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Небесная энциклопедия

Космические корабли и станции, автоматические КА и методы их проектирования, бортовые комплексы управления, системы и средства жизнеобеспечения, особенности технологии производства ракетно-космических систем

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Мониторинг СМИ

Мониторинг СМИ и социальных сетей. Сканирование интернета, новостных сайтов, специализированных контентных площадок на базе мессенджеров. Гибкие настройки фильтров и первоначальных источников.

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Поддерживает ввод нескольких поисковых фраз (по одной на строку). При поиске обеспечивает поддержку морфологии русского и английского языка
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Применить Всего найдено 3007. Отображено 100.
09-02-2012 дата публикации

Antireflective Coatings for High-Resolution Photolithographic Synthesis of DNA Array

Номер: US20120035083A1
Автор: Bei-Shen Sywe, Dana Truong, Glenn H. McGall, Lisa T. Kajisa, Mark O. Trulson, Martin J. Goldberg, Richard P. Rava
Принадлежит: Affymetrix Inc

The present invention provides an array of polymers and methods of forming arrays of polymers by providing a substrate having a first layer including one or more dielectric coatings on a solid support and a second layer including a plurality of polymers disposed on the first layer. The invention also provides methods for forming an array of polymers on a substrate using light-directed synthesis by providing a substrate having a first layer including one or more dielectric coatings on a solid support, derivatizing the first layer by contacting the first layer with a silanation reagent, and a second layer disposed on said first layer wherein the second layer includes functional groups protected with a photolabile protecting group.

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Номер записи: 1
30-08-2012 дата публикации

Methods and Microfluidic Devices for the Manipulation of Droplets in High Fidelity Polynucleotide Assembly

Номер: US20120220497A1
Автор: Joseph Jacobson, Larry Li-Yang Chu, Senthil Ramu
Принадлежит: GEN 9 Inc

Methods and devices are provided for manipulating droplets on a support using surface tension properties, moving the droplets along a predetermined path and merging two droplets together enabling a number of chemical reactions. Disclosed are methods for controlling the droplets volumes. Disclosed are methods and devices for synthesizing at least one oligonucleotide having a predefined sequence. Disclosed are methods and devices for synthesizing and/or assembling at least one polynucleotide product having a predefined sequence from a plurality of different oligonucleotides having a predefined sequence. In exemplary embodiments, the methods involve synthesis and/or amplification of different oligonucleotides immobilized on a solid support, release of synthesized/amplified oligonucleotides in solution to form droplets, recognition and removal of error-containing oligonucleotides, moving or combining two droplets to allow hybridization and/or ligation between two different oligonucleotides, and further chain extension reaction following hybridization and/or ligation to hierarchically generate desired length of polynucleotide products.

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Номер записи: 2
06-09-2012 дата публикации

Apparatus and method for separation of liquid phases of different density and for fluorous phase organic syntheses

Номер: US20120223025A1
Автор: Michal Lebl
Принадлежит: Illumina Inc

A simple, efficient apparatus and method for separating layers of immiscible or partially miscible liquids useful in methods of high-throughput combinatorial organic synthesis or parallel extraction of large libraries or megaarrays of organic compounds is disclosed. The apparatus and method are useful, whether as part of an automated, robotic or manual system for combinatorial organic synthesis or purification (extraction). In a preferred embodiment, an apparatus and method for separating layers of immiscible or partially miscible liquids compatible with microtiter plate type array(s) of reaction vessels is disclosed. Another application of centrifugation based liquid removal was found for washing the plates in biological assays or synthesis on modified substrates.

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Номер записи: 3
04-10-2012 дата публикации

Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays

Номер: US20120252700A1
Автор: Francis Barany, George Barany, Herman Blok, Maria Kempe, Monib Zirvi, Robert P. Hammer
Принадлежит: Cornell Research Foundation Inc

The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.

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Номер записи: 4
08-11-2012 дата публикации

Potentiometric dna microarray, process for producing the same and method of analyzing nucleic acid

Номер: US20120283119A1
Автор: Kenji Yasuda, Kumiko Hattori, Yuji Miyahara
Принадлежит: Individual

A DNA microarray system whereby measurement can be performed at a low running cost, a low price and yet a high accuracy. A nucleic acid probe ( 3 ) is immobilized on the surface of a gate insulator of an electric field effect transistor and then hybridized with a target gene on the surface of the gate insulator. A change in the surface electric charge density thus arising is detected by using the electric effect.

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Номер записи: 5
03-01-2013 дата публикации

Arrays Of Biological Membranes And Methods And Use Thereof

Номер: US20130005611A1
Автор: Anthony G. Frutos, Joydeep Lahiri, Peter J. Kalal, Steven J. Jonas, YE Fang
Принадлежит: Individual

The present invention overcomes the problems and disadvantages associated with prior art arrays by providing an array comprising a plurality of biological membrane microspots associated with a surface of a substrate that can be produced, used and stored, not in an aqueous environment, but in an environment exposed to air under ambient or controlled humidities. Preferably, the biological membrane microspots comprise a membrane bound protein. Most preferably, the membrane bound protein is a G-protein coupled receptor, an ion channel, a receptor serine/threonine kinase or a receptor tyrosine kinase.

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Номер записи: 6
18-04-2013 дата публикации

Microfluidic chip

Номер: US20130096031A1
Автор: Chin-Feng Wan
Принадлежит: Individual

A microfluidic chip includes a base layer, a fluid layer, and a gas regulating layer. The base layer includes a microarray detecting zone. The microarray detecting zone includes a substrate, a photoresist pattern layer, a blocking layer, a bonding layer, at least one linker molecule, and a probe molecule. The bonding layer is covalently attached to the photoresist pattern layer. The at least one linker molecule is covalently bonded to the binding layer. The probe molecule is covalently bonded to the at least one linker molecule for specifically reacting with an under-test molecule. The fluid layer is disposed over the base layer, and includes plural flow channels for introducing or collecting detecting reagents. The gas regulating layer is disposed over the fluid layer for controlling open/close statuses of the flow channels, thereby controlling a flowing condition of a fluid in the fluid layer.

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Номер записи: 7
26-12-2013 дата публикации

Bead sealing method, method for detecting target molecule, array, kit, and target molecule detection device

Номер: US20130345088A1
Автор: Hiroyuki Noji, Ryota Iino, Suguru ARAKI
Принадлежит: JAPAN SCIENCE AND TECHNOLOGY AGENCY

This invention provides a technique enabling to detect target molecules of low concentration with high sensitivity. This invention includes (i) a step of introducing a hydrophilic solvent ( 42 ) containing beads ( 40 ),( 41 ′) into a space ( 30 ) between (a) a lower layer section ( 10 ) including a plurality of receptacles ( 13 ) each of which is capable of storing only one of the beads ( 41 ),( 41 ′) and which are separated from each other by a side wall ( 12 ) having a hydrophobic upper surface and (b) an upper layer section ( 20 ) facing a surface of the lower layer section ( 10 ) on which surface the plurality of receptacles ( 13 ) are provided; and (ii) a step of introducing a hydrophobic solvent ( 43 ) into the space ( 30 ), the step (ii) being carried out after the step (i).

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Номер записи: 8
06-02-2014 дата публикации

Device and method for the generation of molecular microarrays

Номер: US20140038854A1
Автор: Günter Roth, Jugen Burger
Принадлежит: Albert Ludwigs Universitaet Freiburg

The invention relates to a device and a method for the generation of molecular microarrays. The invention relates therefore to a universal approach for the generation of protein microarrays, DNA microarrays and RNA microarrays (in general nucleic acid microarrays), by production of an output molecule from a template molecule microarray via enzymatic or chemical processes and transfer of the output molecule onto the desired molecular microarray.

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Номер записи: 9
03-02-2022 дата публикации

APPARATUS, SYSTEM, AND METHOD USING IMMISCIBLE-FLUID-DISCRETE-VOLUMES

Номер: US20220033896A1
Автор: Cox David M., Lee Linda G., Ma Congcong, Oldham Mark F., REEL Richard T., SCHROEDER Benjamin G., SORENSON Jon M., WIYATNO Willy, WOO Sam L.
Принадлежит: APPLIED BIOSYSTEMS, LLC

Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure. 1. A method comprising:contacting a stream of aqueous sample fluid flowing in a first conduit with a stream of non-aqueous spacing fluid that is immiscible with the aqueous sample fluid to form discrete volumes of the aqueous sample fluid separated from one another by the non-aqueous spacing fluid, wherein the aqueous sample fluid comprises target nucleic acid, and wherein a first plurality of the discrete volumes contains at least one molecule comprising the target nucleic acid and a second plurality of the discrete volumes contains no molecules comprising the target nucleic acid;amplifying the target nucleic acid in one or more of the first plurality of the discrete volumes to form an amplicon;in a second conduit, detecting a fluorescence signal from the amplicon in the one or more of the first plurality of the discrete volumes; andbased on the detecting, discriminating between the one or more of the first plurality of the discrete volumes and the second plurality of the discrete volumes.2. The method of claim 1 , wherein the contacting comprises continuously flowing at least one of the aqueous sample fluid and the non-aqueous spacing fluid into the first conduit.3. The method of claim 1 , further comprising separating the second plurality of the discrete volumes from the first plurality of the discrete volumes.4. The method of claim 1 , wherein less than 37% of the first plurality of the discrete volumes comprise a single molecule comprising the target nucleic acid.5. The method of claim 4 , wherein 1% or more of the first plurality ...

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Номер записи: 10
15-01-2015 дата публикации

Method for detecting the presence of a target nucleic acid sequence in a sample

Номер: US20150017709A1
Автор: James F. Brown, Jonathan E. Silver
Принадлежит: APPLIED BIOSYSTEMS LLC, US Department of Health and Human Services

A method comprises loading a sample portion into a sample chamber which comprises means for minimizing diffusion of the sample portion, subjecting the sample portion to an amplification step, and determining whether the sample portion contains at least one molecule of a target nucleic acid. If the sample portion contains a single molecule of the target nucleic acid, the sample portion would attain a detectable concentration of the target nucleic acid after a single round of amplification. Also, a microfluidic device comprising a sample portion and a sample chamber comprising means for minimizing diffusion of the sample portion. Also, a microfluidic device comprising a sample chamber and an amplification targeting reagent positioned in the first sample chamber.

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Номер записи: 11
16-01-2020 дата публикации

HEATED DEVICE FOR ARRAY SYNTHESIS

Номер: US20200016567A1
Автор: WOODBURY Neal, Zhao Zhan-Gong
Принадлежит:

The manufacturing of molecular arrays often requires the coordination of various physical, chemical, and thermal parameters. Hence, the quality and homogeneity of many molecular arrays can be very dependent on the method of manufacturing. The instant disclosure provides a device that is configured to consistently yield peptide arrays of high quality. The device distributes optimum levels of heat and coupling solution during the chemical coupling and manufacturing of peptide array. 1. A device for the manufacture of a molecular array , the device comprising:a) a heating component, whereby the heating component provides a level of thermal uniformity across a surface that varies by no more than 5° C. as measured from a center to an edge of the surface; 'whereby the contemporaneous use of the heating component and the spinning component in the manufacture of the molecular array provides a homogeneous coupling of the one or more molecular monomers to at least 80% of the surface exposed to the monomer.', 'b) a spinning component coupled to the heating component; whereby the spinning component distributes a continuous or a semi-continuous amount of a fluid comprising one or more molecular monomers, a coupling solution, or a wash solution to the surface,'}2. The device of claim 1 , wherein the heating component provides a desired thermal uniformity across at least 90% of the surface.3. The device of claim 2 , wherein the thermal uniformity varies by no more than 1° C. between the center and the edge of the surface.4. The device of claim 1 , wherein the heating component provides a desired specific heat across at least 90% of the surface.5. The device of claim 4 , wherein the specific heat is less than 1.05 J/g ° C.6. The device of claim 1 , wherein the spinning component effectively distributes the amount of fluid comprising the one or more molecular monomers claim 1 , the coupling solution claim 1 , or the wash solution to at least 80% of the surface.7. The device of claim ...

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Номер записи: 12
18-01-2018 дата публикации

PROCESS FOR MAKING AN ARRAY

Номер: US20180017551A1
Автор: KAM Lance Cameron, LAW Bee Khuan Jaslyn, Low Hong Yee, NG Zheng Jie, SHEETZ Michael Patrick, SURYANA Mona, TEO Kim Kiat, WEE Kee Fong, YIM King Fai Evelyn
Принадлежит:

There is disclosed a method of making an array for cell assays comprising the step of providing an array of structures on a substrate, each of said structures having a pre-defined topography thereon, and wherein at least one structure has a different topography from at least one other structure. 157.-. (canceled)58. A method of making an array for cell assays comprising the step of providing an array of structures that each extend from a substrate and having a pre-defined topography thereon , wherein at least one structure (A) has a different topography from at least one other structure (B) , wherein structure (A) is imprinted separately to structure (B) , and wherein structure (A) is capable of being imprinted at an imprinting condition (A) that is different to imprinting condition (B) of structure (B).59. The method as claimed in claim 58 , wherein the structures are generally elongate and have a proximal end that extends from the substrate and a distal end that is opposite to said proximal end.60. The method as claimed in claim 59 , wherein the topography of said structures is provided on said proximal end.61. The method as claimed in claim 60 , wherein the elongate structures have a longitudinal axis extending from their proximal end to their distal end and wherein said longitudinal axis is generally normal to a planar surface of said substrate.62. The method as claimed in claim 58 , wherein the providing step comprises the step of adhering said structures to said substrate.63. The method as claimed in claim 62 , wherein said adhering step comprises the step of providing an adhesive layer on said substrate before said adhering step.64. The method as claimed in claim 63 , wherein said providing an adhesive layer on said substrate comprises the step of spin-coating a polymer solution onto said substrate.65. The method as claimed in claim 64 , removing the polymer solution while said array of structures are disposed in said polymer solution to form a polymer layer ...

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Номер записи: 13
01-02-2018 дата публикации

DE NOVO SYNTHESIZED GENE LIBRARIES

Номер: US20180029001A1
Автор: Banyai William, Chen Siyuan, FERNANDEZ Andres, Indermuhle Pierre, Peck Bill James
Принадлежит:

De novo synthesized large libraries of nucleic acids are provided herein with low error rates. Further, devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Longer nucleic acids can be synthesized in parallel using microfluidic assemblies. Further, methods herein allow for the fast construction of large libraries of long, high-quality genes. Devices for the manufacturing of large libraries of long and high-quality nucleic acids are further described herein. 1. A polynucleotide cDNA library based on instructions provided in a computer readable non-transient medium , the library comprising at least 20 ,000 polynucleotides based on the instructions provided in the computer readable non-transient medium , wherein the at least 20 ,000 polynucleotides collectively encode cDNA sequences for at least 500 genes or gene fragments , and wherein the at least 20 ,000 polynucleotides encode sequences with an aggregate error rate of less than 1 in 800 bases compared to sequences received in the instructions provided in the computer readable non-transient medium.2. The polynucleotide cDNA library of claim 1 , wherein the at least 20 claim 1 ,000 polynucleotides encode sequences with an aggregate error rate of less than 1 in 1000 bases compared to sequences received in the instructions provided in the computer readable non-transient medium.3. The polynucleotide cDNA library of claim 1 , wherein each of the at least 20 claim 1 ,000 polynucleotides comprises a first overlap region which is complementary to a second overlap region of another polynucleotide of the at least 20 claim 1 ,000 polynucleotides.4. The polynucleotide cDNA library of claim 3 , wherein the first overlap region comprises a GC content of 35% to 65%.5. The polynucleotide cDNA library of claim 3 , wherein the first overlap region comprises 10 to 100 bases in length.6. The polynucleotide cDNA library of claim 3 , wherein the at least 20 claim 3 ,000 ...

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Номер записи: 14
04-02-2016 дата публикации

Functionalized grids for locating and imaging biological specimens and methods of using the same

Номер: US20160032281A1
Автор: Mark Utlaut, N. William Parker
Принадлежит: FEI Co

A functionalized specimen support for use in charged particle microscopy is provided that includes a specimen support surface configured to support specimens during an interrogation of the specimens with a charged particle microscope, the specimen support surface having functionalized sites, each functionalized site configured to maintain position of a portion of one of the specimens at the functionalized site by way of attachment, attraction, or a combination thereof.

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Номер записи: 15
07-02-2019 дата публикации

COMPOSITIONS AND METHODS FOR ENTRAPPING PROTEIN ON A SURFACE

Номер: US20190039041A1
Автор: Hogan Michael E.
Принадлежит: GENOMICS USA, INC.

The present invention provides a formulation to link protein to a solid support that comprises one or more proteins, Oligo-dT and one or more non-volatile, water-soluble protein solvents, solutes or combination thereof in an aqueous solution. Further provided is a method of attaching a protein to a surface of a substrate. The formulations provided herein are contacted onto the substrate surface, printed thereon and air dried. The substrate surface is irradiated with UV light to induce thymidine photochemical crosslinking via the thymidine moieties of the Oligo-dT. 1. A formulation to link protein to a solid support , comprising:one or more proteins;Oligo-dT; andone or more non-volatile, water-soluble protein solvents, solutes or combination thereof in an aqueous solution.wherein the water-soluble protein solvent comprises propanediol or the water-soluble protein solvent and solids comprise propanediol and at least one of sucrose, trehalose or sorbitol.2. The formulation of claim 1 , wherein said sucrose claim 1 , trehalose or sorbitol is present at a mass ratio of about 0.5:1 up to about 4:1 relative to propanediol.3. The formulation of claim 1 , wherein the water soluble protein solvents and solids comprise glycerol and propanediol and at least one of sucrose claim 1 , trehalose or sorbitol.4. The formulation of claim 1 , wherein the solid support is an amino-silane layer disposed upon an underlying surface.5. The formulation of claim 4 , wherein said underlying surface is a metal surface claim 4 , a glass surface or a ceramic surface. This application is a divisional application of U.S. application Ser. No. 15/668,169, filed Aug. 3, 2017, now allowed; which is a divisional application of U.S. application Ser. No. 14/120,278, filed May 14, 2014, now U.S. Pat. No. 9,751,069, issued Sept. 5, 2017; which claims benefit of priority under 35 U.S.C. § 119(e) of provisional application U.S. Ser. No. 61/823,065, filed May 14, 2013, the entirety of which are hereby ...

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Номер записи: 16
06-02-2020 дата публикации

KINETIC EXCLUSION AMPLIFICATION OF NUCLEIC ACID LIBRARIES

Номер: US20200040386A1
Автор: Boutell Jonathan Mark, Bowen M. Shane, Gunderson Kevin L., Ronaghi Mostafa, Shen Min-Jui Richard, Stephens Kathryn M., Venkatesan Bala Murali, Vijayan Kandaswamy
Принадлежит: Illumina, Inc.

A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated. 1. A method for amplifying nucleic acids , comprising (i) an array of amplification sites having one or more capture agents, and', '(ii) an amplification reagent comprising a solution comprising a plurality of different target nucleic acids,', 'wherein the number of the different target nucleic acids in the solution exceeds the number of amplification sites in the array,', 'wherein the different target nucleic acids have fluidic access to the plurality of amplification sites, and', 'wherein each of the amplification sites is capable of being occupied by several target nucleic acids of the plurality of different target nucleic acids; and, '(a) providing'}(b) reacting the amplification reagent with the array of amplification sites, such that a plurality of amplification sites each comprises clonal amplicons from an individual target nucleic acid from the solution; (i) transporting the different target nucleic acids to the amplification sites to seed at the amplification sites, and', '(ii) amplifying the target nucleic acids that are seeded at the amplification ...

