Настройки

Укажите год
-

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

Подробнее
-

Мониторинг СМИ

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

Подробнее

Форма поиска

Поддерживает ввод нескольких поисковых фраз (по одной на строку). При поиске обеспечивает поддержку морфологии русского и английского языка
Ведите корректный номера.
Ведите корректный номера.
Ведите корректный номера.
Ведите корректный номера.
Укажите год
Укажите год
Применить Всего найдено 26. Отображено 24.
20-12-2012 дата публикации

ISOLATION OF POLYMERASE-NUCLEIC ACID COMPLEXES

Номер: US20120322666A1
Автор: Bhamidipati Arunashree, Clark Tyson A., Korlach Jonas, Olivares Eric, Pham Thang, Travers Kevin
Принадлежит: Pacific Biosciences of California, Inc.

Compositions, methods and systems are provided for the isolation of polymerase-nucleic acid complexes. Complexes can be separated from free enzyme by using hook molecules to target single stranded regions on the nucleic acid. Active complexes can be isolated from mixtures having both active and inactive complexes by initiating nucleic acid synthesis so as to open up a portion of a double stranded region rendering that region single stranded. Hook molecules are targeted to bind the sequences that are thus exposed. The hook molecules bound to active polymerase-nucleic acid complex are isolated, and the active polymerase-nucleic acid complexes released. 1. A method for isolating a polymerase-nucleic acid complex comprising:forming a polymerase-nucleic acid complex by mixing: (a) a polymerase enzyme comprising strand displacement activity and (b) a nucleic acid comprising a double stranded portion comprising a first strand and a complementary second strand;initiating nucleic acid synthesis by the polymerase enzyme to produce a nascent strand complementary to the first strand, thereby displacing a portion of the second strand;halting or reducing the rate of nucleic acid synthesis;hybridizing a hook oligonucleotide to the complex through a capture region on the hook oligonucleotide that is complementary to at least some of the displaced portion of the second strand; andisolating the complex using the hook oligonucleotide.2. The method of further comprising loading the isolated complex onto a substrate.3. The method of further comprising carrying out single-molecule nucleic acid sequencing with the polymerase-nucleic acid complex on the substrate.4. The method of wherein the nucleic acid is a circular nucleic acid.5. The method of wherein the nucleic acid comprises a double stranded central region and single stranded hairpin end regions.6. The method of wherein the nucleic acid comprises a linear nucleic acid comprising a linear double-stranded adaptor.7. The method of ...

Подробнее
Номер записи: 1
14-11-2013 дата публикации

METHODS AND COMPOSITIONS FOR SEQUENCING MODIFIED NUCLEIC ACIDS

Номер: US20130303385A1
Автор: Clark Tyson A., Korlach Jonas, Turner Stephen
Принадлежит:

Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid. 111-. (canceled)12. A method for identifying sequence differences between two nucleic acids from different sources , the method comprising:a) providing a first nucleic acid from a first sample;b) providing a second nucleic acid from a second sample;c) treating the first nucleic acid to produce a modified nucleic acid;d) denaturing the modified nucleic acid and the second nucleic acid;e) annealing the modified nucleic acid to the second nucleic acid, thereby producing hybrid nucleic acids that comprise a first modified strand from the first sample and a second unmodified strand from the second sample, and further wherein a portion of the hybrid nucleic acids comprise non-complementary regions of one or more base pairs where the first modified strand and the second unmodified strand are non-complementary;f) binding a non-complementary-region-specific binding agent to the portion of the hybrid nucleic acids, wherein the non-complementary-region-specific binding agent comprises a selectable tag;g) capturing the portion of the hybrid nucleic acids bound to the non-complementary-region-specific binding agent using the selectable tag;h) removing nucleic acids not bound to the non-complementary-region-specific binding agent;i) subjecting the portion of the hybrid nucleic acids to a single type of sequencing reaction in which both the first and second strands of the hybrid nucleic acids are sequenced and both sequence data and modification data are provided in a single sequence read;j) for each sequence read, ...

Подробнее
Номер записи: 2
02-01-2014 дата публикации

IDENTIFICATION OF 5-METHYL-C IN NUCLEIC ACID TEMPLATES

Номер: US20140004511A1
Автор: Clark Tyson A., HE Chuan, Korlach Jonas, Lu Xingyu, Zhang Liang
Принадлежит:

A method for identifying a 5-MeC in a template nucleic is provided. The method comprises providing a template having 5-MeC, converting the 5-MeC into a futher modification selected from 5-caC and 5-FC. The converted template is then sequenced, and a change in sequencing is detected that is indicative of the further modification, allowing for identifying the 5-MeC in the template nucleic acid. 1. A method for identifying a 5-MeC in a template nucleic acid , the method comprising:a) providing a template nucleic acid comprising the 5-MeC;b) converting the 5-MeC into a further modification by treating the template nucleic acid with a Tet protein, wherein the further modification is selected from 5-caC and 5-fC;c) sequencing the template nucleic acid;d) monitoring the sequencing; ande) detecting a change in the sequencing that is indicative of the further modification, thereby indentifying the 5-MeC in the template nucleic acid.2. The method of claim 1 , wherein the template nucleic acid is a circular nucleic acid.3. The method of claim 2 , wherein the sequencing comprises rolling-circle synthesis of a nascent nucleic acid strand.4. The method of claim 1 , wherein the template nucleic acid is an RNA or DNA molecule.5. The method of claim 1 , wherein the enzyme is a polymerase enzyme.6. The method of claim 1 , wherein the sequencing results in the synthesis of a nascent nucleic acid strand.7. The method of claim 1 , wherein the sequencing is a single-molecule sequencing reaction.8. The method of claim 6 , wherein the monitoring detects incorporation of single nucleotides into the nascent nucleic acid strand to generate a sequence read that is complementary to the template nucleic acid.9. The method of claim 8 , wherein the change occurs at the further modification.10. The method of claim 8 , wherein the change occurs at one or more positions upstream or downstream of the further modification.11. The method of claim 8 , wherein the single nucleotides are differentially ...

Подробнее
Номер записи: 3
12-01-2017 дата публикации

Delaying real-time sequencing

Номер: US20170009289A1
Автор: Cheryl Heiner, Erik Miller, Jonas Korlach, Kevin Travers, Tyson A. Clark
Принадлежит: Pacific Biosciences of California Inc

Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.

Подробнее
Номер записи: 4
24-01-2019 дата публикации

Methods and compositions for sequencing modified nucleic acids

Номер: US20190024162A1
Автор: Jonas Korlach, Stephen Turner, Tyson A. Clark
Принадлежит: Pacific Biosciences of California Inc

Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.

Подробнее
Номер записи: 5
15-05-2014 дата публикации

COMPOSITIONS AND METHODS FOR SELECTION OF NUCLEIC ACIDS

Номер: US20140134610A1
Автор: Clark Tyson A., Korlach Jonas, Pham Thang-Tat, Tsai Yu-Chih, Turner Stephen
Принадлежит: Pacific Biosciences of California, Inc.

Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations. 1. A method for enrichment of a target region in a nucleic acid sample comprising:a) digesting the nucleic acid sample with a restriction enzyme that cuts a defined distance from its recognition site to produce a population of double-stranded nucleic acid fragments, wherein fragments containing the target region have known single-stranded overhangs on each end, each overhang being different;b) ligating two types of stem-loop adapters to the population of nucleic acid fragments, wherein one type of stem-loop adapter has a single-stranded overhang sequence complementary to a first of the known single-strand overhangs at one end of the fragment comprising the target region, and the other type of stem-loop adapter has a single-stranded overhang sequence complementary to a second of the known single-stranded overhangs on the other end of the fragment comprising the target region;c) treating the sample with one or more exonucleases to digest the double-stranded nucleic acid fragments that have one or no stem-loop adapter linked thereto, thus enriching for the target region in the nucleic acid sample.2. The method of claim 1 , wherein one or more restriction enzymes chosen to cleave fragments other than the fragments comprising the target region are added to the population of fragments prior to or during said treating.3. The method of claim 1 , wherein a primer binding sequence is present within at least one of the adapters.4. The method of claim 3 , wherein a primer is bound to the primer binding ...