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Номер записи: 17
14-02-2019 дата публикации

GEL PATTERNED SURFACES

Номер: US20190046943A1
Автор: Barnard Steven M., Bowen M. Shane, Brown Andrew A., George Wayne N., Rogert Bacigalupo Maria Candelaria, Tsay James
Принадлежит:

An example method includes contacting a substrate coated with a sol-gel material with a stamp that includes a plurality of protruding features. While contacting the coated sol-gel material with the stamp, the example method further includes curing the coated sol-gel material so as to form a patterned sol-gel layer that includes a plurality of wells. The stamp is separated from the patterned sol-gel layer. 128-. (canceled)29. A method comprising:contacting a substrate coated with a sol-gel material with a stamp that includes a plurality of protruding features;while contacting the coated sol-gel material with the stamp, curing the coated sol-gel material so as to form a patterned sol-gel layer that comprises a plurality of wells; andseparating the stamp from the patterned sol-gel layer.30. The method of claim 29 , further comprising forming the coated substrate by coating the substrate with the sol-gel material claim 29 , wherein the coating is performed by spin-coating claim 29 , dipping claim 29 , or spray-coating.31. The method of claim 29 , wherein the curing the coated sol-gel material is performed by exposing the coated sol-gel material to light.32. The method of claim 29 , wherein the curing the coated sol-gel material is performed by exposing the coated sol-gel material to heat.33. The method of claim 29 , further comprising claim 29 , after separating the stamp from the patterned sol-gel layer claim 29 , sintering the patterned sol-gel layer.34. The method of claim 29 , further comprising depositing a gel material in the wells claim 29 , wherein the gel material is adapted to promote capture and/or amplification of target nucleic acids.35. The method of claim 34 , where depositing the gel material in the wells comprises:coating the gel material on the patterned sol-gel layer such that the gel material enters the wells and coats interstitial regions between the wells; andpolishing the patterned sol-gel layer so as to remove the gel material from the ...

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Номер записи: 18
23-02-2017 дата публикации

PROBE INVERSION PROCESS FOR IN SITU SYNTHESIZED PROBE ARRAYS

Номер: US20170050162A1
Автор: McGall Glenn, SINGH Vijay, Zhou Wei
Принадлежит:

The present disclosure relates to processes for inverting oligonucleotide probes in an in situ synthesized array. These processes can be used to reverse the orientation of probes with respect to the substrate from 3′-bound to 5′-bound. These processes can also be used to reduce or eliminate the presence of truncated probe sequences from an in situ synthesized array. 1. A method , comprising:(a) providing a substrate with a plurality of branched linkers coupled to said substrate, wherein said substrate comprises a plurality of hydroxyalkyl groups, wherein each branched linker comprises (i) a first branch comprising a first alkyne and (ii) a second branch, wherein said second branch comprises a first cleavable linker coupled to a 3′ end of a first oligonucleotide, and wherein a 5′ end of said first oligonucleotide is coupled to a first azide group; and(b) circularizing said first oligonucleotide by reacting said first azide group with a second alkyne, wherein said second alkyne is said first alkyne or a neighboring alkyne;wherein efficiency of said circularization increases when said second branch further comprises a capping moiety.2. The method of claim 1 , wherein the ratio between said cleavable linker and said first alkyne is about 5 claim 1 , about 4 claim 1 , about 3 claim 1 , about 2 claim 1 , about 1 claim 1 , about 0.5 claim 1 , about 0.33 claim 1 , about 0.25 claim 1 , about 0.2 claim 1 , or about 0.1.3. The method of claim 1 , further comprising (c) cleaving said first cleavable linker claim 1 , thereby decoupling said 3′ end of said first oligonucleotide from said second branch.4. The method of claim 3 , wherein another second branch comprises a second cleavable linker coupled to a 3′ end of a second oligonucleotide claim 3 , wherein said second oligonucleotide is shorter than said first oligonucleotide claim 3 , and wherein said cleaving releases said second oligonucleotide from said substrate.5. A method claim 3 , comprising:(a) providing a substrate;(b) ...

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Номер записи: 19
03-03-2016 дата публикации

METHODS OF MAKING AND USING MICROARRAYS SUITABLE FOR HIGH-THROUGHPUT DETECTION

Номер: US20160059202A1
Автор: Blair Steven M., Chagovetz Alexander, Wilson Colby
Принадлежит: UNIVERSITY OF UTAH RESEARCH FOUNDATION

Disclosed are high density microarrays and methods for making and using such microarrays. The microarrays of the present invention can have uniformly shaped and sized sensing zones and are designed to allow high-throughput detection assays with minimal noise. 138-. (canceled)39. A microarray , comprising:a substrate;cladding material deposited on the substrate in the form of a continuous layer of cladding material that laterally defines an array of discontinuous wells, wherein a base portion of said wells includes the substrate; anda ligand having a basal functional group and an apical functional group attached to the wells, wherein the basal functional group is configured to bind to the substrate but not to the cladding layer material so that bound ligand is confined to the wells and the cladding layer remains free of bound ligand.40. The microarray of claim 39 , wherein the ligand comprises a photolabile functional group that requires radiant light energy in order to bind to a surface.41. The microarray of claim 40 , wherein the radiant light energy passes through the upper surface only in the wells claim 40 , thereby causing the photolabile functional group in the wells to bind to the upper surface; wherein the bound ligand is confined to the wells and the cladding layer remains free of bound ligand.42. The microarray of claim 41 , wherein the photolabile functional group is immobilized in the well claim 41 , wherein radiant light energy de-protects the photolabile functional group claim 41 , wherein the de-protected group can bind to an oligonucleotide probe or other biomolecule.43. The microarray of wherein a probe is attached to the apical functional group of the bound ligand.44. The microarray of wherein the ligand is a member selected from the group consisting of DNA claim 39 , RNA claim 39 , PNA claim 39 , LNA claim 39 , and other modified synthetic or naturally occurring nucleic acids claim 39 , peptides claim 39 , proteins claim 39 , antibodies claim 39 , ...

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Номер записи: 20
04-03-2021 дата публикации

MICROARRAY SYNTHESIS AND ASSEMBLY OF GENE-LENGTH POLYNUCLEOTIDES

Номер: US20210062185A1
Автор: Oleinikov Andrew V.
Принадлежит: Gen9, Inc.

There is disclosed a process for in vitro synthesis and assembly of long, gene-length polynucleotides based upon assembly of multiple shorter oligonucleotides synthesized in situ on a microarray platform. Specifically, there is disclosed a process for in situ synthesis of oligonucleotide fragments on a solid phase microarray platform and subsequent, “on device” assembly of larger polynucleotides composed of a plurality of shorter oligonucleotide fragments. 1. (canceled)2. A method for producing a polynucleotide comprising a target sequence , the method comprising: [ is identical to an overlapping sequence region of another double-stranded oligonucleotide in the plurality of double-stranded oligonucleotides; and', 'comprises a Type II restriction endonuclease cleavage site; and, '(i) an internal sequence identical to a portion of the target sequence, wherein the internal sequence, at one or both ends, comprises an overlapping sequence region that, '(ii) one or more flanking sequences, wherein each flanking sequence comprises a Type II restriction endonuclease recognition site corresponding to the Type II restriction endonuclease cleavage site of the internal sequence;, '(a) providing a plurality of double-stranded oligonucleotides, each double-stranded oligonucleotide comprising(b) digesting the plurality of double-stranded oligonucleotides with a Type II restriction endonuclease that recognizes the Type II restriction endonuclease recognition site; and(c) ligating the digested oligonucleotides to produce the polynucleotide comprising the target sequence.3. The method of claim 2 , wherein each double-stranded oligonucleotide in (a) comprises a flanking sequence at each end.4. The method of claim 2 , wherein the plurality of double-stranded oligonucleotides are digested in (b) with a Type IIS restriction endonuclease.5. The method of claim 2 , wherein the Type IIS restriction endonuclease includes at least one of MylI claim 2 , BspMI claim 2 , BsaXI claim 2 , BsrI ...

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Номер записи: 21
02-03-2017 дата публикации

SYSTEM AND METHOD FOR ANALYSIS OF PEPTIDE SYNTHESIS FIDELITY

Номер: US20170059578A1
Автор: Bannen Ryan, Barilovits Sarah, PATEL Jigar, SULLIVAN Eric, Tan John
Принадлежит:

The present invention provides a system and method for assessing the fidelity of a synthetic peptide population including interrogating a population of peptide features in the presence of a receptor having an affinity for a plurality of binder sequences. A first amino acid is at a defined position within a first one of the binder sequences, and the population of peptide features includes a first control peptide feature synthesized to have an amino acid sequence including the first one of the binder sequences. The system and method further includes detecting a signal output characteristic of an interaction of the receptor with the first control peptide feature. The signal output is indicative of the fidelity of incorporation of the first amino acid into the first control peptide at the defined position within the first one of the binder sequences. 1. A method of assessing the fidelity of a synthetic peptide population , the method comprising:interrogating a population of peptide features in the presence of a receptor having an affinity for a plurality of binder sequences, a first amino acid at a defined position within a first one of the binder sequences, the population of peptide features including a first control peptide feature synthesized to have an amino acid sequence including the first one of the binder sequences; anddetecting a signal output characteristic of an interaction of the receptor with the first control peptide feature, the signal output indicative of the fidelity of incorporation of the first amino acid into the first control peptide at the defined position within the first one of the binder sequences.2. The method of claim 1 , further comprising detecting a signal output characteristic of an interaction of the receptor with a second control peptide feature claim 1 , the signal output indicative of the fidelity of incorporation of a second amino acid into the second control peptide at a defined position within a second one of the binder sequences ...

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Номер записи: 22
28-02-2019 дата публикации

High-density nucleic acid arrays on polyester substrates

Номер: US20190060860A1
Автор: David M. Lynn, Lloyd M. Smith, Matthew C.D. Carter, Matthew T. Holden
Принадлежит: WISCONSIN ALUMNI RESEARCH FOUNDATION

Described is a method of synthesizing nucleic acids on polyester substrates and the resulting compositions of matter. The method synthesizes nucleic acids from surface hydroxyl initiation points present on the substrate surface. These surface hydroxyls are present either naturally, or as a result of a chemical treatment to cleave ester bonds on the substrate surface. The preferred polyester substrate contains PET.

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Номер записи: 23
17-03-2022 дата публикации

NANOSCALE BIOCHEMICAL SAMPLE PREPARATION AND ANALYSIS

Номер: US20220080420A1
Автор: Kelly Ryan T., Smith Richard D., Zhu Ying
Принадлежит: BATTELLE MEMORIAL INSTITUTE

Provided herein are methods and systems for biochemical analysis, including compositions and methods for processing and analysis of small cell populations and biological samples (e.g., a robotically controlled chip-based nanodroplet platform). In particular aspects, the methods described herein can reduce total processing volumes from conventional volumes to nanoliter volumes within a single reactor vessel (e.g., within a single droplet reactor) while minimizing losses, such as due to sample evaporation. 1. A platform for biological sample preparation , comprising:{'sup': '2', '#text': 'a substrate comprising at least one reactor vessel having one or more hydrophilic surfaces configured for containment of a biological sample, wherein the hydrophilic surfaces have a non-zero total surface area less than 25 mm;'}a spacer containing an aperture, wherein the aperture is dimensioned to surround the at least one reactor vessel when the spacer is positioned on the substrate; anda cover positioned on the spacer.2. The platform of claim 1 , further comprising a membrane interposed between the spacer and the cover claim 1 , the membrane configured to form a gas-tight seal between the spacer and the cover to minimize evaporation.3. The platform of claim 1 , wherein the platform is formed from a material that is substantially optically transparent.4. The platform of claim 1 , wherein the platform is formed from glass.5. The platform of claim 1 , further comprising at least one hydrophobic surface surrounding the at least one reactor vessel.6. The platform of claim 1 , further comprising at least two reactor vessels claim 1 , wherein the at least two reactor vessels are separated by a hydrophobic surface.7. The platform of claim 1 , wherein the hydrophilic surface is formed on an upper surface of a pillar and defines the lateral boundary of the least one reactor vessel.8. The platform of claim 1 , wherein the at least one reactor vessel is a well having a depth extending below a ...

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Номер записи: 24
09-03-2017 дата публикации

Fluid Deposition Apparatus and Method

Номер: US20170065958A1
Автор: Cheng Chun-Wen, Lai Fei-Lung, Liu Yi-Shao, Peng Jung-Huei, Tsai Shang-Ying
Принадлежит:

The present disclosure relates to a method of depositing a fluid onto a substrate. In some embodiments, the method may be performed by mounting a substrate to a micro-fluidic probe card, so that the substrate abuts a cavity within the micro-fluidic probe card that is in communication with a fluid inlet and a fluid outlet. A first fluidic chemical is selectively introduced into the cavity via the fluid inlet of the micro-fluidic probe card. 1. A method of depositing a fluid onto a substrate , comprising:mounting a substrate to a micro-fluidic probe card, so that the substrate abuts a cavity within the micro-fluidic probe card that is in communication with a fluid inlet and a fluid outlet; andselectively introducing a first fluidic chemical to the cavity via the fluid inlet of the micro-fluidic probe card.2. The method of claim 1 , further comprising:dismounting the micro-fluidic probe card from the substrate.3. The method of claim 1 , further comprising:removing the first fluidic chemical from the cavity via the fluid outlet of the micro-fluidic probe card; andselectively introducing a second fluidic chemical to the cavity via the fluid inlet of the micro-fluidic probe card.4. The method of claim 1 , further comprising:selectively introducing a drying agent, which is configured to dry the substrate, to the cavity via the fluid inlet of the micro-fluidic probe card.5. The method of claim 4 , wherein the drying agent comprises nitrogen gas.6. The method of claim 1 , further comprising:performing a performance check to determine if the first fluidic chemical has been deposited onto the substrate prior to dismounting the micro-fluidic probe card from the substrate.7. The method of claim 6 , wherein the micro-fluidic probe card comprises a transparent surface positioned between the substrate and a performance monitoring element that is configured to perform the performance check.8. The method of claim 7 , wherein performing the performance check comprises:directing light ...

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Номер записи: 25
27-02-2020 дата публикации

IN VITRO DNA WRITING FOR INFORMATION STORAGE

Номер: US20200063119A1
Автор: Farzadfard Fahim, Lu Timothy Kuan-Ta
Принадлежит: Massachusetts Institute of Technology

Provided herein are compositions, systems, and methods for information (e.g., artificial or digital information) recording and storage in nucleic acids (e.g., DNA). Information can be recorded and stored on pre-synthesized storage medium. 1. A method of storing information , comprising:(i) providing a storage medium comprising a plurality of nucleic acid molecules, each nucleic acid molecule comprising one or more information storage regions, each information storage region comprising a write address followed by a read address; and (a) a modifying enzyme comprising a DNA binding domain fused to a base editing enzyme that edits one or more target nucleotides in the write address of the plurality of nucleic acid molecules, and', '(b) a plurality of guide RNAs (gRNAs), each gRNA comprising a specificity determining sequence (SDS) that is complementary to one type of information storage region in the plurality of nucleic acid molecules;, '(ii) contacting, in vitro, the storage medium withwherein the contacting results in the editing of the one or more target nucleotides in the write address of the plurality of nucleic acid molecules.2. The method of claim 1 , wherein the DNA binding domain is a catalytically-inactive Cas9 (dCas9) or a Cas9 nickase (nCas9).3. The method of claim 1 , wherein the DNA binding domain is a catalytically-inactive Cpf1 (dCpf1).4. The method of claim 1 , wherein the plurality of nucleic acid molecules are isolated genomic DNA molecules claim 1 , plasmids claim 1 , or synthetic oligonucleotides.58.-. (canceled)9. The method of claim 1 , wherein each of the plurality of nucleic acid molecules further comprises a protospacer adjacent motif (PAM) following each information storage region.10. The method of claim 1 , wherein the plurality of nucleic acid molecules do not each comprise a PAM following each information storage region claim 1 , and the method further comprises contacting the storage medium with a PAM-presenting oligonucleotide (PAMmer). ...

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Номер записи: 26
24-03-2016 дата публикации

METHOD FOR COMBINATORIAL PARTICLE MANIPULATION FOR PRODUCING HIGH-DENSITY MOLECULE ARRAYS, IN PARTICULAR PEPTIDE ARRAYS, AND MOLECULE ARRAYS THAT CAN BE OBTAINED BY MEANS THEREOF

Номер: US20160082406A1
Автор: Breitling Frank, Bykovskaya Valentina, LEIBE Klaus, Löffler Felix, MÄRKLE Frieder, NESTEROV-MÜLLER Alexander, SCHILLO Sebastian, VON BOJNICIC-KNINSKI Clemens
Принадлежит:

The present invention relates to a method for combinatorial particle manipulation for producing high-density molecule arrays, and to the high-density molecule arrays obtained therefrom. In particular, the present invention relates to a method for producing high-density molecule arrays, in particular peptide or oligonucleotide arrays, by combinatorial patterning of particles, wherein the patterning is achieved by the selective and direct action of electromagnetic radiation. 1. A method for producing high-density molecule arrays having a pitch of 300 μm or less , the method comprising:(i) providing a target substrate having a plurality of discrete spots,(ii) conditioning selected spots of the target substrate by electromagnetic radiation, and(iii) reacting at least one monomer with reactants present in immobilized form in the selected spots of the target substrate.2. The method of claim 1 , wherein there is provided at least one starting substrate having a material layer selected from the group consisting of a particle layer and a film layer in which the at least one monomer is present claim 1 , and wherein step (ii) of conditioning selected spots comprises the selective transfer of material from the starting substrate to the target substrate and the site-specific fixing of the material to the target substrate claim 1 , wherein the selective transfer and/or the site-specific fixing is by electromagnetic radiation.3. The method of claim 2 , wherein one or more intermediate layers which assist the transfer of material is arranged between the starting substrate and the material layer.4. The method of claim 2 , wherein one or more intermediate layers is arranged between the starting substrate and the material layer which protect the at least one monomers to be transferred or the target substrate and the reactants situated thereon from the electromagnetic radiation.5. The method of claim 2 , wherein the selective transfer of material from the starting substrate and the ...

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Номер записи: 27
26-03-2015 дата публикации

Device, Array, And Methods For Disease Detection And Analysis

Номер: US20150087543A1
Автор: COLEMAN Matthew A., Lane Stephen M., Matthews Dennis L., Rao Rupa S.
Принадлежит:

A device and array coupled to capture molecules are provided. Specifically, the device and array can be used for detecting the presence and concentration of biomarkers in a sample from a subject. The device and array can also allow the use of a method for scoring a sample for, e.g., the purpose of diagnosing a disease. The method can also be advantageous to applications where there is a need to accurately determine the disease stage of a subject for the purpose of making therapeutic decisions. 1. A multiplex immunoassay detection device for measurement of breast cancer markers in a patient sample , comprising:a glass solid support comprising a plurality of distinct spots arranged in an array format, each spot comprising a distinct capture antibody capable of binding to a breast cancer marker, the distinct capture antibody selected from the group consisting of antibody Clone 191924 for HER2, antibody Clone 36006.211 for MMP-2, antibody Clone M8071022 for CA-15-3 and antibody Clone 190312 for osteopontin;a glass cover plate, wherein the glass cover plate forms an upper surface positioned above the solid support;a vertical support comprising adhesive silicone, wherein the vertical support forms a connection between the solid support and the cover plate, the connection forming at least one channel surrounding the array of capture antibodies, and wherein the channel comprises a first end and a second end and wherein the first end of the channel comprises an opening; andan absorbent material comprising a nitrocellulose membrane connected to the second end.2. A kit comprising the multiplex immunoassay detection device of and set of biotinylated detection antibodies for detection of breast cancer markers bound to the capture antibodies claim 1 , the detection antibodies comprising antibody AF-1129 for HER2 claim 1 , Antibody AF-902 for MMP-2 claim 1 , Antibody Clone M8071021 for CA 15-3 and antibody AF-1433 for osteopontin.3. A multiplex immunoassay method for detection of ...

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Номер записи: 28
31-03-2022 дата публикации

ARTICLES HAVING LOCALIZED MOLECULES DISPOSED THEREON AND METHODS OF PRODUCING SAME

Номер: US20220098660A1
Автор: Cicero Ron L., Korlach Jonas, Lyle John, Otto Geoff, Peluso Paul, Rank David R., Roitman Daniel, Turner Stephen, Wegener Jeffery, XU YUE
Принадлежит:

Methods of producing substrates having selected active chemical regions by employing elements of the substrates in assisting the localization of active chemical groups in desired regions of the substrate. The methods may include optical, chemical and/or mechanical processes for the deposition, removal, activation and/or deactivation of chemical groups in selected regions of the substrate to provide selective active regions of the substrate. 113-. (canceled)14. A method of preferentially localizing desired molecules within optical confinements disposed upon a substrate , comprising:depositing the desired molecules over the surface of the substrate; andselectively removing the desired molecules from the surface of the substrate that is not within the optical confinements.15. The method of claim 14 , wherein the substrate comprises an opaque layer on a transparent layer claim 14 , and wherein the optical confinements comprise nanoscale wells disposed through the opaque layer and exposing part of the transparent layer.16. The method of claim 15 , wherein the transparent layer comprises SiO.17. The method of claim 15 , wherein the opaque layer comprises a metal or metal oxide.18. The method of claim 15 , wherein the opaque layer comprises aluminum and the transparent layer comprises SiO.19. The method of claim 14 , wherein the optical confinements comprise zero mode waveguides.20. The method of claim 14 , wherein selectively removing the desired molecules from the surface of the substrate that is not within the optical confinements comprises contacting the substrate with a deactivation component coupled to an exclusionary component claim 14 , which exclusionary component is at least partially excluded from entering into the optical confinements.21. The method of claim 20 , wherein the deactivation component comprises an enzyme.22. The method of claim 21 , wherein the enzyme is selected from the group consisting of a protease claim 21 , a nuclease claim 21 , and a ...

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Номер записи: 29
25-03-2021 дата публикации

CONDITIONED SURFACES FOR IN SITU MOLECULAR ARRAY SYNTHESIS

Номер: US20210086159A1
Автор: WOODBURY Neal, ZHAO Zhang-Gong
Принадлежит:

Described herein are in situ synthesized arrays and methods of making them, wherein array signal sensitivity and robustness is enhanced by carrying out conditioning steps and/or generating linkers during synthesis. An array comprises a surface with a collection of features, wherein the features comprise molecules or polymers attached to the surface. In certain embodiments of the invention, carrying out conditioning steps during array synthesis can yield arrays with improved signal. In other embodiments, linkers are synthesized on the array surface prior to synthesis of functional molecules, wherein increasing linker length can correspond to an improvement in the signal generated by the array. 1a. performing a conditioning step on a surface of the array in the absence of monomers;b. repeating step (a) at least once;c. performing a synthesis step upon the surface to add at least one monomer; andd. repeating step (c) at least once to form a sequence, wherein the conditioning step performed prior to synthesizing the sequence enhances attachment of the sequence to the surface of the array.. A method for making an array comprising: This application is a continuation of U.S. patent application Ser. No. 15/264,426, filed Sep. 13, 2016 with claims the benefit of U.S. Provisional Application No. 62/218,418, filed Sep. 14, 2015, each of which is incorporated herein by reference in its entirety.This invention was made with government support under MCB-1243082 awarded by the National Science Foundation. The government has certain rights in the invention.The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Nov. 28, 2016, is named 42206-708_201_SL.txt and is 3,456 bytes in size.Array technologies allow for large-scale, quantitative analyses of biological samples. However, the density and robustness of such technologies should be improved to ...

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Номер записи: 30
29-03-2018 дата публикации

Flow Cell Array and Uses Thereof

Номер: US20180085727A1
Автор: Colgan Evan, Lvov Alexey Y., Polonsky Stanislav
Принадлежит:

Apparatus, computer program products, and methods for using a flow cell array are provided herein. A computer program product includes a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a device to cause the device to determine placement of one or more reaction sites on a first component; provide a material for the reaction sites in one or more surface channels of the first component; connect the first component to a second component to form an array, wherein the surface channels of the first component connect the reaction sites with one or more vias, and wherein the second component comprises the vias connected to multiple sub-surface channels; and align the surface channels of the first component with the vias of the second component to form a connection between the first component and the second component. 1. A computer program product comprising a computer readable storage medium having program instructions embodied therewith , the program instructions executable by a device to cause the device to:determine placement of one or more reaction sites on a first component;provide a material for the one or more reaction sites in one or more surface channels of the first component;connect the first component to a second component to form an array, wherein the one or more surface channels of the first component connect the one or more reaction sites with one or more vias, and wherein the second component comprises the one or more vias connected to multiple sub-surface channels; andalign the one or more surface channels of the first component with the one or more vias of the second component to form a connection between the first component and the second component.2. The computer program product of claim 1 , wherein said determining is based on use of a Gauss number if the number of the one or more reaction sites represents a sum of two integer squares.3. The computer program product of claim 1 , ...

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Номер записи: 31
29-03-2018 дата публикации

Flow Cell Array and Uses Thereof

Номер: US20180085728A1
Автор: Colgan Evan, Lvov Alexey Y., Polonsky Stanislav
Принадлежит:

Systems and methods for using a flow cell array are provided herein. A system includes at least one processor coupled to a memory and configured for determining placement of one or more reaction sites on a first component; providing a material for the one or more reaction sites in one or more surface channels of the first component; connecting the first component to a second component to form an array, wherein the one or more surface channels of the first component connect the one or more reaction sites with one or more vias, and wherein the second component comprises the one or more vias connected to multiple sub-surface channels; and aligning the one or more surface channels of the first component with the one or more vias of the second component to form a connection between the first component and the second component. 1. A system comprising:a memory; and determining placement of one or more reaction sites on a first component;', 'providing a material for the one or more reaction sites in one or more surface channels of the first component;', 'connecting the first component to a second component to form an array, wherein the one or more surface channels of the first component connect the one or more reaction sites with one or more vias, and wherein the second component comprises the one or more vias connected to multiple sub-surface channels; and', 'aligning the one or more surface channels of the first component with the one or more vias of the second component to form a connection between the first component and the second component., 'at least one processor coupled to the memory and configured for2. The system of claim 1 , wherein said determining is based on use of a Gauss number if the number of the one or more reaction sites represents a sum of two integer squares.3. The system of claim 1 , wherein said determining is based on use of numerical approximation.4. The system of claim 1 , wherein the at least one processor is further configured for:independently ...

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Номер записи: 32
21-03-2019 дата публикации

Apparatus, System, And Method Using Immiscible-Fluid-Discrete-Volumes

Номер: US20190085387A1
Автор: Cox David M., Lee Linda G., Ma Congcong, Oldham Mark F., REEL Richard T., SCHROEDER Benjamin G., SORENSON Jon M., WIYATNO Willy, WOO Sam L.
Принадлежит:

Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure. 1. A method comprising:amplifying a nucleic acid in at least one conduit to form an amplicon, the at least one conduit comprising an inner wall;attaching the amplicon to the inner wall to form an attached amplicon; anddetecting the attached amplicon or an attached derivative thereof, in the at least one conduit.2. A method comprising:sequentially contacting an aqueous sample fluid in a conduit with a non-aqueous spacing fluid that is immiscible with the aqueous sample, to form a plurality of discrete volumes of the aqueous sample fluid separated from one another by the non-aqueous spacing fluid, the aqueous sample fluid comprising a plurality of target nucleic acid sequences, wherein at least one of the discrete volumes contains at least one target nucleic acid sequence;amplifying the at least one target nucleic acid in the conduit to form an amplicon; andsubjecting the amplicon to a nucleic acid sequencing reaction in the conduit.3. The method of claim 2 , wherein subjecting the nucleic acid sequence to a sequencing reaction forms a detectable product claim 2 , and the method further comprises detecting the detectable product.4. The method of claim 3 , wherein the detectable product is detected inside the conduit.5. The method of claim 3 , wherein the detectable product is detected with a flow cell.6. The method of claim 2 , wherein the sequencing reaction comprises a Sanger sequencing reaction.7. The method of claim 2 , further comprising dividing the at least on nucleic acid containing discrete volume into two or more portions before ...

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Номер записи: 33
05-05-2022 дата публикации

System and method for patterning flow cell substrates

Номер: US20220134333A1
Автор: Dajun Yuan, Randall Smith, Steven MODIANO
Принадлежит: Illumina Inc

A method for patterning flow cell substrates using photo-initiated chemical reactions that includes fabricating a planar waveguide flow cell by forming a layer of light coupling gratings on a glass substrate layer; depositing a core layer on the layer of light coupling gratings; depositing a cladding layer on the core layer; and forming nanowells in the cladding layer; silanizing the cladding layer; coating the silanized cladding layer and nanowells with a first group of reactants; introducing a second group of reactants into the nanowells, wherein the second group of reactants includes a target reactant and a light-sensitive photoinitiator system; coupling a light source to the light coupling gratings and directing light internally within the planar waveguide flow cell for photo-initiating a chemical reaction between the first and second groups of reactants, wherein the photo-initiated chemical reaction covalently binds the target reactant to only the bottom portion of each nanowell.

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Номер записи: 34
05-04-2018 дата публикации

Flow Cell Array and Uses Thereof

Номер: US20180093243A1
Автор: Colgan Evan, Lvov Alexey Y., Polonsky Stanislav
Принадлежит:

Systems, computer program products, and methods for using a flow cell array are provided herein. A computer program product includes a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a device to cause the device to determine placement of multiple reaction site openings, wherein each reaction site opening is connected to a first sub-surface channel; connect the first sub-surface channel to two or more additional sub-surface channels by multiple vias; and provide a material for multiple reaction sites, wherein an overlap of the multiple reaction site openings and the material delineate the multiple reaction sites. 1. A computer program product comprising a computer readable storage medium having program instructions embodied therewith , the program instructions executable by a device to cause the device to:determine placement of multiple reaction site openings, wherein each reaction site opening is connected to a first sub-surface channel;connect the first sub-surface channel to two or more additional sub-surface channels by multiple vias; andprovide a material for multiple reaction sites, wherein an overlap of the multiple reaction site openings and the material delineate the multiple reaction sites.2. The computer program product of claim 1 , wherein the program instructions executable by a computing device further cause the computing device to:incorporate a cover to seal the multiple reaction site openings.3. The computer program product of claim 2 , wherein said incorporating comprises temporarily securing the cover.4. The computer program product of claim 2 , wherein said incorporating comprises permanently securing the cover.5. The computer program product of claim 1 , wherein said determining is based on use of a Gauss number if the number of the multiple reaction site openings represents a sum of two integer squares.6. The computer program product of claim 1 , wherein said determining is ...

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Номер записи: 35
05-04-2018 дата публикации

Flow Cell Array and Uses Thereof

Номер: US20180093244A1
Автор: Alexey Y. Lvov, Evan Colgan, Stanislav Polonsky
Принадлежит: International Business Machines Corp

Systems, computer program products, and methods for using a flow cell array are provided herein. A system includes at least one processor coupled to a memory and configured for determining placement of multiple reaction site openings, wherein each reaction site opening is connected to a first sub-surface channel; connecting the first sub-surface channel to two or more additional sub-surface channels by multiple vias; and providing a material for multiple reaction sites, wherein an overlap of the multiple reaction site openings and the material delineate the multiple reaction sites.

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Номер записи: 36
05-04-2018 дата публикации

Flow Cell Array and Uses Thereof

Номер: US20180093245A1
Автор: Colgan Evan, Lvov Alexey Y., Polonsky Stanislav
Принадлежит:

Systems, computer program products, and methods for using a flow cell array are provided herein. A computer program product includes a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a device to cause the device to deliver multiple items of chemical matter independently to multiple reaction sites of a flow cell array across multiple distinct instances of time; image multiple parallel chemical reactions at the multiple reaction sites of the flow cell array; and record an emission from each of the multiple chemical reactions site. 1. A computer program product comprising a computer readable storage medium having program instructions embodied therewith , the program instructions executable by a device to cause the device to:deliver multiple items of chemical matter independently to multiple reaction sites of a flow cell array across multiple distinct instances of time;image multiple parallel chemical reactions at the multiple reaction sites of the flow cell array; andrecord an emission from each of the multiple chemical reactions site.2. The computer program product of claim 1 , wherein said multiple distinct instances of time comprise multiple non-overlapping instances of time determined based on at least one of the multiple parallel chemical reactions and the multiple items of chemical matter. Embodiments of the invention generally relate to information technology, and, more particularly, to biological sequencing.Existing deoxyribonucleic acid (DNA) sequencing techniques, such as sequencing-by-synthesis (SBS), sequencing-by-ligation, and pyro-sequencing, use imaging of parallel cyclical chemical reactions. For example, reversible dye-terminators (RDTs) add one fluorescently-labeled nucleotide to a template (single-stranded DNA, for example) per cycle and determine the type of incorporated nucleotide based on the color of the fluorescent label. Such reactions require changing chemicals at every ...

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Номер записи: 37
05-04-2018 дата публикации

Flow Cell Array and Uses Thereof

Номер: US20180093246A1
Автор: Colgan Evan, Lvov Alexey Y., Polonsky Stanislav
Принадлежит:

Systems, computer program products, and methods for using a flow cell array are provided herein. A system includes at least one processor coupled to a memory and configured for delivering multiple items of chemical matter independently to multiple reaction sites of a flow cell array across multiple distinct instances of time; imaging multiple parallel chemical reactions at the multiple reaction sites of the flow cell array; and recording an emission from each of the multiple chemical reactions site. 1. A system comprising:a memory; and delivering multiple items of chemical matter independently to multiple reaction sites of a flow cell array across multiple distinct instances of time;', 'imaging multiple parallel chemical reactions at the multiple reaction sites of the flow cell array; and', 'recording an emission from each of the multiple chemical reactions site., 'at least one processor coupled to the memory and configured for2. The system of claim 1 , wherein said multiple distinct instances of time comprise multiple non-overlapping instances of time determined based on at least one of the multiple parallel chemical reactions and the multiple items of chemical matter. Embodiments of the invention generally relate to information technology, and, more particularly, to biological sequencing.Existing deoxyribonucleic acid (DNA) sequencing techniques, such as sequencing-by-synthesis (SBS), sequencing-by-ligation, and pyro-sequencing, use imaging of parallel cyclical chemical reactions. For example, reversible dye-terminators (RDTs) add one fluorescently-labeled nucleotide to a template (single-stranded DNA, for example) per cycle and determine the type of incorporated nucleotide based on the color of the fluorescent label. Such reactions require changing chemicals at every cycle and rely on fluidic cells to deliver the chemicals to multiple reaction sites. Typically, each cycle of an RDT chemical reaction includes the steps of detritylation, coupling, capping and ...

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Номер записи: 38
06-04-2017 дата публикации

DE NOVO SYNTHESIZED GENE LIBRARIES

Номер: US20170095785A1
Автор: Banyai William, Chen Siyuan, FERNANDEZ Andres, Indermuhle Pierre, Peck Bill James
Принадлежит:

De novo synthesized large libraries of nucleic acids are provided herein with low error rates. Further, devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Longer nucleic acids can be synthesized in parallel using microfluidic assemblies. Further, methods herein allow for the fast construction of large libraries of long, high-quality genes. Devices for the manufacturing of large libraries of long and high-quality nucleic acids are further described herein. 1. A device for nucleic acid collection , comprising: a base layer of the plate; and', a side wall that extends vertically from the base layer;', 'an interior region of the well; and', 'an exterior region of the well, wherein the exterior region of the well has a lower surface energy than the interior region of the well; and, 'one or more wells, wherein each well of the one or more wells comprises], 'a) a plate, the plate comprisingb) a flexible, solid support structure, wherein the flexible, solid support structure comprises a plurality of clusters, wherein each cluster comprises a plurality of loci, wherein each locus comprises (i) a microwell comprising a single fluidic opening, or (ii) a microchannel comprising two fluidic openings and extending through the flexible, solid support structure, and wherein each cluster is vertically aligned to a respective well.2. The device of claim 1 , wherein the flexible claim 1 , solid support structure is a sheet claim 1 , tubing claim 1 , gel claim 1 , or film.3. The device of claim 1 , wherein the flexible claim 1 , solid support structure comprises nylon claim 1 , nitrocellulose claim 1 , or polypropylene.4. The device of claim 1 , wherein the flexible claim 1 , solid support structure comprises silicon claim 1 , polystyrene claim 1 , agarose claim 1 , dextran claim 1 , cellulosic polymer claim 1 , polyacrylamide claim 1 , or polydimethylsiloxane (PDMS).5. The device of claim 1 , wherein the plate is silicon or ...

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Номер записи: 39
14-04-2016 дата публикации

Flow Cell Array and Uses Thereof

Номер: US20160101401A1
Автор: Alexey Y. Lvov, Evan C. Colgan, Stanislav Polonsky
Принадлежит: International Business Machines Corp

Apparatus and methods for using a flow cell array are provided herein. A method includes determining placement of one or more reaction sites on a first component; providing a material for the one or more reaction sites in one or more surface channels of the first component; connecting the first component to a second component to form an array, wherein the one or more surface channels of the first component connect the one or more reaction sites with one or more vias, and wherein the second component comprises the one or more vias connected to multiple sub-surface channels; and aligning the one or more surface channels of the first component with the one or more vias of the second component to form a connection between the first component and the second component.

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Номер записи: 40
19-04-2018 дата публикации

METHODS FOR MULTIPLEX ANALYTICAL MEASUREMENTS IN SINGLE CELLS OF SOLID TISSUES

Номер: US20180104663A1
Автор: Finski Alexei, MacBeath Gavin
Принадлежит: President and Fellows of Harvard College

The invention provides a method for the isolation of a single cell embedded in a tissue while preserving the state of molecules of the cell, and therefore allows for transformation of a single target cell in live tissue into a format that can be evaluated using analytical methods. 1. A method of lysing a single cell present in a tissue , the method comprising:a) identifying a cell from a tissue;b) contacting a detergent-containing lysis buffer with the intracellular space of the identified cell;c) allowing the lysis buffer to spread within the intracellular space of the identified cell for a period of time, wherein the cell is lysed from the inside of the cell; andd) collecting the lysate.2. The method of claim 1 , wherein the method occurs in the absence of tissue fixation and tissue disaggregation.3. The method of claim 1 , wherein the isolated cell is in an organotypic culture.4. The method of claim 1 , wherein the lysate is collected by suctioning the lysate using a suction channel.5. The method of claim 4 , wherein the suction channel is a bent suction micropipette.6. The method of claim 1 , wherein the collected lysate is further applied to a nitrocellulose pad.7. The method of claim 6 , wherein a standard is also applied to the nitrocellulose pad.8. The method of claim 1 , wherein the lysate is evaluated using an analytical method.9. The method of claim 8 , wherein the analytical method is selected from the group consisting of mass spectrometry claim 8 , protein microarray claim 8 , RT-qPCR claim 8 , RNA-Seq claim 8 , and MALDI-MS.10. The method of claim 1 , wherein the cell is part of a live solid tissue.11. The method of claim 1 , wherein the detergent is sodium dodecyl sulfate.12. A method of analyzing a cell present in a tissue claim 1 , the method comprising:a) identifying a cell from a tissue;b) contacting a detergent-containing lysis buffer to the intracellular space of the identified cell;c) allowing the lysis buffer to spread within the intracellular ...

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Номер записи: 41
23-04-2015 дата публикации

POLYMERIZED MICROARRAYS

Номер: US20150111764A1
Автор: Bian Shudan, Braunschweig Adam B., Zieba Sylwia
Принадлежит: New York University

Micropatterns of glycan-bearing brush polymers generated by the initiation of oligomerization of acrylate and methacrylate monomers from thiol-terminated surfaces. Chain lengths are controlled in situ by varying exposure time, and these multivalent glycan scaffolds detect glycan binding proteins at sub-micromolar concentrations. 1. A microarray comprising:a thiol-terminated substrate;a plurality of polymer brushes bound via thiol-(meth)acrylate polymerization to the thiol-terminated substrate.2. The microarray of claim 1 , wherein the polymer brushes exhibit a linear length growth rate from the substrate.3. The microarray of claim 1 , wherein the polymer brushes comprise a polymer grown by free radical polymerization.4. The microarray of claim 1 , wherein the polymer brushes comprise a materials selected from n (meth)acrylate oligomer and poly((meth)acrylate polymer.5. The microarray of claim 1 , wherein each of the polymer brushes comprise a plurality of binding sites for molecules selected from the group consisting of glycans claim 1 , glycan binding proteins claim 1 , antibodies claim 1 , peptides claim 1 , small molecules claim 1 , and DNA.7. The method of claim 6 , wherein the initiator is selected from the group consisting of a photoinitiator or a radical initiator.8. The method of claim 7 , wherein the initiator is a photoinitiator.9. The method of claim 8 , wherein the deposition of the (meth)acrylate-containing monomers and deposition of the photoinitiator is done simultaneously.10. The method of claim 8 , wherein the deposition of the (meth)acrylate-containing monomers and deposition of the photoinitiator is by polymer pen lithography and further wherein the acrylate-containing monomers and the photoinitiator are constituents of an ink for polymer pen lithography.11. The method of claim 8 , wherein the irradiation is by beam pen lithography.12. The method of wherein the photoinitiator is selected from the group consisting of 2 claim 8 ,2-dimethoxy-2- ...

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Номер записи: 42
19-04-2018 дата публикации

POLYPEPTIDE ARRAYS AND METHODS OF ATTACHING POLYPEPTIDES TO AN ARRAY

Номер: US20180106795A1
Автор: Bei Kang, Jayaraman Vasanth, Krishnamurthy Hari Krishnan, Rajasekaran John J., Wang Tianhao
Принадлежит:

Disclosed herein are formulations, substrates, and arrays. In certain embodiments, methods of attaching a biomolecule to an array using a photoactivated conjugation compound are disclosed. Methods of generating site-specific attachment of biomolecules to an array are also disclosed. Arrays generated by these methods and methods of using these arrays are also disclosed. 1. A method of attaching a biomolecule to a surface , comprising:obtaining a surface comprising a plurality of attachment groups attached to said surface;attaching a photoactivatable conjugation compound to said attachment group;contacting said surface with a biomolecule: andselectively exposing said surface to electromagnetic radiation, wherein said electromagnetic radiation activates said attached photoactivatable conjugation compound and wherein said attached activated photoactivatable conjugation compound binds to said biomolecule, thereby attaching said biomolecule to said surface.2. The method of claim 1 , wherein said photoactivatable conjugation compound comprises a functional group selected from the group consisting of: an NHS ester claim 1 , a sulfo-NHS ester claim 1 , an amine claim 1 , a primary alcohol claim 1 , a secondary alcohol claim 1 , a phenol claim 1 , a thiol claim 1 , an aniline claim 1 , a hydroxamic acid claim 1 , a primary amide claim 1 , an aliphatic amine claim 1 , and a sulfonamide.3. The method of claim 1 , wherein said photoactivatable conjugation compound comprises an ester.4. The method of claim 1 , wherein said photoactivatable conjugation compound comprises a carboxylic acid group.5. The method of claim 4 , wherein said carboxylic group is activated.6. The method of claim 1 , wherein said photoactivatable conjugation compound comprises an N-hydroxy succinimide moiety.7. The method of claim 1 , wherein said photoactivatable conjugation compound comprises an amine group.8. The method of claim 1 , wherein said photoactivatable conjugation compound comprises a ...

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Номер записи: 43
18-04-2019 дата публикации

PLATFORM FOR DISCOVERY AND ANALYSIS OF THERAPEUTIC AGENTS

Номер: US20190112730A1
Автор: Boutell Jonathan Mark, Golynskiy Misha, He Molly, KELLINGER Matthew William, Peisajovich Sergio, Previte Michael
Принадлежит: Illumina, Inc.

A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent. 1. A method of characterizing candidate agents , comprising(a) providing a library of candidate agents, wherein each candidate agent is attached to a nucleic acid tag haying a tag sequence;(b) conflicting the library of candidate agents with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed comprising individual features on the solid support that each attach to an individual candidate agent from the library;(c) contacting the array of candidate agents with a screening agent, wherein one or more candidate agents in the array react with the screening agent;(d) detecting the array during or after the contacting of the array with the screening agent, thereby determining that at least one candidate agent in the array reacts with the screening agent;(e) sequencing the nucleic acid tags on the array to determine the tag sequence that is attached to each of the candidate agents; and(f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.2. The method of claim 1 , wherein the ...

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Номер записи: 44
18-04-2019 дата публикации

ARRAY-BASED PEPTIDE LIBRARIES FOR THERAPEUTIC ANTIBODY CHARACTERIZATION

Номер: US20190113522A1
Автор: Greving Matthew, SAINI Gaurav, Smith David
Принадлежит:

Provided herein are methods, chemical library and simulation system for performing in situ patterned chemistry. Methods, systems and assays comprising the use of the synthesized chemical libraries, which increase explored protein space in a knowledge-based manner, are also provided for characterizing antibody-target interactions including: identifying target proteins of antibodies, characterizing antibody-binding regions in target proteins, identifying linear and structural epitopes in target proteins, and determining the propensity of antibody binding to target proteins. 1. A method of in situ synthesizing a chemical library on a substrate , the chemical library comprising a plurality of molecules , the method comprising:(a) receiving a biological sequence and a number of synthesis steps;(b) determining a plurality of patterned masks, wherein each patterned mask is assigned an activated or inactivated designation to each feature on the substrate, and wherein about 1% to about 75% of the activated designation features in each sequential patterned mask overlaps with the activated designation features of an immediately preceding patterned mask;(c) assigning at least one monomer to each patterned mask; and(d) coupling the monomers onto the features to form molecules;wherein (c) and (d) assembles one said synthesis step and the synthesis step is repeated.2. The method of claim 1 , wherein the number of synthesis steps is larger than 50% claim 1 , 60% claim 1 , 70% claim 1 , 80% claim 1 , 90% claim 1 , 100% claim 1 , 110% claim 1 , 120% claim 1 , 130% claim 1 , 140% claim 1 , 150% claim 1 , 160% claim 1 , 170% claim 1 , 180% claim 1 , 190% claim 1 , or 200% of a length of the biological sequence.3. The method of claim 1 , wherein the input biological sequence comprises a disease-related epitope.4. The method of claim 1 , wherein the input biological sequence comprises a peptide sequence.5. The method of claim 1 , wherein the input biological sequence comprises an epitope ...

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Номер записи: 45
04-05-2017 дата публикации

SYSTEM AND METHOD FOR LONGITUDINAL ANALYSIS OF PEPTIDE SYNTHESIS

Номер: US20170120212A1
Автор: Bannen Ryan, Barilovits Sarah, PATEL Jigar, SULLIVAN Eric, Tan John
Принадлежит:

The present invention provides a system and method for assessing a synthetic peptide population including interrogating a population of peptide features in the presence of a receptor having an affinity for a binder sequence. The population of peptide features is synthesized over a plurality of synthesis periods and includes a plurality of control peptide features synthesized to have an amino acid sequence including the binder sequence. The control peptide features include a first feature synthesized beginning with a first one of the synthesis periods, and a second feature synthesized beginning after the first one of the synthesis periods such that synthesis of the second control peptide feature is delayed by at least one synthesis period. The method further includes detecting a signal output characteristic of an interaction of the receptor with the control peptide features, the signal output indicative of the fidelity of synthesis of the population of peptide features. 1. A method of assessing a synthetic peptide population , the method comprising: a first control peptide feature synthesized beginning with a first one of the plurality of synthesis periods; and', 'a second control peptide feature synthesized beginning after the first one of the plurality of synthesis periods such that synthesis of the second control peptide feature is delayed by at least one synthesis period; and, 'interrogating a population of peptide features in the presence of a receptor having an affinity for a binder sequence, the population of peptide features synthesized over a plurality of synthesis periods, the population of peptide features including a plurality of control peptide features synthesized to have an amino acid sequence including the binder sequence, the plurality of control peptide features includingdetecting a signal output characteristic of an interaction of the receptor with the plurality of control peptide features, the signal output indicative of the fidelity of synthesis ...

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Номер записи: 46
01-09-2022 дата публикации

STRUCTURED SUBSTRATES FOR OPTICAL SURFACE PROFILING

Номер: US20220276174A1
Автор: Bergstein David A., Goldberg Bennett B., Ruane Michael F., ÜNLÜ M. Selim
Принадлежит:

This disclosure provides methods and devices for the label-free detection of target molecules of interest. The principles of the disclosure are particularly applicable to the detection of biological molecules (e.g., DNA, RNA, and protein) using standard SiO2-based microarray technology. 115-. (canceled)16. An optical detection apparatus comprising:(i) a light source, wherein said light source produces an illumination beam comprising one or more wavelength(s);(ii) a reflective substrate comprising capture molecules bound to an uppermost surface, wherein the illumination beam is directed onto the reflective substrate;(iii) a flow cell into which the reflective substrate is incorporated to allow delivery of target molecules to the capture molecules in a fluid environment; and(iv) a photodetector array operably linked to a central processor capable of measuring an intensity of light from the illumination beam reflected from the reflective substrate.1756-. (canceled)57. The optical detection apparatus of claim 16 , wherein the light source is a laser.58. The optical detection apparatus of claim 57 , wherein the laser is a tunable laser.59. The optical detection apparatus of claim 16 , wherein the illumination beam comprises substantially a single wavelength.60. The optical detection apparatus of claim 16 , wherein the reflective substrate comprises silicon dioxide (SiO).61. The optical detection apparatus of claim 16 , wherein the reflective substrate comprises a plurality of spatially distinct binding locations claim 16 , each location comprising a plurality of substantially identical capture molecules that specifically bind a single type of target molecule.62. The optical detection apparatus of claim 16 , comprising one or more objectives to focus the illumination beam and/or imaged light.63. The optical detection apparatus of claim 16 , wherein the photodetector array and central processor operably linked thereto are capable of recording an image comprising pixels ...

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Номер записи: 47
21-05-2015 дата публикации

METHODS FOR PERFORMING PATTERNED CHEMISTRY

Номер: US20150141296A1
Автор: Gupta Nidhi, Rajesekaran John, WOODBURY Neal
Принадлежит: The Arizona Board of Regents, A Body Corporate of the State of Arizona, acting for and on behalf of

Provided are methods for performing patterned chemistry and arrays prepared thereby. 1. A method of making an array of molecules , comprising:providing a substrate having a surface wherein the surface has a plurality of features, each of the features being defined by a perimeter and at least some of the features comprising a first plurality of active sites, wherein the perimeter is a metal,applying a first chemical reaction mixture onto the surface such that the first chemical reaction mixture is evenly distributed across the plurality of active sites, wherein the first chemical reaction mixture comprises a first molecule having a first functional group capable of attaching to the active site, a second functional group capable of forming a covalent bond and a protecting group capping the second functional group, whereby the first molecule is coupled to the first plurality of active sites.2. The method of further comprisingselectively forming a second plurality of active sites in at least some of the features,applying a second chemical reaction mixture onto the surface such that the second chemical reaction mixture is evenly distributed across the second plurality of active sites, wherein the second chemical reaction mixture comprises a second molecule having a first functional group capable of attaching to the active site, a second functional group capable of forming a covalent bond and a protecting group capping the second functional group, whereby the second molecule is coupled to the second plurality of active sites.3. The method of claim 1 , wherein after the first chemical reaction mixture is applied onto the surface claim 1 , the method further comprises heating the substrate.4. The method of claim 3 , wherein the heating the substrate comprises heating the substrate with a hot plate.5. The method of claim 2 , wherein selectively forming a second plurality of active sites in at least some of the features comprisesdepositing a photosensitive layer over the ...

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Номер записи: 48
21-05-2015 дата публикации

METHOD OF MANUFACTURING PROBE-IMMOBILIZED CARRIER

Номер: US20150141298A1
Автор: Kawamura Masashi, Okabe Tetsuo
Принадлежит:

A probe-immobilized carrier for detecting a target substance is manufactured such that a spot is prevented from being contaminated with another spot and a probe is prevented from nonspecifically adsorbing a background area in the manufacture of the probe-immobilized carrier and nonspecific adsorption cannot be occurred even after the formation of an array. A substrate containing a reactive group for immobilizing a probe thereon is used and the steps of: (i) supplying a liquid droplet containing a probe on the substrate; (ii) inactivating a reactive group existing in an area other than a supplying area of the substrate, and (iii) removing an unreacted probe existing in the supplied liquid droplet are carried out. 117-. (canceled)18. A method of manufacturing a probe-immobilized carrier , comprising the steps of:(i) introducing a reactive group for immobilizing a probe to a surface of a substrate;(ii) supplying a liquid droplet containing the probe to an area on the surface of the substrate;(iii) immobilizing the probe on the substrate through the reactive group;(iv) inactivating the reactive group existing in an area other than the area supplied with the liquid droplet on the substrate, by applying a blocking compound to a region on the substrate including the area supplied with the liquid droplet so as not to spread the liquid droplet on the surface; and(v) subsequently removing the unreacted probe existing in the supplied liquid droplet.19. The method of manufacturing a probe-immobilized carrier according to claim 18 , wherein the liquid droplet is supplied by spotting.20. The method of manufacturing a probe-immobilized carrier according to claim 18 , wherein the blocking compound is applied to the region by a gas-phase treatment.21. The method of manufacturing a probe-immobilized carrier according to claim 20 , wherein the gas-phase treatment is effected by confining the substrate supplied with the liquid droplet containing a probe in a closed chamber filled with ...

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Номер записи: 49
18-05-2017 дата публикации

GEL PATTERNED SURFACES

Номер: US20170136434A1
Автор: Barnard Steven M., Bowen M. Shane, Brown Andrew A., George Wayne N., Rogert Bacigalupo Maria Candelaria, Tsay James
Принадлежит:

Provided is an array including a solid support having a surface, the surface having a plurality of wells, the wells containing a gel material, the wells being separated from each other by interstitial regions on the surface, the interstitial regions segregating the gel material in each of the wells from the gel material in other wells of the plurality; and a library of target nucleic acids in the gel material, wherein the gel material in each of the wells comprises a single species of the target nucleic acids of the library. Methods for making and using the array are also provided. 128.-. (canceled)29. A method comprising:coating at least a portion of the support with a gel material, the solid support comprising a planar surface interrupted by a plurality of concave features bordered by one or more interstitial regions on the planar surface, wherein the portion comprises at least some of the concave features and at least some of the interstitial regions; andpolishing the gel material from the at least some of the interstitial regions while maintaining the gel material in the at least some of the concave features, including on bottom surfaces of the at least some of the concave features.30. The method of claim 29 , wherein the support comprises a solid support.31. The method of claim 30 , wherein the solid support comprises glass claim 30 , silicon claim 30 , or a plastic material claim 30 , or a combination thereof.32. The method of claim 29 , wherein coating comprises contacting the solid support with a preformed gel material.33. The method of claim 29 , wherein coating comprises contacting the solid support with a liquid that subsequently forms the gel material.34. The method of claim 29 , wherein the gel comprises poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) that non-covalently associates with the at least some of the concave features.35. The method of claim 34 , wherein the concave features comprise a non-silanized surface.36. The method of claim 29 ...

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Номер записи: 50
18-05-2017 дата публикации

Arrays, substrates, devices, methods and systems for detecting target molecules

Номер: US20170138942A1
Автор: Habib Ahmad, James R. Heath, Rong Fan
Принадлежит: California Institute of Technology CalTech

Arrays and substrates comprising a material, in particular capture agents and/or detectable targets, attached to the substrates along substantially parallel lines forming a barcoded pattern and related methods and systems.

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Номер записи: 51
24-05-2018 дата публикации

PLATFORM FOR DISCOVERY AND ANALYSIS OF THERAPEUTIC AGENTS

Номер: US20180142378A1
Автор: Boutell Jonathan Mark, Golynskiy Misha, He Molly, KELLINGER Matthew William, Peisajovich Sergio, Previte Michael
Принадлежит:

A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent. 1. A method of characterizing candidate agents , comprising(a) providing a library of candidate agents, wherein each candidate agent is attached to a nucleic acid tag having a tag sequence;(b) contacting the library of candidate agents with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed comprising individual features on the solid support that each attach to an individual candidate agent from the library;(c) contacting the array of candidate agents with a screening agent, wherein one or more candidate agents in the array react with the screening agent;(d) detecting the array during or after the contacting of the array with the screening agent, thereby determining that at least one candidate agent in the array reacts with the screening agent;(e) sequencing the nucleic acid tags on the array to determine the tag sequence that is attached to each of the candidate agents; and(f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.2. The method of claim 1 , wherein the ...

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Номер записи: 52
25-05-2017 дата публикации

Method for producing polymers

Номер: US20170147748A1
Автор: Cord F. Staehler, Manfred Mueller, Peer F. STAEHLER
Принадлежит: Synthetic Genomics Inc

Synthesis of polymers (I) comprising constructing oligomeric building blocks (II) on a carrier by parallel synthesis, releasing (II) from the carrier and combining (II) to form (I), is new.

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Номер записи: 53
17-06-2021 дата публикации

NUCLEIC ACID IMMOBILIZATION ARTICLE AND METHODS THEREOF

Номер: US20210178353A1
Автор: "OMalley Shawn Michael", LYNN JEFFREY GLENN
Принадлежит:

An article including: a substrate; and at least one immobilization site on the substrate comprising at least one nucleic acid immobilization site, each site having a first layer of a tie agent in contact with the substrate, and a second layer of a dendrimer mobilizing agent in contact with the first layer. Also disclosed is a method of making and a method of using the article. 116-. (canceled)17. A method comprising:coating a substrate with a photoresist adhesion promoter to form an adhesion promoted substrate;coating the adhesion promoted substrate with a photoresist and developing the photoresist by selective light exposure to form a selected pattern;developing the selected pattern with a photoresist etchant to form an etched patterned substrate;selectively coating etched areas of the etched patterned substrate by chemical vapor deposition with a tie agent to form a tie agent coated etched patterned substrate;removing the photoresist from the tie agent coated etched patterned substrate; andcontacting the tie agent coated etched patterned substrate with a dendrimer, either before or after removing the photoresist from the tie agent coated etched patterned substrate, to form a patterned nucleic acid immobilization surface.18. The method of claim 17 , wherein the tie agent comprises (3-glycidyloxypropyl) trimethoxysilane (GLYMO).19. The method of claim 17 , wherein the dendrimer comprises a polyamidoamine (PAMAM) dendrimer.20. The method of claim 17 , wherein the photoresist adhesion promoter comprises hexamethyldisilazane (HMDS).21. The method of claim 17 , comprising immobilizing a plurality of DNA nanoballs on a corresponding array of patches of the patterned nucleic acid immobilization surface.22. The method of claim 21 , wherein the immobilizing the plurality of DNA nanoballs comprises electrostatically immobilizing the plurality of DNA nanoballs on the corresponding array of patches of the patterned nucleic acid immobilization surface.23. The method of claim 21 ...

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Номер записи: 54
07-05-2020 дата публикации

STRUCTURED SUBSTRATES FOR OPTICAL SURFACE PROFILING

Номер: US20200141875A1
Автор: Bergstein David A., Goldberg Bennett B., Ruane Michael F., ÜNLÜ M. Selim
Принадлежит:

This disclosure provides methods and devices for the label-free detection of target molecules of interest. The principles of the disclosure are particularly applicable to the detection of biological molecules (e.g., DNA, RNA, and protein) using standard SiO-based microarray technology. 1. A layered substrate comprising a base layer , at least one coating layer having a refractive index different from the refractive index of said base layer , and a plurality of spatially distinct binding locations , wherein each of said binding locations comprises capture molecules bound to the topmost coating layer.2. The layered substrate of claim 1 , wherein said base layer has a high refractive index.3. The layered substrate of claim 1 , wherein the refractive index of said at least one coating layer is between about 1.1 and about 1.7.4. The layered substrate of claim 1 , wherein the refractive index of said at least one coating layer is about 1.4.5. The layered substrate of claim 1 , wherein said base layer comprises silicon.6. The layered substrate of claim 1 , wherein at least one of said coating layers comprises SiO.7. The layered substrate of claim 1 , wherein at least one of said coating layers comprises SiN.8. The layered substrate of claim 1 , wherein at least one of said coating layers comprises gold.9. The layered substrate of claim 1 , wherein said substrate comprises at least two different coating layers.10. The layered substrate of claim 1 , wherein said substrate further comprises a plurality of reaction wells.11. The layered substrate of claim 1 , wherein each of said binding locations comprise a single type of capture molecule.12. The layered substrate of claim 1 , wherein said capture molecules are selected from the group consisting of DNA claim 1 , RNA claim 1 , and protein.13. The layered substrate of claim 1 , wherein said capture molecules are covalently bound to said topmost coating layer.14. The layered substrate of claim 1 , having one coating layer and ...

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Номер записи: 55
21-08-2014 дата публикации

Protein Chips for High Throughput Screening of Protein Activity

Номер: US20140235507A1
Автор: Heng Zhu, James Frank Klemic, Mark Reed, Michael Snyder
Принадлежит: YALE UNIVERSITY

The present invention relates to protein chips useful for the large-scale study of protein function where the chip contains densely packed reaction wells. The invention also relates to methods of using protein chips to assay simultaneously the presence, amount, and/or function of proteins present in a protein sample or on one protein chip, or to assay the presence, relative specificity, and binding affinity of each probe in a mixture of probes for each of the proteins on the chip. The invention also relates to methods of using the protein chips for high density and small volume chemical reactions. Also, the invention relates to polymers useful as protein chip substrates and methods of making protein chips. The invention further relates to compounds useful for the derivatization of protein chip substrates.

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Номер записи: 56
07-06-2018 дата публикации

NON-FOULING POLYMERIC SURFACE MODIFICATION AND SIGNAL AMPLIFICATION METHOD FOR BIOMOLECULAR DETECTION

Номер: US20180155763A1
Автор: Chilkoti Ashutosh
Принадлежит:

An article such as a biosensor having a nonfouling surface thereon is described. The article comprises: (a) a substrate having a surface portion; (b) a linking layer on the surface portion; (c) a polymer layer comprising brush molecules formed on the linking layer; and (d) optionally but preferably, a first member of a specific binding pair (e.g., a protein, peptide, antibody, nucleic acid, etc.) coupled to the brush molecules. The polymer layer is preferably formed by the process of surface-initiated polymerization (SIP) of monomeric units thereon. Preferably, each of the monomeric units comprises a monomer (for example, a vinyl monomer) core group having at least one protein-resistant head group coupled thereto, to thereby form the brush molecule on the surface portion. Methods of using the articles are also described. 1. A biomolecular detector , comprising:(a) a substrate having a surface portion;(b) a linking layer on said surface portion; and(c) a polymer layer formed on said linking layer by the process of surface-initiated polymerization of monomeric units thereon, with each of said monomeric units comprising a monomer core group having at least one protein-resistant head group coupled thereto, to thereby form a brush molecule on said surface portion;said brush molecule comprising a stem formed from the polymerization of said monomer core groups, and a plurality of branches formed from said head group projecting from said stem; and(d) a first member of a specific binding pair coupled to said brush molecule.242-. (canceled) This application claims the benefit of U.S. Provisional Patent Application Ser. No. 60/717,430; filed Sep. 15, 2005, the disclosure of which is incorporated by reference herein in its entirety.This application is related to Ashutosh Chilkoti and Hongwei Ma, A tunable nonfouling surface of oligoethylene glycol, U.S. patent application Ser. No. 10/783,054, filed Feb. 20, 2004 (Docket No. 5405-318), the disclosure of which is incorporated by ...

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Номер записи: 57
14-05-2020 дата публикации

COMPOSITIONS AND METHODS FOR ENTRAPPING PROTEIN ON A SURFACE

Номер: US20200147580A1
Автор: Hogan Michael E.
Принадлежит:

The present invention provides a formulation to link protein to a solid support that comprises one or more proteins, Oligo-dT and one or more non-volatile, water-soluble protein solvents, solutes or combination thereof in an aqueous solution. Further provided is a method of attaching a protein to a surface of a substrate. The formulations provided herein are contacted onto the substrate surface, printed thereon and air dried. The substrate surface is irradiated with UV light to induce thymidine photochemical crosslinking via the thymidine moieties of the Oligo-dT. 1. A composition for measuring binding to HLA proteins , comprising:a substrate having a surface; anda first array of HLA protein spots indirectly attached to the surface of the substrate, wherein each HLA protein within each spot is entrapped within a matrix that retains the native three dimensional structure of the HLA protein while the HLA protein is indirectly attached to the surface.2. The composition of claim 1 , wherein the matrix that retains the native three dimensional structure of the HLA protein comprises a cross-linked Oligo-dT network bound to the surface of the substrate.3. The composition of claim 2 , wherein each Oligo-dT in the network comprises 30-100 nucleotides.4. The composition of claim 1 , wherein the first array of HLA protein spots comprises glycerol claim 1 , propanediol claim 1 , sorbitol or trehalose.5. The composition of claim 4 , wherein the first array of HLA protein spots comprises glycerol claim 4 , propanediol claim 4 , sorbitol or trehalose in a concentration of 0.5% to 1%.6. The composition of claim 1 , wherein the first array of HLA protein spots comprises the HLA proteins at a concentration of 5 μg/ml-500 μg/ml.7. The composition of claim 1 , further comprising a second array of HLA protein spots indirectly attached to the surface of the substrate claim 1 , wherein the second array of HLA protein spots comprises different HLA proteins than the first array of HLA ...

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Номер записи: 58
14-05-2020 дата публикации

CATALYTICALLY ACTIVE SUBSTANCES

Номер: US20200147595A1
Автор: Kraft Lewis J.
Принадлежит:

A catalytically active substance includes a copper (I) sulfide mineral particle, and an alkyne functionalized molecule bound to a surface of the copper (I) sulfide mineral particle. In an example method, a copper (I) sulfide mineral is reacted with an alkyne functionalized molecule to form a catalytically active substance. The catalytically active substance is reacted with an azide functionalized molecule to couple the catalytically active substance with the azide functionalized molecule. 1. A catalytically active substance , comprising:a copper (I) sulfide mineral particle; andan alkyne functionalized molecule bound directly to a surface of the copper (I) sulfide mineral particle.2. The catalytically active substance as defined in claim 1 , wherein the copper (I) sulfide mineral particle is selected from the group consisting of chalcocite claim 1 , djurleite claim 1 , and digenite.3. The catalytically active substance as defined in claim 1 , wherein the alkyne functionalized molecule is a primer having an alkyne functional group attached at the 5′ terminus of the primer.4. The catalytically active substance as defined in claim 1 , wherein a coordinate bond binds the alkyne functionalized molecule to the surface of the copper (I) sulfide mineral particle.5. A method of making a triazole claim 1 , comprising reacting an alkyne functionalized molecule with an azide functionalized molecule in the presence of a copper (I) sulfide mineral.6. The method as defined in claim 5 , wherein:the copper (I) sulfide mineral reacts with the alkyne functionalized molecule to form a catalytically active substance; andthe catalytically active substance reacts with the azide functionalized molecule to couple the catalytically active substance with the azide functionalized molecule.7. The method as defined in claim 5 , wherein prior to reacting the copper (I) sulfide mineral with the alkyne functionalized molecule claim 5 , the method further comprises adding a stoichiometric excess of ...

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Номер записи: 59
14-05-2020 дата публикации

DEVICE AND METHOD FOR MAKING DISCRETE VOLUMES OF A FIRST FLUID IN CONTACT WITH A SECOND FLUID, WHICH ARE IMMISCIBLE WITH EACH OTHER

Номер: US20200149099A1
Автор: Cox David, GREINER Douglas, LEE Linda, LEHTO Dennis, NURSE James, REEL Richard, WIYATNO Willy K., WOJTOWICZ Janusz, WOO Sam
Принадлежит: APPLIED BIOSYSTEMS, LLC

A system may include a first conduit configured to form a first batch of discrete volumes of aqueous fluid separated by spacing liquid disposed between consecutive volumes of aqueous fluid, the spacing liquid being immiscible with the aqueous fluid volumes; a second conduit, fluidically coupled to the first conduit, the second conduit configured to statically hold the first batch of discrete volumes of aqueous fluid; and a third conduit configured to receive the first batch of discrete volumes of aqueous fluid from the second conduit. The third conduit can be configured to transfer the discrete volumes of aqueous fluid of the first batch for downstream processing. 1. A system comprising:a first conduit configured to form a first batch of discrete volumes of aqueous fluid separated by spacing liquid disposed between consecutive volumes of aqueous fluid, the spacing liquid being immiscible with the aqueous fluid volumes;a second conduit, fluidically coupled to the first conduit, the second conduit configured to statically hold the first batch of discrete volumes of aqueous fluid; anda third conduit configured to receive the first batch of discrete volumes of aqueous fluid from the second conduit;wherein the third conduit is configured to transfer the discrete volumes of aqueous fluid of the first batch for downstream processing.2. The system according to claim 1 , wherein the downstream processing comprises a thermal cycling nucleic acid sequence amplification process.3. The system according to claim 2 , wherein the downstream processing comprises a fluorescence detection process.4. The system according to claim 1 , wherein the downstream processing comprises a fluorescence detection process.5. The system according to claim 1 , further comprising a vessel configured to contain the aqueous fluid and another fluid immiscible with the aqueous fluid claim 1 , wherein the vessel is fluidically coupled to flow the aqueous fluid to the first conduit.6. The system of claim 1 ...

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Номер записи: 60
23-05-2019 дата публикации

METHOD FOR DETECTING TARGET MOLECULE

Номер: US20190154682A1
Автор: ARAKI Suguru, IINO Ryota, NOJI Hiroyuki
Принадлежит: JAPAN SCIENCE AND TECHNOLOGY AGENCY

This invention provides a technique enabling to detect target molecules of low concentration with high sensitivity. This invention includes (i) a step of introducing a hydrophilic solvent () containing beads (),(′) into a space () between (a) a lower layer section () including a plurality of receptacles () each of which is capable of storing only one of the beads (),(′) and which are separated from each other by a side wall () having a hydrophobic upper surface and (b) an upper layer section () facing a surface of the lower layer section () on which surface the plurality of receptacles () are provided; and (ii) a step of introducing a hydrophobic solvent () into the space (), the step (ii) being carried out after the step (i). 112-. (canceled)13: A detecting method using a kit and a deaerating device , [ a lower layer section provided with a plurality of receptacles being separated from each other by a side wall having a hydrophobic upper surface; and', 'an upper layer section facing, via a space, a surface of the lower layer section on which surface the plurality of receptacles are provided;, 'an array having a flow cell structure, said array including, 'beads;', 'a hydrophilic solvent; and', 'a hydrophobic solvent;', 'each of the plurality of receptacles is capable of storing only one of the beads; and', 'said space is used as a flow path for allowing a fluid to flow between the lower layer section and the upper layer section;, 'wherein said kit comprises said deaerating device is set for removing air in the plurality of receptacles while keeping the hydrophilic solvent as it is in the plurality of receptacles;', 'said kit and said deaerating device being used to carry out a method for sealing the beads, the method comprising the steps of:', '(i) introducing the hydrophilic solvent containing the beads into the space between the lower layer section and the upper layer section;', '(ii) deaerating to remove air in the plurality of receptacles while keeping the ...

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Номер записи: 61
24-06-2021 дата публикации

CATALYST-FREE SURFACE FUNCTIONALIZATION AND POLYMER GRAFTING

Номер: US20210189082A1
Автор: Berti Lorenzo, Brown Andrew A., George Wayne N.
Принадлежит:

Some embodiments described herein relate to a substrate with a surface comprising a silane or a silane derivative covalently attached to optionally substituted cycloalkene or optionally substituted heterocycloalkene for direct conjugation with a functionalized molecule of interest, such as a polymer, a hydrogel, an amino acid, a nucleoside, a nucleotide, a peptide, a polynucleotide, or a protein. In some embodiments, the silane or silane derivative contains optionally substituted norbornene or norbornene derivatives. Method for preparing a functionalized surface and the use in DNA sequencing and other diagnostic applications are also disclosed. 1. A substrate comprising a first surface comprising silane or a silane derivative covalently bound to a functionalized molecule through a first plurality of unsaturated moieties selected from cycloalkenes , cycloalkynes , heterocycloalkenes , heterocycloalkynes , or optionally substituted variants or combinations thereof covalently attached to silicon atoms of said silane or silane derivative.2. The substrate of claim 1 , wherein said first plurality of unsaturated moieties are selected from norbornene claim 1 , heteronorbornenes claim 1 , norbornene derivatives claim 1 , trans-cyclooctene claim 1 , trans-cyclooctene derivatives claim 1 , cyclooctyne claim 1 , bicycloalkynes claim 1 , or optionally substituted variants or combinations thereof.3. The substrate of claim 1 , wherein said first plurality of unsaturated moieties are selected from optionally substituted norbornene claim 1 , optionally substituted cyclooctyne claim 1 , optionally substituted bicyclononyne claim 1 , or optionally substituted bicyclo[6.1.0]non-4-yne.4. The substrate of claim 1 , further comprising linkers covalently attached between silicon atoms of said silane or silane derivative and the first plurality of unsaturated moieties.5. The substrate of claim 4 , wherein the linkers are selected from optionally substituted alkylenes claim 4 , optionally ...

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Номер записи: 62
21-05-2020 дата публикации

Substrates, Peptide Arrays, and Methods

Номер: US20200156036A1
Автор: Hari Krishnan KRISHNAMURTHY, John J. Rajasekaran, Kang Bei, Tianhao WANG, Vasanth JAYARAMAN
Принадлежит: Vibrant Holdings LLC

Disclosed herein are formulations, substrates, and arrays. Also disclosed herein are methods for manufacturing and using the formulations, substrates, and arrays. Also disclosed are methods for identifying peptide sequences useful for diagnosis and treatment of disorders, and methods for using the peptide sequences for diagnosis and treatment of disorders, e.g., celiac disorder. In certain embodiments, substrates and arrays comprise a porous layer for synthesis and attachment of polymers or biomolecules.

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Номер записи: 63
25-06-2015 дата публикации

MICROARRAY SYSTEM WITH IMPROVED SEQUENCE SPECIFICITY

Номер: US20150176067A1
Автор: BEHLKE Mark Aaron, Gunning Kerry B.
Принадлежит:

The invention provides a novel array method for nucleic acid sequence detection with improved specificity which allows for detection of genetic variation, from simple SNPs (where the variation occurs at a fixed position and is of limited allelic number) to more complex sequence variation patterns (such as with multigene families or multiple genetic strains of an organism where the sequence variation between the individual members is neither fixed nor consistent). The array is comprised of short, synthetic oligonucleotide probes attached to a solid surface which are hybridized to single-stranded targets. Single stranded targets can be produced using a method that employs primers modified on the 5′ end to prohibit degradation by a 5′-exonuclease that is introduced to degrade the unprotected strand. The invention further provides for printing buffers/solutions for the immobilization of oligonucleotide probes to an array surface. The invention also provides hybridization and wash buffers and conditions to maximize hybridization specificity and signal intensity, and reduce hybridization times. 1. An array comprising a surface comprising epoxide moieties and a plurality of oligonucleotides each comprising a 5′ hydrazide linker attached to the surface of the array through a bond formed between the linker and an epoxide moiety.2. A method of forming a microarray on a surface comprising epoxide moieties , comprising:depositing a plurality of samples onto the surface in discrete domains, each sample comprising a spotting buffer and an oligonucleotide comprising a 5′ hydrazide linker, under conditions that allow formation of a bond between the hydrazide linker and the epoxide moiety.3. The method of claim 2 , wherein the spotting buffer has a pH of less than about 8.5 and comprises monobasic sodium phosphate claim 2 , an ethylene oxide based nonionic detergent claim 2 , and ethylene glycol.4. The method of claim 3 , wherein the nonionic detergent is Nonidet P-40.5. The method ...

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Номер записи: 64
23-06-2016 дата публикации

COVALENTLY-IMMOBILIZED HYDROGEL ARRAYS IN MULTI-WELL PLATES

Номер: US20160175800A1
Автор: Le Ngoc Nhi, Murphy William
Принадлежит:

Hydrogel arrays, methods for preparing hydrogel arrays and methods for screening cell-substrate interactions using the hydrogel arrays are disclosed. Advantageously, the hydrogel arrays include individual hydrogel posts that are completely isolatable, allowing for systematic and independent control of the chemical composition and physical dimensions of each hydrogel post. 1. A method of preparing a hydrogel array comprising a multi-well plate , the multi-well plate comprising a plurality of wells wherein the plurality of wells independently comprises a hydrogel post , the method comprisingthiol-functionalizing a bottom surface of the plurality of wells;adding a hydrogel precursor solution to at least one well of the plurality of wells;selectively polymerizing a portion of the hydrogel precursor solution in the at least one well; andremoving unpolymerized hydrogel precursor solution from the plurality of wells, wherein the polymerized hydrogel forms a hydrogel post covalently immobilized within the at least one well.2. The method of wherein the thiol-functionalizing of the bottom surface of the plurality of the wells is by silanization.3. The method of further comprising assembling the multi-well plate with a negative insert claim 1 , wherein the negative insert fills a portion of a volume of the well.4. The method of wherein the multi-well plate is selected from the group consisting of a glass-bottom multi-well plate and a polystyrene multi-well plate.5. The method of claim 4 , wherein the multi-well plate is selected from the group consisting of 4-well plates claim 4 , 6-well plates claim 4 , 8-well plates claim 4 , 12-well plates claim 4 , 24-well plates claim 4 , 32-well plates claim 4 , 96-well plates claim 4 , and 384-well plates.6. The method of wherein the hydrogel precursor solution is polymerized by exposure to ultraviolet light.7. The method of further comprising forming a hydrogel layer on the hydrogel post.8. The method of wherein the hydrogel precursor ...

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Номер записи: 65
22-06-2017 дата публикации

THREE-DIMENSIONAL POLYMER NETWORKS WITH CHANNELS SITUATED THEREIN

Номер: US20170175176A1
Автор: BEDNAR Sonja, KLAPPROTH Holger
Принадлежит: Safeguard Biosystems Holdings Ltd.

The disclosure provides three-dimensional crosslinked polymer networks comprising one or more channels extending from the surface and/or near the surface of the network into the interior of the network, arrays comprising the networks, processes for making the networks, and uses of the networks and arrays. 131-. (canceled)32. A three-dimensional network having a surface and an interior , said three-dimensional network comprising:(a) a water-soluble polymer that has been cross-linked and covalently attached to the surface of a substrate;(b) at least 5 channels that converge at a point in the interior of the network such that the lateral distance between the channels decreases from the surface toward the point in the interior; and(c) probe molecules covalently attached to the polymer.33. The three-dimensional network of claim 32 , which comprises at least 10 channels that converge at a point in the interior of the network such that the lateral distance between the channels decreases from the surface toward the point in the interior.34. The three-dimensional network of claim 32 , wherein at least a majority of channels in the network extends into the interior from a point that is less than 10 microns from the surface of the network or extends into the interior from a point on the surface of the network.35. The three-dimensional network of claim 34 , wherein at least a majority of channels in the network extends into the interior from a point that is less than 5 microns from the surface of the network or extends into the interior from a point on the surface of the network.36. The three-dimensional network of claim 32 , wherein at least a majority of channels in the network has a length that is at least 10% of the largest dimension of the network.37. The three-dimensional network of claim 36 , wherein at least a majority of channels in the network has a length that is at least 20% of the largest dimension of the network.38. The three-dimensional network of claim 32 , ...

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Номер записи: 66
28-05-2020 дата публикации

METHODS AND COMPOSITIONS FOR SINGLE MOLECULE COMPOSITION LOADING

Номер: US20200164335A1
Автор: Pham Thang, Popovich Natasha, Shen Gene, Sun Lei, Turner Stephen
Принадлежит:

The present invention provides methods, compositions, and systems for distributing single polymerase molecules into array regions. In particular, the methods, compositions, and systems of the present invention result in a distribution of single polymerase molecules into array regions at a percentage that is larger than the percentage expected to be occupied under a Poisson distribution. 1. A method of distributing single polymerase molecules into array regions , the method comprising;(a) providing a surface comprising a plurality of array regions, wherein each array region comprises several binding elements; and 'wherein the exposing is conducted under conditions such that the multiple functional moieties of the linear DNA structure react with available binding elements in a given array region and prevent other polymerase enzyme compositions from loading in that given array region,', '(b) exposing the surface to a solution comprising polymerase enzyme compositions, wherein each polymerase enzyme composition comprises a polymerase bound to a linear DNA structure comprising multiple functional moieties, wherein the multiple functional moieties comprise biotin moieties or avidin moieties, and wherein the multiple functional moieties are attached to the linear DNA structure through flexible linkers comprising a polymeric structure selected from the group consisting of polyethylene glycol, a peptide, and an aliphatic carbon chain,'}thereby distributing single polymerase molecules into array regions.2. The method of claim 1 , wherein the flexible linkers are attached to the linear DNA structure via a modified base.3. The method of claim 2 , wherein the modified base is a member selected from the group consisting of aminoallyl-dT claim 2 , aminopropargyl-dT claim 2 , a thiol-modified base claim 2 , an azide modified base claim 2 , and an alkyl-modified base.4. The method of claim 1 , wherein the flexible linkers have a length of about 0.5 nm to about 3 nm.5. The method of ...

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Номер записи: 67
08-07-2021 дата публикации

PROTEIN ARRAYS AND METHODS OF USING AND MAKING THE SAME

Номер: US20210207132A1
Автор: Chu Larry Li-Yang, Hudson Michael E., Jacobson Joseph
Принадлежит: Gen9, Inc.

Methods and devices are provided for preparing a protein array having a plurality of proteins. In one embodiment, the method includes providing a plurality of nucleic acids each having a predefined sequence and expressing in vitro a plurality of proteins from the plurality of nucleic acids. In another embodiment, protein arrays having a solid surface and a microvolume are also provided. The solid surface can have a plurality of anchor oligonucleotides capable of hybridizing with a plurality of nucleic acids. The microvolume can cover each of the plurality of anchor oligonucleotides and can be configured to produce a polypeptide from each of the plurality of nucleic acids. 1. A method for preparing a protein array having a plurality of proteins , the method comprising:(a) providing a plurality of nucleic acids each having a predefined sequence; and(b) expressing in vitro a plurality of proteins from the plurality of nucleic acids, wherein the plurality of proteins are expressed on an array.2. The method of further comprising (c) measuring an activity of each of the plurality of proteins.3. The method of claim 1 , wherein the plurality of nucleic acids are synthesized on a solid surface.4. The method of claim 1 , wherein each of the plurality of nucleic acids comprises a regulatory genetic sequence.5. The method of claim 1 , wherein each of the plurality of proteins is expressed in vitro in a well of a micro-well plate.6. The method of claim 1 , wherein each of the plurality of proteins is expressed in vitro at a different feature of a solid surface.7. A method for preparing a protein array having a plurality of proteins claim 1 , the method comprising:(a) providing a first microvolume comprising a population of nucleic acids having a plurality of distinct, predefined sequences;(b) immobilizing the nucleic acid sequences onto an array comprising a plurality of anchor oligonucleotides having a sequence complementary to a terminus sequence of the nucleic acids;(c) ...

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Номер записи: 68
05-07-2018 дата публикации

ELECTRICALLY ACTIVE COMBINATORIAL CHEMICAL (EACC) CHIP FOR BIOCHEMICAL ANALYTE DETECTION

Номер: US20180187249A1
Автор: Georger, JR. Jacque H., Su Xing, Sun Lei B.
Принадлежит:

Apparatus and methods are disclosed for electrically active combinatorial-chemical (EACC) chips for biochemical analyte detection. An apparatus includes a substrate that has an array of regions defining multiple cells, wherein each of the cells includes a reaction cavity that contains multiple functional binding groups. A method of detecting an analyte providing the reaction cavity between a source and a drain or a pair of electrodes, applying a voltage and monitoring a parameter indicative of an analyte characteristic. A process of fabricating an EACC include bonding an analyte to the multiple functional binding groups of each reaction cavity, and forming an analyte sensing structure including the substrate. 150-. (canceled)51. An apparatus , comprising a substrate including an array of regions defining a plurality of cells , each of the plurality of cells including a reaction cavity containing multiple functional binding groups , wherein the array of regions comprises a first gradient of a first functional binding group and a second gradient of a second functional binding group , wherein an inter-molecular distance between the first functional binding group and the second functional binding group corresponds to a distance between binding locations on a biochemical analyte , wherein the plurality of cells comprise a chip for analyte detection having a feature size between 0.5 microns and 500 microns and analyte detection comprises creation of a binding site with one or more of the multiple functional binding groups.52. The apparatus of claim 51 , wherein the multiple functional binding groups are coupled to the substrate via hybridized DNA.53. The apparatus of claim 51 , wherein the plurality of cells each comprise an electrical sensing circuit.54. The apparatus of claim 51 , wherein the plurality of cells comprise a protein chip having a feature size between 0.5 microns and 500 microns.55. The apparatus of claim 51 , wherein the plurality of cells comprise a ...

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Номер записи: 69
11-06-2020 дата публикации

MICROARRAY SYNTHESIS AND ASSEMBLY OF GENE-LENGTH POLYNUCLEOTIDES

Номер: US20200181603A1
Автор: Oleinikov Andrew V.
Принадлежит: Gen9, Inc.

There is disclosed a process for in vitro synthesis and assembly of long, gene-length polynucleotides based upon assembly of multiple shorter oligonucleotides synthesized in situ on a microarray platform. Specifically, there is disclosed a process for in situ synthesis of oligonucleotide fragments on a solid phase microarray platform and subsequent, “on device” assembly of larger polynucleotides composed of a plurality of shorter oligonucleotide fragments. 1. (canceled)2. A method for producing a polynucleotide comprising a target sequence , the method comprising: [ is identical to an overlapping sequence region of another double-stranded oligonucleotide in the plurality of double-stranded oligonucleotides; and', 'comprises a Type II restriction endonuclease cleavage site; and, '(i) an internal sequence identical to a portion of the target sequence, wherein the internal sequence, at one or both ends, comprises an overlapping sequence region that, '(ii) one or more flanking sequences, wherein each flanking sequence comprises a Type II restriction endonuclease recognition site corresponding to a Type II restriction endonuclease cleavage site of the internal sequence;, '(a) providing a plurality of double-stranded oligonucleotides, each double-stranded oligonucleotide comprising(b) digesting the plurality of double-stranded oligonucleotides with a Type II restriction endonuclease that recognizes the Type II restriction endonuclease recognition site; and(c) ligating the digested oligonucleotides to produce the polynucleotide comprising the target sequence.3. The method of claim 2 , wherein each double-stranded oligonucleotide in (a) comprises a flanking sequence at each end.4. The method of claim 2 , wherein the plurality of double-stranded oligonucleotides are digested in (b) with a Type IIS restriction endonuclease.51. The method of claim 4 , wherein the Type IIS restriction endonuclease includes at least one of MylI claim 4 , BspMI claim 4 , BsaXI claim 4 , BsrI ...

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Номер записи: 70
11-06-2020 дата публикации

PROTEIN ARRAYS AND METHODS OF USING AND MAKING THE SAME

Номер: US20200181604A1
Автор: Chu Larry Li-Yang, Hudson Michael E., Jacobson Joseph
Принадлежит: Gen9, Inc.

Methods and devices are provided for preparing a protein array having a plurality of proteins. In one embodiment, the method includes providing a plurality of nucleic acids each having a predefined sequence and expressing in vitro a plurality of proteins from the plurality of nucleic acids. In another embodiment, protein arrays having a solid surface and a microvolume are also provided. The solid surface can have a plurality of anchor oligonucleotides capable of hybridizing with a plurality of nucleic acids. The microvolume can cover each of the plurality of anchor oligonucleotides and can be configured to produce a polypeptide from each of the plurality of nucleic acids. 120-. (canceled)21. A method for preparing a plurality of proteins comprising: wherein the plurality of wells comprises a plurality of nucleic acids, each nucleic acid having a predefined sequence and encoding a protein; and', 'wherein the nucleic acids of each well are immobilized on one or more supports; and, '(a) providing a plate comprising a plurality of wells 'wherein the proteins are expressed in the wells of the plate in volumes having a size of 0.5 picoliters to 100 nanoliters.', '(b) expressing in vitro a plurality of proteins from the plurality of nucleic acids,'}22. The method of claim 21 , wherein the plurality of nucleic acids is immobilized on beads.23. The method of claim 21 , wherein the nucleic acids of each well are immobilized on one bead.24. The method of claim 21 , wherein the plurality of nucleic acids is immobilized on the surface of the plate.25. The method of claim 21 , wherein each well in the plurality of wells comprises a nucleic acid having a unique predetermined sequence.26. The method of claim 25 , wherein the plurality of proteins comprises a plurality of different proteins.27. The method of claim 21 , wherein the plurality of nucleic acids comprises nucleic acids having different predetermined sequences.28. The method of claim 27 , wherein the nucleic acids of each ...

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Номер записи: 71
13-07-2017 дата публикации

MICROARRAY FABRICATION SYSTEM AND METHOD

Номер: US20170197193A1
Автор: Beierle John M., Berti Lorenzo, Bowen M. Shane, Gunderson Kevin L., Lin Shengrong, Park Sang Ryul, Rogert Bacigalupo Maria Candelaria, Tsay James, Venkatesan Bala Murali, Vijayan Kandswamy, Wu Yir-Shyuan
Принадлежит:

A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites comprise base pads, such as polymer base pads, that promote the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create a layout of base pads in a desired pattern. Further, the microarrays may include features to encourage clonality at the sites. 1. A biological microarray system , comprising:an array of base pads at predetermined sites on a substrate;a molecule binding substance disposed over each of the base pads and linked to no more than a nucleic acid molecule;a porous attachment layer disposed over the base pads; andcopies of each of the nucleic acid molecules linked to the porous attachment layer disposed over each of the respective base pads.2. The system of claim 1 , wherein a single nucleic acid molecule is linked to each and every base pad in the array.3. The system of claim 1 , wherein a single nucleic acid molecule is linked to fewer than all of the base pads in the array.4. The system of claim 1 , wherein the nucleic acid molecules comprise nucleotides or nucleotide-like components.5. The system of claim 1 , wherein the substrate comprises a glass.6. The system of claim 1 , wherein the base pads comprise gold.7. The system of claim 1 , wherein the porous attachment layer is patterned.8. The system of claim 1 , wherein the porous attachment layer comprises a plurality of regions at least partially surrounding each of the base pads.9. The system of claim 1 , wherein the porous attachment layer extends substantially continuously over the plurality of base pads.10. The system of claim 1 , wherein the porous attachment layer comprises acrylamide.11. The system of claim 1 , wherein the porous attachment layer is a porous hydrogel.12. The system of claim 1 , wherein the porous attachment layer at least partially covers the base pads.13. The system of claim 1 , wherein the ...

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Номер записи: 72
30-07-2015 дата публикации

DEVICE AND METHOD FOR REAL-TIME DETECTION OF MOLECULAR ACCUMULATIONS AND/OR MONITORING THE PRODUCTION PROCESS OF A MOLECULAR MICROARRAY

Номер: US20150209752A1
Автор: ROTH Guenter
Принадлежит:

The invention relates to a method for producing a microarray, wherein the production of this array is detected in real time from the accumulation of the product molecules being produced. The invention further relates to a microarray produced by this method, and to a device for the real-time detection of molecular accumulations on an array surface during the production of microarrays. 1. A method for producing a microarray , comprisinga) providing a first original array comprising a first support surface, to which at least one template molecule is bound,b) providing a second support surface (receiver surface), which is brought into a spatial orientation relative to the first support surfacec) providing a liquid, containing an enzymatic and/or chemical reaction system, between the first and second support surfaces, so that regions of the two surfaces are in contact with one another via the liquid,d) producing a product molecule using the template molecule and the enzymatic and/or chemical reaction system,e) transferring the product molecule to the second support surface via the liquid between the first and second support surfaces, wherein a correlation exists between a binding site of the template molecule to the first support surface and an accumulation of the corresponding product molecule on the second support surface, andf) detecting the accumulation of the product molecule on the receiver surface in real time.2. The method according to claim 1 , whereina gap exists between the first and second support surface, which is filled with the liquid before, after or during the spatial orientation of the first and second support surfaces.3. The method according to claim 1 , whereinthe first support surface comprises reference spots that comprise reference molecules, wherein product molecules are produced from these reference molecules in d), and a production of these product molecules according to steps e) and f) is detected in real time, and wherein the producing of d), ...

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Номер записи: 73
18-06-2020 дата публикации

METHODS AND COMPOSITIONS OF LOCALIZING NUCLEIC ACIDS TO ARRAYS

Номер: US20200188871A1
Автор: Horgan Adrian Martin, Rasolonjatovo Isabelle Marie Julia, Sabot Andrea, Smith Mark Edward Brennan, Sohna Sohna Jean-Ernest, Swerdlow Harold Philip
Принадлежит:

Methods and compositions are disclosed relating to the localization of nucleic acids to arrays such as silane-free arrays, and of sequencing the nucleic acids localized thereby. 1. (canceled)2. A population of template nucleic acids , wherein each template nucleic acid comprises a first end , and a second end capable of hybridizing to SEQ ID NO:05 , wherein a plurality of the template nucleic acids in the population are different from each other.3. The population of claim 2 , wherein the second end comprises SEQ ID NO:04.4. The population of claim 2 , wherein the first end is capable of hybridizing to SEQ ID NO:03.5. The population of claim 2 , wherein the first end comprises SEQ ID NO:11.6. The population of claim 2 , wherein a remainder polynucleotide is disposed between the first end and the second end.7. The population of claim 2 , wherein the template nucleic acids have a length greater than 300 nucleotides.8. The population of claim 2 , wherein the template nucleic acids comprise genomic DNA.9. The population claim 2 , wherein the first end or second end is capable of hybridizing at 5×SSC and 40° C.10. A composition comprising the population of template nucleic acids of hybridized to a plurality of first oligonucleotides via the first ends of the template nucleic acids claim 2 , wherein the first oligonucleotides are immobilized on a substrate.11. The composition of claim 10 , wherein the first ends are capable of hybridizing to SEQ ID NO:03.12. The composition of claim 10 , wherein a plurality of the first ends comprise SEQ ID NO:11.13. The composition of claim 10 , wherein the first oligonucleotides comprise SEQ ID NO:03.14. The composition of claim 10 , wherein a plurality of the second ends of the template nucleic acids comprise SEQ ID NO:04.15. The composition of claim 10 , further comprising a plurality of second oligonucleotides immobilized on a substrate.16. The composition of claim 15 , wherein the plurality of second oligonucleotides comprise SEQ ID ...

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Номер записи: 74
29-07-2021 дата публикации

Devices, Systems, and Methods of Electronic Modulation of Polymerase for DNA Synthesis

Номер: US20210229059A1
Автор: Hessel Andrew, Wang Hua
Принадлежит:

A method of synthesis of a nucleotide chain, the nucleotide chain including an ordered plurality of nucleotides, the method including: identifying a first nucleotide of the ordered plurality of nucleotides; controlling a polymerase enzyme to assemble the first nucleotide onto the nucleotide chain by electrically modulating an electrode; identifying a subsequent nucleotide in the ordered plurality of nucleotides as a current nucleotide; and controlling the polymerase enzyme to assemble the current nucleotide onto an end of the nucleotide chain by electrically modulating the electrode. 1. A method of synthesis of a nucleotide chain , the nucleotide chain including an ordered plurality of nucleotides , the method comprising:identifying a first nucleotide of the ordered plurality of nucleotides;controlling a polymerase enzyme to assemble the first nucleotide onto the nucleotide chain by electrically modulating an electrode;identifying a subsequent nucleotide in the ordered plurality of nucleotides as a current nucleotide; andcontrolling the polymerase enzyme to assemble the current nucleotide onto an end of the nucleotide chain by electrically modulating the electrode.2. The method of further comprising:controlling the polymerase enzyme to assemble a telomere by electrically modulating the electrode, the polymerase enzyme assembling the first nucleotide onto an end of the telomere.3. The method of further comprising:repeatedly identifying a subsequent nucleotide in the ordered plurality of nucleotides as the current nucleotide and controlling the polymerase enzyme to assemble the current nucleotide onto the end of the nucleotide chain until the polymerase enzyme assembles a complete nucleotide chain.4. The method of claim 3 , further comprising claim 3 , after assembly of the complete nucleotide chain claim 3 , controlling the polymerase enzyme to assemble a telomere to the end of the complete nucleotide chain by electrically modulating the electrode.5. The method of ...

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Номер записи: 75
27-06-2019 дата публикации

ARRAYS, SUBSTRATES, DEVICES, METHODS AND SYSTEMS FOR DETECTING TARGET MOLECULES

Номер: US20190195869A1
Автор: Ahmad Habib, Fan Rong, Heath James R.
Принадлежит:

Arrays and substrates comprising a material, in particular capture agents and/or detectable targets, attached to the substrates along substantially parallel lines forming a barcoded pattern and related methods and systems. 1. An array for detecting at least one target in a sample , the array comprising:at least one capture agent or component thereof attached to a substrate, the at least one capture agent capable of specifically binding the at least one target to form a capture agent target binding complex,the at least one capture agent or component thereof arranged on the array so that capture agent target binding complexes are detectable along substantially parallel lines forming a barcoded pattern.2. The array of claim 1 , wherein the at least one target is a plurality of targets claim 1 , and the at least one capture agent or component thereof is a plurality of capture agents or components thereof claim 1 , each capture agent of the plurality of capture agents bindingly distinguishable and positionally distinguishable from another claim 1 , each capture agent of the plurality of capture agents capable of specifically binding each target of the plurality of targets to form a capture agent target binding complex.35-. (canceled)6. The array of claim 1 , wherein said substantially parallel lines are formed by microfluidic channels or portions thereof claim 1 , the microfluidic channels being microfluidic channels of the array.78-. (canceled)9. A microfluidic device comprising the array of .10. The microfluidic device of claim 9 , further comprising a separating unit for separating a fluidic component of a fluid sample claim 9 , the separating unit comprisinga flowing microfluidic channel in fluidic communication with the inlet, the flowing microfluidic channel having a flowing channel resistance, andan assaying microfluidic channel in fluidic communication with the flowing channel, the assaying microfluidic channel having an assaying channel resistance,wherein the ...

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Номер записи: 76
26-07-2018 дата публикации

METHODS AND COMPOSITIONS OF LOCALIZING NUCLEIC ACIDS TO ARRAYS

Номер: US20180207606A1
Автор: Horgan Adrian Martin, Rasolonjatovo Isabelle Marie Julia, Sabot Andrea, Smith Mark Edward Brennan, Sohna Sohna Jean-Ernest, Swerdlow Harold Philip
Принадлежит:

Methods and compositions are disclosed relating to the localization of nucleic acids to arrays such as silane-free arrays, and of sequencing the nucleic acids localized thereby. 1. (canceled)2. A population of template nucleic acids , wherein each template nucleic acid comprises a first end capable of hybridizing to SEQ ID NO:03 , and a second end , wherein the template nucleic acids are different from each other.3. The population of claim 2 , wherein the first end comprises SEQ ID NO:11.4. The population of claim 2 , wherein the second end is capable of hybridizing to SEQ ID NO:05.5. The population of claim 2 , wherein the second end comprises SEQ ID NO: 4.6. The population of claim 2 , wherein a remainder polynucleotide is disposed between the first end and the second end.7. The population of claim 2 , wherein the template nucleic acids have a length greater than 300 nucleotides.8. The population of claim 2 , wherein the template nucleic acids comprise genomic DNA.9. The population claim 2 , wherein the first end is capable of hybridizing at 5×SSC and 40° C.10. A composition comprising: the population of template nucleic acids of hybridized to a plurality of first oligonucleotides via the first ends of the template nucleic acids claim 2 , wherein the first oligonucleotides are immobilized on a substrate.11. The composition of claim 10 , wherein the first oligonucleotides comprise SEQ ID NO:03.12. The composition of claim 10 , wherein the second ends of the template nucleic acids are capable of hybridizing to SEQ ID NO:05.13. The composition of claim 12 , wherein the second ends of the template nucleic acids comprise SEQ ID NO: 4.14. The composition of claim 10 , further comprising a plurality of second oligonucleotides immobilized on a substrate.15. The composition of claim 14 , wherein the plurality of second oligonucleotides comprise SEQ ID NO:04.16. The composition of claim 10 , wherein the immobilized first oligonucleotides each comprise a polyT spacer ...

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Номер записи: 77
26-07-2018 дата публикации

POLYMER SHEETS FOR SEQUENCING APPLICATIONS

Номер: US20180207920A1
Автор: Barnard Steven M., Chen Kenny, Venkatesan Bala Murali
Принадлежит:

Embodiments of the present application relate to patterned polymer sheets and processes to prepare the same for sequencing applications. In particular, flexible micro- and nano-patterned polymer sheets are prepared and used as a template surface in sequencing reaction and new polish-free methods of forming isolated hydrogel plugs in nanowells are described. 1. A process for preparing a polymer sheet for sequencing applications , comprising:providing a substrate with a surface;depositing a layer of a polymer composition onto the surface of the substrate, wherein the polymer composition comprises functional groups for grafting oligonucleotides;forming the polymer composition into a polymer sheet on the surface; andremoving said polymer sheet from the surface of the substrate.2. The process of claim 1 , wherein the polymer composition comprises a hydrogel.3. The process of or claim 1 , wherein the polymer composition comprises poly(N-(5-azidoacetamidylpentyl) acrylamide-co-acrylamide) (PAZAM).4. The process of any one of to claim 1 , wherein the forming of the polymer sheet comprises dehydrating the polymer composition.5. The process of claim 4 , wherein the dehydrating is performed at an elevated temperature.6. The process of claim 5 , wherein the dehydrating occurs at about 60° C.7. The process of any one of to claim 5 , wherein the surface of the substrate comprises micro-scale or nano-scale patterns.8. The process of claim 7 , wherein the micro-scale or nano-scale patterns comprise channels claim 7 , trenches claim 7 , posts claim 7 , wells claim 7 , or combinations thereof.9. The process of or claim 7 , wherein an imprint of the micro-scale or nano-scale patterns of the patterned surface is transferred to the polymer sheet to form a patterned polymer sheet.10. A process for preparing a substrate surface for sequencing applications claim 7 , comprising:providing a polymer sheet comprising a first plurality of functional groups;contacting said polymer sheet with a ...

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Номер записи: 78
25-06-2020 дата публикации

ARRAYS AND METHODS OF MANUFACTURE

Номер: US20200198286A1
Автор: Bates David James, Haynes Andrew, Kannappan Karthik, Partridge Ashton Cyril
Принадлежит: Digital Sensing Ltd.

The invention relates to a microarray structure that may include a substrate material layer, a continuous three-dimensional (3D) surface layer on the substrate material layer that is capable of functionalisation for use as an array, and an inert material. The structure may include accurately defined and functionalisable isolated areas which are millimeter to nanometer in size. The functionalisable areas may be part of the continuous 3D surface layer and may be isolated by the inert material but interconnected within the structure by the continuous 3D surface layer. 128-. (canceled)29. A microarray structure including a substrate material layer , a continuous three-dimensional (3D) surface layer on the substrate material layer that is capable of functionalisation for use as an array , and an inert material;wherein the structure includes accurately defined and functionalisable isolated areas which are millimeter to nanometer in size; andwherein the functionalisable areas are part of the continuous 3D surface layer and are isolated by the inert material but which are interconnected within the structure by the continuous 3D surface layer.30. An intermediate structure for use in fabricating an array , wherein the intermediate structure includes a substrate material layer that includes an accurately defined 3D pattern to a millimeter to nanometer scale , and a continuous 3D surface layer on the substrate material layer that is capable of functionalisation for use as an array over at least part of the pattern.31. A method for the formation of an intermediate structure , wherein the method includes the steps of:a. placing an accurately defined 3D pattern at the millimeter to nanometer scale on the surface of a substrate material; andb. coating at least part of the patterned substrate material with a continuous 3D surface layer.32. The method of claim 31 , wherein the method is for the formation of a structure capable of functionalisation as an array claim 31 , the method ...

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Номер записи: 79
04-07-2019 дата публикации

MOLECULAR CHAIN SYNTHESIZER

Номер: US20190201863A1
Автор: Frank Ian W., Korn Jeffrey A., Magyar Andrew P., Patel Neil S.
Принадлежит:

An apparatus for optically-verified de novo DNA synthesis includes a microfluidic system that has channels leading in and out of a synthesis chamber having a functionalized region on a floor thereof on which a single-strand of DNA to which a nucleotide is to be attached can be fixed. The chamber is in optical communication with both an illumination system, which excites an electron in a fluorophore that is attached to the DNA strand, a detection system, which detects a signature photon emitted as the excited electron decays into its ground state. 1. An apparatus comprising a microfluidic system , a detection system , and an excitation system , wherein said microfluidic system includes a first manufacturing unit , wherein said first manufacturing unit includes a chamber , a first channel , a second channel , and a functionalized region , wherein said functionalized region is configured for holding a molecular chain to which a monomer is to be attached , wherein said functionalized region is disposed in said chamber , wherein said chamber is in optical communication with said detection system , wherein said chamber is in optical communication with said excitation system , wherein said first channel connects to said chamber , wherein said second channel connects to said chamber , wherein said detection system comprises a detector tuned to detect a signature photon from a fluorophore that is attached to said single strand , said single strand having been attached to said functionalized region , and wherein said excitation system comprises a light source disposed for illuminating said fluorophore , said light source being configured to stimulate a specific electronically excited state.2. The apparatus of claim 1 , wherein said microfluidic system is formed on a substrate claim 1 , said apparatus further comprising a second manufacturing unit that has the same structure as said first manufacturing unit claim 1 , wherein said second manufacturing unit is formed on said ...

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Номер записи: 80
04-08-2016 дата публикации

Chemiluminescent Protein Chip, Method and Kit for Detecting Seroglycoid Fucosylation Index

Номер: US20160223556A1
Автор: Aiying Zhang, Ning Li, Shengqi Wang, YANG Ke, Yonghong Zhang
Принадлежит: Beijing Youan Hospital

A chemiluminescent protein chip, kit and method for detecting seroglycoid fucosylation index, in the field of protein detection technology. The chemiluminescent protein chip includes a substrate slide, at least one detection subarea, detection spot areas and one control spot area. The detection spots are formed by fixed aplha fetoprotein (AFP)-specific antibodies.

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Номер записи: 81
20-08-2015 дата публикации

Gel-based bio chip for electrochemical synthesis and electrical detection of polymers

Номер: US20150231633A1
Автор: Nikolay Suetin, Valery M. Dubin
Принадлежит: Intel Corp

An embodiment of the invention relates to a biochip comprising at least two measurement electrodes, a synthesis electrode, a ground electrode, a gap between the at least two measurement electrodes, a porous dielectric isolation layer and a gel comprising a probe in the gap, wherein the porous dielectric isolation layer is between the synthesis electrode and the gel. Yet other embodiments relate to the method of manufacturing the biochip and using the biochip for electrical detection of bio-species.

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Номер записи: 82
16-08-2018 дата публикации

Ultra high-density oligomer arrays and method of production thereof

Номер: US20180229204A1
Автор: Alexander Nesterov-Mueller, Barbara Ridder, Clemens Matthias von Bojnicic-Kninski, Daniela Silke Althuon, Felix Friedrich Loeffler, Frank Breitling, Roman Popov, Valentina BYKOVSKAYA
Принадлежит: Karlsruher Institut fuer Technologie KIT

The present invention relates to a method of producing an oligomer array. The invention comprises the steps of: providing a substrate with a multitude of recesses; introducing a first particle with a first molecule into a recess; releasing the first molecule from the first particle; binding the first molecule to a second molecule to form an oligomer while immobilizing the second molecule in the recess; optionally repeating the steps, wherein at least one of the first particles and/or the first molecules comprises a detectable marker.

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Номер записи: 83
03-09-2015 дата публикации

METHODS FOR MULTIPLEX ANALYTICAL MEASUREMENTS IN SINGLE CELLS OF SOLID TISSUES

Номер: US20150246335A1
Автор: Finski Alexei, MacBeath Gavin
Принадлежит:

The invention provides a method for the isolation of a single cell embedded in a tissue while preserving the state of molecules of the cell, and therefore allows for transformation of a single target cell in live tissue into a format that can be evaluated using analytical methods. 1. A method of lysing a single cell present in a tissue , the method comprising:a) identifying a cell from a tissue;b) contacting a detergent-containing lysis buffer with the intracellular space of the identified cell;c) allowing the lysis buffer to spread within the intracellular space of the identified cell for a period of time, wherein the cell is lysed from the inside of the cell; andd) collecting the lysate.212-. (canceled)13. The method of claim 1 , wherein the method occurs in the absence of tissue fixation and tissue disaggregation.14. The method of claim 1 , wherein the isolated cell is in an organotypic culture.15. The method of claim 1 , wherein the lysate is collected by suctioning the lysate using a suction channel.16. The method of claim 15 , wherein the suction channel is a bent suction micropipette.17. The method of claim 1 , wherein the collected lysate is further applied to a nitrocellulose pad.18. The method of claim 17 , wherein a standard is also applied to the nitrocellulose pad.19. The method of claim 1 , wherein the lysate is evaluated using an analytical method.20. The method of claim 19 , wherein the analytical method is selected from the group consisting of mass spectrometry claim 19 , protein microarray claim 19 , RT-qPCR claim 19 , RNA-Seq claim 19 , and MALDI-MS.21. The method of claim 1 , wherein the cell is part of a live solid tissue.22. The method of claim 1 , wherein the detergent is sodium dodecyl sulfate.23. A method of analyzing a cell present in a tissue claim 1 , the method comprising:a) identifying a cell from a tissue;b) contacting a detergent-containing lysis buffer to the intracellular space of the identified cell;c) allowing the lysis buffer to ...

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Номер записи: 84
20-11-2014 дата публикации

Arrays and methods of manufacture

Номер: US20140342128A1
Автор: Andrew Haynes, Ashton Cyril Partridge, David James Bates, Karthik Kannappan
Принадлежит: Digital Sensing Ltd

The invention relates to a microarray structure including a substrate material layer, a continuous three-dimensional (3D) surface layer on the substrate material layer that is capable of functionalisation for use as an array, and an inert material wherein the structure includes accurately defined and functionalisable isolated areas which are millimeter to nanometer in size. The functionalised areas are part of the continuous 3D surface layer and are isolated by the inert material and are interconnected within the structure by the continuous 3D surface layer.

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Номер записи: 85
20-11-2014 дата публикации

Compositions and methods for entrapping protein on a surface

Номер: US20140342947A1
Автор: Michael E. Hogan
Принадлежит: Individual

The present invention provides a formulation to link protein to a solid support that comprises one or more proteins, Oligo-dT and one or more non-volatile, water-soluble protein solvents, solutes or combination thereof in an aqueous solution. Further provided is a method of attaching a protein to a surface of a substrate. The formulations provided herein are contacted onto the substrate surface, printed thereon and air dried. The substrate surface is irradiated with UV light to induce thymidine photochemical crosslinking via the thymidine moieties of the Oligo-dT.

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Номер записи: 86
14-09-2017 дата публикации

Spot array substrate, method for producing same, and nucleic acid polymer analysis method and device

Номер: US20170260573A1
Автор: Masatoshi Narahara, Naoshi Itabashi, Sonoko Migitaka, Tomohiro Shoji, Yukio Ono
Принадлежит: Hitachi High Technologies Corp

In order to reduce the cost of producing a spot array substrate and reduce the cost of nucleic acid polymer analysis, a spot array substrate is used which is produced by preparing a resin substrate 402 having a surface on which an uneven pattern is formed and a plurality of bead sitting positions set in a two-dimensional array within the uneven pattern, and loading surface-modified beads onto the bead sitting positions of the resin substrate.

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Номер записи: 87
20-09-2018 дата публикации

DE NOVO SYNTHESIZED GENE LIBRARIES

Номер: US20180264428A1
Автор: Banyai William, Chen Siyuan, FERNANDEZ Andres, Indermuhle Pierre, Peck Bill James
Принадлежит:

De novo synthesized large libraries of nucleic acids are provided herein with low error rates. Further, devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Longer nucleic acids can be synthesized in parallel using microfluidic assemblies. Further, methods herein allow for the fast construction of large libraries of long, high-quality genes. Devices for the manufacturing of large libraries of long and high-quality nucleic acids are further described herein. 1. A method for synthesizing oligonucleotides , comprising:synthesizing a plurality of oligonucleotides at a rate of extending of at least 15 nucleotides per hour, wherein each of the oligonucleotides has a preselected sequence, and wherein the synthesizing comprises extending each oligonucleotide by a single base in an extension reaction.2. The method of claim 1 , wherein the rate of extending is at least 20 nucleotides per hour.3. The method of claim 1 , wherein the rate of extending is at least 25 nucleotides per hour.4. The method of claim 1 , wherein the plurality oligonucleotides are synthesized in parallel.5. The method of claim 1 , wherein at least 20 claim 1 ,000 oligonucleotides are synthesized.6. The method of claim 1 , wherein at least 500 claim 1 ,000 oligonucleotides are synthesized.7. The method of claim 1 , wherein each of the oligonucleotides is at least 25 bases in length.8. The method of claim 1 , wherein the plurality of oligonucleotides are synthesized on a solid substrate.9. The method of claim 8 , wherein the solid substrate comprises silicon claim 8 , silicon dioxide or silicon nitride.10. The method of claim 1 , wherein each of the oligonucleotides has a different preselected sequence.11. The method of claim 1 , wherein each of the oligonucleotides comprises 100 to 200 nucleotides in length and is synthesized in less than 5 hours.12. A method of synthesizing oligonucleotides claim 1 , comprising:a. providing a solid substrate;b. ...

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Номер записи: 88
20-09-2018 дата публикации

Position-defined cell culture and characterization platform

Номер: US20180264466A1
Автор: Wei Cai, Yu Jui (Roger) Chiu, Yu-Hwa Lo
Принадлежит: UNIVERSITY OF CALIFORNIA

Methods, systems, and devices are disclosed for culturing and characterizing individual cellular entities including cells organoids, or tissue. In one aspect, a device includes a first substrate structured to include an array of hydrophilic regions surrounded by a hydrophobic surface including nanostructures protruding from the hydrophobic surface, in which the array of hydrophilic regions are capable to adhere an individual cellular entity and the hydrophobic surface is configured to prevent the cellular entity from adherence; and a second substrate including a coating of antibodies corresponding to a type of cellular substance secreted by the cellular entity, in which the second substrate is operable to be placed upon the first substrate such that the coating of antibodies makes contact with the individual cellular entities adhered to the hydrophilic regions.

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Номер записи: 89
20-09-2018 дата публикации

CATALYST-FREE SURFACE FUNCTIONALIZATION AND POLYMER GRAFTING

Номер: US20180265660A1
Автор: Berti Lorenzo, Brown Andrew A., George Wayne N.
Принадлежит:

Some embodiments described herein relate to a substrate with a surface comprising a silane or a silane derivative covalently attached to optionally substituted cycloalkene or optionally substituted heterocycloalkene for direct conjugation with a functionalized molecule of interest, such as a polymer, a hydrogel, an amino acid, a nucleoside, a nucleotide, a peptide, a polynucleotide, or a protein. In some embodiments, the silane or silane derivative contains optionally substituted norbornene or norbornene derivatives. Method for preparing a functionalized surface and the use in DNA sequencing and other diagnostic applications are also disclosed. 1. A method of grafting primers on a first surface of a substrate , the method comprising:providing pre-conjugated primers comprising oligonucleotides covalently bonded to a functionalized molecule, wherein the functionalized molecule comprises functional groups; andcontacting the pre-conjugated primers with a substrate having a first surface comprising a silane or a silane derivative, wherein the silane or silane derivative comprises a first plurality of unsaturated moieties selected from the group consisting of cycloalkenes, cycloalkynes, heterocycloalkenes, heterocycloalkynes, and optionally substituted variants and combination thereof covalently attached thereto, and wherein the pre-conjugated primers are covalently bound to the first surface of the substrate through the reaction of the functional groups of the functionalized molecule with the first plurality of unsaturated moieties of the silane or silane derivative.2. The method of claim 1 , wherein the pre-conjugated primers are prepared by reacting the functional groups of the functionalized molecule with a second plurality of unsaturated moieties of the oligonucleotides to form covalent bonding claim 1 , and wherein the second plurality of unsaturated moieties of the oligonucleotide are selected from the group consisting of alkynes claim 1 , cycloalkenes claim 1 , ...

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Номер записи: 90
20-09-2018 дата публикации

PROGRAMMABLE ARRAYS

Номер: US20180267029A1
Автор: Brunner Al, Kahn Peter, LaBaer Joshua, Magee Mitch, Qiu Ji, Takulapalli Bharath, Wiktor Peter
Принадлежит:

Biomolecule arrays on a substrate are described which contain a plurality of biomolecules, such as coding nucleic acids and/or isolated polypeptides, at a plurality of discrete, isolated, locations. The arrays can be used, for example, in high throughput genomics and proteomics for specific uses including, but not limited molecular diagnostics for early detection, diagnosis, treatment, prognosis, monitoring clinical response, and protein crystallography. 1(a) a first substrate; and(b) biomolecules comprising at least 10 isolated coding nucleic acids and/or at least 10 isolated polypeptides, wherein each nucleic acid and/or polypeptide is physically confined at a discrete location on the first substrate, and wherein each nucleic acid is capable of expressing its encoded product in situ at its discrete location on the substrate, and/or wherein each polypeptide is capable of a characteristic activity in situ at its discrete location on the substrate; wherein the discrete locations are separated from each other on the first substrate by a center to center spacing of between about 20 nm and about 1 mm.. A biomolecule array, comprising This application is a continuation of U.S. patent application Ser. No. 14/345,032, filed Mar.14, 2014, which is the national stage entry of International Patent Application Ser. No. PCT/US2012/061702, filed Oct. 24, 2012, which claims priority to U.S. Provisional Patent Application Ser. No. 61/551,128, filed Oct. 25, 2011, each of which is hereby incorporated by reference herein in its entirety.This invention was made with government support under grant number R42 RR031446 awarded by National Institutes of Health. The government has certain rights in the invention.Microarrays have revolutionized molecular biology by enabling thousands of experiments to be performed simultaneously within the size of a single microscope slide. Originally microarrays consist of thousands of spots of short nucleotide polymers that are either synthesized ...

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Номер записи: 91
29-08-2019 дата публикации

SUBSTRATES, SYSTEMS, AND METHODS FOR NUCLEIC ACID ARRAY SYNTHESIS

Номер: US20190262794A1
Автор: Rajasekaran John J.
Принадлежит:

Disclosed herein are formulations, substrates, and arrays for the synthesis of PNA chains and PNA-DNA chimera on microarrays. In some embodiments, the formulations include a photo-protective compound that shields any PNA monomers, PNA polymers, or PNA-DNA chimera already attached to a microarray from radiation exposure during the synthesis of the PNA or PNA-DNA chains. In some embodiments, substrates and arrays comprise a porous or a planar layer for synthesis and attachment of PNA or DNA monomers, or PNA or PNA-DNA polymers. In some embodiments, disclosed herein are formulations and methods for high efficiency coupling of PNA monomers or PNA polymers to a microarray substrate. 1. An array of features attached to a surface at positionally-defined locations , each of said features comprising:a plurality of PNA polymers of determinable sequence and intended length, wherein said plurality of PNA polymers comprises a distribution of lengths characterized by a coupling efficiency of at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 98.5%, 99%, or 99.5%.2. The array of claim 1 , wherein the distribution of lengths of said plurality of PNA polymers less than the intended length is characterized by the equation F(N)=10−10wherein N=the actual length of the PNA polymer and E=coupling efficiency claim 1 , wherein E is at least 90% claim 1 , 91% claim 1 , 92% claim 1 , 93% claim 1 , 94% claim 1 , 95% claim 1 , 96% claim 1 , 97% claim 1 , 98% claim 1 , 98.5% claim 1 , 99% claim 1 , or 99.5%.3. The array of claim 1 , wherein the proportion of PNA polymers of intended length is characterized by the equation: F(N)=10 claim 1 , wherein N=the intended length of the PNA polymer and E=average coupling efficiency claim 1 , wherein E is at least 90% claim 1 , 91% claim 1 , 92% claim 1 , 93% claim 1 , 94% claim 1 , 95% claim 1 , 96% claim 1 , 97% claim 1 , 98% claim 1 , 98.5% claim 1 , 99% claim 1 , or 99.5%.4. The array of claim 1 , wherein said array comprises at least 10 claim 1 , ...

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Номер записи: 92
20-08-2020 дата публикации

THREE-DIMENSIONAL POLYMER NETWORKS WITH CHANNELS SITUATED THEREIN

Номер: US20200261880A1
Автор: BEDNAR Sonja, KLAPPROTH Holger
Принадлежит: Safeguard Biosystems Holdings Ltd.

The disclosure provides three-dimensional crosslinked polymer networks comprising one or more channels extending from the surface and/or near the surface of the network into the interior of the network, arrays comprising the networks, processes for making the networks, and uses of the networks and arrays. 1. A three-dimensional network having a surface and an interior , said three-dimensional network comprising:(a) a crosslinked polymer covalently attached to the surface of a substrate;(b) one or more channels; and(c) probe molecules covalently attached to the polymer.2. The three-dimensional network of claim 1 , wherein at least one of the channels is characterized by one claim 1 , two claim 1 , or three of the following properties:(a) the channel extends into the interior from a point that is less than 5 microns from the surface of the network or extends into the interior from a point on the surface of the network;(b) the channel has a length that is at least 10% of the largest dimension of the network; and(c) the channel has a minimum cross-section of at least 5 times the network's mesh size.3. The three-dimensional network of or claim 1 , comprising at least 5 channels claim 1 , wherein a plurality of channels converge at a point in the interior of the network such that the lateral distance between the channels decreases from the surface toward the point in the interior.4. The three-dimensional network of any one of to claim 1 , wherein the crosslinked polymer is water-swellable.5. The three-dimensional network of claim 4 , wherein the network has in its hydrated state a mesh size of 5 to 75 nm.6. The three-dimensional network of any one of to claim 4 , wherein a majority of probe molecules are in the interior of the network and/or adjoin a channel.7. The three-dimensional network of any one of to claim 4 , wherein the polymer comprises a polymer polymerized from dimethylacrylamide (DMAA) claim 4 , methacryloyloxybenzophenone (MABP) claim 4 , and sodium 4- ...

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Номер записи: 93
22-10-2015 дата публикации

Method for positioning structures in indentations and arrangements thus obtainable

Номер: US20150298090A1
Автор: ACUNA Guillermo, PIBIRI Enrico, TINNEFELD Philip
Принадлежит:

Positioning structures in at least one indentation present on a or in a support, wherein said indentation is an indentation having a diameter in the nanometer range, makes it possible to position the structure in the indentation substantially centrally with defined orientation. A support having at least one indentation, wherein this is one having a size in the nanometer range, includes a predetermined structure which is arranged substantially centrally within said indentation and which optionally has a functional unit diametrically opposite to the side pointing to the bottom surface. The arrangement is especially suitable for single molecule analysis and, here especially, for single molecule sequencing and other high-throughput methods. 2. Method according to claim 1 , wherein at least two claim 1 , such as three or four claim 1 , second binding partners are present on the one side of the structure and said at least two claim 1 , such as three or four claim 1 , second binding partners are arranged around the center of the structure.3. Method according to claim 1 , wherein the ratio of the diameter of the structure to the diameter of the indentation is at least 0.5.4. Method according to claim 1 , wherein the ratio of the diameter of the structure to the diameter of the indentation is at least 0.6.5. Method according to claim 1 , wherein the indentation is a nanoaperture.6. Method according to claim 1 , wherein the side having the second binding partner of the structure and the bottom surface of the support that is exposed in the indentation are positioned substantially parallel to one another.7. Method according to claim 1 , wherein the bond between the first binding partner and the second binding partner to form the binding pair is covalent or noncovalent.8. Method according to wherein one binding partner of said first and second binding partners is biotin.9. Method according to claim 1 , wherein the functional unit is arranged diametrically opposite to the side ...

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Номер записи: 94
11-10-2018 дата публикации

NUCLEIC ACID CAPTURE METHOD AND KIT

Номер: US20180291436A1
Автор: Wang Qing, Zhang Ming
Принадлежит: MyOmicsDx, Inc

A kit and a method for enriching target nucleic acid sequences from a biological sample are disclosed. The method includes preparing, and contacting with the biological sample, a first RNA probe set and a second RNA probe set respectively targeting both of the two antiparallel strands of a duplex segment in each target nucleic acid sequence. Each RNA probe in the first RNA probe set and the second RNA probe set can be generated by chemical synthesis or by in vitro or in vivo transcription, and can be biotin-labelled to thereby allow capturing of the target nucleic acid sequences by magnetic beads labelled with streptavidin, or can be engineered to a microfluidic channel to facilitate the capturing. The method can be applied to capture double-stranded nucleic acid sequences or single-stranded nucleic acid sequences having duplex segments, and the nucleic acid sequences can include DNAs, RNAs, or DNA-RNA hybrid molecules. 1. A kit for enriching at least one target nucleic acid sequence from a biological sample , comprising:at least one pair of RNA probe sets, each pair comprising a first RNA probe set and a second RNA probe set configured to respectively target two antiparallel strands of a duplex segment in each of the at least one target nucleic acid sequence, wherein each RNA probe in any of the first RNA probe set and the second RNA probe set is labelled with an immobilization portion; anda solid support labelled with a coupling partner on a surface thereof, wherein the coupling partner is configured to be able to form a secure coupling to the immobilization portion to thereby allow immobilization of each RNA probe in any of the first RNA probe set and the second RNA probe set in the each of the at least one pair of RNA probe sets onto the solid support.2. The kit of claim 1 , wherein each RNA probe in any of the first RNA probe set and the second RNA probe set in the each of the at least one pair of RNA probe sets has a length of about 100-150 nt claim 1 ,3. The ...

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Номер записи: 95
27-10-2016 дата публикации

Methods and Compositions for Single Molecule Composition Loading

Номер: US20160310926A1
Автор: Pham Thang, Popovich Natasha, Shen Gene, Sun Lei, Turner Stephen
Принадлежит: Pacific Biosciences of California, Inc.

The present invention provides methods, compositions, and systems for distributing single polymerase molecules into array regions. In particular, the methods, compositions, and systems of the present invention result in a distribution of single polymerase molecules into array regions at a percentage that is larger than the percentage expected to be occupied under a Poisson distribution. 150-. (canceled)51. A method of distributing single polymerase molecules into array regions , the method comprising;(a) providing a surface comprising a plurality of array regions, wherein each array region comprises several binding elements; (i) the multiple functional moieties comprise a member selected from the group consisting of biotin and avidin,', '(ii) the exposing is conducted under conditions such that the multiple functional moieties of the polymeric structure react with available binding elements in a given array region and prevent other polymerase enzyme compositions from loading in that given array region,, '(b) exposing the surface to a solution comprising polymerase enzyme compositions, wherein each polymerase enzyme composition comprises a polymerase bound to a polymeric structure comprising multiple functional moieties, whereinthereby distributing single polymerase molecules into array regions.52. The method of claim 51 , wherein the polymeric structure comprises DNA claim 51 , and the multiple functional moieties are incorporated into the polymeric structure through attachment to a nucleobase.53. The method of claim 51 , wherein the multiple functional moieties are attached to the polymeric structure through flexible linkers.54. (canceled)55. The method of claim 53 , wherein the flexible linkers comprise a member selected from the group consisting of polyethylene glycol claim 53 , a peptide claim 53 , an oligonucleotide claim 53 , and an aliphatic carbon chain.5655. The method of claim 53 , wherein the polymeric structure comprises DNA and wherein the flexible ...

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Номер записи: 96
03-10-2019 дата публикации

METHODS AND COMPOSITIONS FOR SINGLE MOLECULE COMPOSITION LOADING

Номер: US20190299187A1
Автор: Pham Thang, Popovich Natasha, Shen Gene, Sun Lei, Turner Stephen
Принадлежит:

The present invention provides methods, compositions, and systems for distributing single polymerase molecules into array regions. In particular, the methods, compositions, and systems of the present invention result in a distribution of single polymerase molecules into array regions at a percentage that is larger than the percentage expected to be occupied under a Poisson distribution. 125-. (canceled)26. A method of distributing single polymerase molecules into array regions , the method comprising:(a) providing a surface comprising a plurality of array regions, wherein each array region comprises several binding elements; (i) a core, and', '(ii) at least three arms comprising avidin moieties attached to DNA molecules,, '(b) exposing the surface to a solution comprising polymerase enzyme compositions, wherein each polymerase enzyme composition comprises a polymerase bound to a scaffold, wherein the scaffold compriseswherein the exposing is conducted under conditions such that the avidin moieties of the scaffold react with available binding elements in a given array region and prevent other polymerase enzyme compositions from loading in that given array region,thereby distributing single polymerase molecules into array regions.27. The method of claim 26 , wherein the core comprises a member selected from the group consisting of: an organic molecule claim 26 , a multi-binding site protein claim 26 , a branched peptide claim 26 , and a branched oligonucleotide.28. The method of claim 26 , wherein the core comprises a multi-armed polyethylene glycol molecule.29. The method of claim 26 , wherein the core comprises an avidin molecule.30. The method of claim 26 , wherein claim 26 , in the multiple arms claim 26 , the avidin moieties are attached to the end of the DNA molecules.31. The method of claim 26 , wherein the avidin moieties are part of an oligonucleotide claim 26 , and wherein the avidin moieties are attached to the DNA molecules through hybridization between ...

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Номер записи: 97
03-11-2016 дата публикации

Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays

Номер: US20160319334A1
Автор: Francis Barany, George Barany, Herman Blok, Maria Kempe, Monib Zirvi, Robert P. Hammer
Принадлежит: Cornell Research Foundation Inc

The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.

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Номер записи: 98
02-11-2017 дата публикации

ANALYSIS METHOD ON THE BASIS OF AN ARRAY

Номер: US20170312727A1
Автор: ROTH Guenter
Принадлежит: Albert-Ludwigs-Universitaet Freiburg

The invention relates to a method for analyzing molecular properties and/or reaction conditions, comprising a step of providing a first store having a first surface, wherein a specific selection of sample molecules is directly or indirectly bonded to the surface in a defined arrangement, a step of producing at least two transfer stores, wherein at least two additional surfaces are provided, and a reaction step, selected from the group comprising a transfer reaction, an amplification reaction, and/or a derivatization reaction, whereby product molecules can arise and said product molecules and/or the sample molecules bond to the surfaces, wherein there is a clear spatial association between the sample molecules of the first store and the product molecules and/or sample molecules of the transfer stores and the first store, the transfer stores, the sample molecules, the product molecules, the transfer reaction, the amplification reaction, and/or the derivatization reaction is analyzed. 1. A method for analysis of molecular properties and/or reaction conditions , comprising: 'a selection of sample molecules is bound directly or indirectly to the surface in a defined arrangement,', 'a) supplying a first storage, comprising a first surface, wherein'} at least two additional surfaces are provided, and', 'carrying out a reaction, the reaction being a transfer reaction, amplification reaction and/or a derivatization reaction, so that product molecules are formed, and these product molecules and/or the sample molecules bind to the surfaces, wherein', 'there is a clear-cut spatial association between the sample molecules of the first storage and the product molecules and/or the sample molecules of the transfer storage,, 'b) of producing at least two transfer storages, wherein'}c) analyzing the first storage, the transfer storage, the sample molecules, the product molecules, the transfer reaction, the amplification reaction and/or the derivatization reaction.2. The method ...

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Номер записи: 99
01-11-2018 дата публикации

METHOD FOR IMMOBILISING A COMPOUND OF INTEREST ON A SUBSTRATE IN A GIVEN PATTERN AND KIT FOR IMPLEMENTING SAME

Номер: US20180311635A1
Автор: FONCY JULIE, FRANCOIS Jean-Marie, SEVERAC CHILDERICK, Trevisiol Emmanuelle
Принадлежит:

A method for immobilizing a compound of interest on the surface of a substrate in a given pattern using a printing pad. The printing pad is made from a polymer material with a face having a hollow profile that geometrically matches the pattern. The compound of interest is deposited on the surface of walls of a recess. A solution of a compound, capable of forming a link with the substrate and a link with the compound of interest, is confined inside the recess between the substrate and the face of the pad, in a solvent capable of penetrating into the polymer material. The confinement is carried out at a temperature and for a period sufficient to allow the solvent to penetrate the polymer material. 112-. (canceled)13. A method for immobilizing a compound of interest on a surface of a substrate according to a given pattern , comprising successive steps of:on a printing pad made from a polymer material comprising a printing face having a profile of recesses that is geometrically complementary to said given pattern, deposition of said compound of interest on a surface of walls of at least one recess;confinement of a solution of a linker compound in a solvent inside said recess between said substrate and said printing face of the pad, said linker compound capable of simultaneously forming a bond with said substrate and a bond with said compound of interest, and the solvent capable of penetrating into said polymer material; andwherein said confinement is carried out at a temperature and for a period of time to allow the solvent inside said recess to penetrate into said polymer material.14. The method as claimed in claim 13 , wherein the printing pad is made from an elastomeric material.15. The method as claimed in claim 13 , wherein the solvent is chosen from a group consisting of toluene and tetrahydrofuran.16. The method as claimed in claim 13 , wherein the linker compound is a phosphorus-comprising dendrimer having a central nucleus and comprising claim 13 , at its ...

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Номер записи: 100