Подробнее
Номер записи: 6
28-02-2019 дата публикации

DELAYING REAL-TIME SEQUENCING

Номер: US20190062833A1
Автор: Clark Tyson A., Heiner Cheryl, Korlach Jonas, Miller Erik, Travers Kevin
Принадлежит:

Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced. 170-. (canceled)7130. A composition comprising a plurality of nucleic acid sequencing templates , wherein each of the plurality nucleic acid sequencing templates comprises an adaptor region and an insert region , wherein the adaptor region comprises a sequencing initiation site and a runway region and the insert region comprises a sequence of interest , wherein the runway region is between the sequencing initiation site and the insert region , and wherein the runway region has a length that delays sequencing the insert region for seconds or more in a nucleic acid sequencing reaction initiated from the sequencing initiation site.72. The composition of claim 71 , wherein the runway region has a length that delays sequencing the insert region is greater than about 30 seconds.73. The composition of claim 72 , wherein the length of the runway region is 200 nucleotides or greater.74. The composition of claim 73 , wherein the length of the runway region is between 200 and 2 claim 73 ,000 nucleotides.75. The composition of claim 71 , wherein the runway region comprises at least one modified base that is absent from the insert region.76. The composition of claim 71 , wherein the runway region in each of the plurality of nucleic acid sequencing templates has substantially the same sequence.77. The composition of claim 71 , wherein each of the plurality of nucleic acid sequencing templates is linear.78. The composition of claim 77 , wherein each of the plurality of nucleic acid sequencing templates comprises a single strand region on at least one end claim 77 , wherein the single strand region comprises the sequencing initiation site.79. The composition of claim 78 , wherein the sequencing initiation site is an initiation ...

Подробнее
Номер записи: 7
05-06-2014 дата публикации

ISOLATION OF POLYMERASE-NUCLEIC ACID COMPLEXES

Номер: US20140155276A1
Автор: Bhamidipati Arunashree, Clark Tyson A., Korlach Jonas, Olivares Eric, Pham Thang, Travers Kevin
Принадлежит: Pacific Biosciences of California, Inc.

Compositions, methods and systems are provided for the isolation of polymerase-nucleic acid complexes. Complexes can be separated from free enzyme by using hook molecules to target single stranded regions on the nucleic acid. Hook oligonucleotides are used to capture polymerase nucleic acid complexes where the nucleic acids comprise circular nucleic acids having a double stranded central region with hairpin regions on each end. Methods for loading such complexes onto substrates and for single molecule sequencing of such complexes are also provided. 1. A method comprising;fragmenting a double stranded DNA sample into double stranded fragments;ligating to each end of the double stranded fragments a hairpin to produce a population of circular DNA templates having a central double stranded region and hairpin regions on each end;exposing the population of circular DNA templates to a DNA polymerase enzyme having strand displacement activity under conditions in which a mixture comprising a population of polymerase-template complexes is formed;adding to the population of complexes a hook oligonucleotide comprising a capture region complementary to a portion of the hairpin region;using the hook oligonucleotide to isolate the complexes to which it hybridized;thereby isolating complexes from the mixture.2. The method of further comprising loading the isolated complex onto a substrate.3. The method of wherein the adding of the hook oligonucleotide is done before the addition of the DNA polymerase enzyme claim 1 , and the hook oligonucleotide comprises a primer for the DNA polymerase enzyme.4. The method of further comprising adding a primer before exposing the templates to the DNA polymerase enzyme claim 1 , then subsequently carrying out the adding of the hook oligonucleotides.5. The method of wherein beads are used to isolate the complexes with the hook oligonucleotide.6. The method of wherein the hook nucleotide also has a retrieval region having a sequence that allows the ...

Подробнее
Номер записи: 8
26-06-2014 дата публикации

COMPOSITIONS AND METHODS FOR SELECTION OF NUCLEIC ACIDS CONTAINING MODIFIED BASES

Номер: US20140179564A1
Автор: Clark Tyson A., Korlach Jonas, Turner Stephen
Принадлежит: Pacific Biosciences of California, Inc.

Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a desired property, or lacking nucleic acids having an undesired property. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations. In addition, such methods allow for analysis of pooled samples. 1. A method of generating a pool of sequencing templates enriched for a type of modified base , the method comprising:a) fragmenting a nucleic acid sample comprising the type of modified base, thereby generating a mixture comprising a first subset of nucleic acid fragments comprising the type of modified base and a second subset of nucleic acid fragments that do not comprise the type of modified base;b) linking adapters to nucleic acid fragments in both the first subset and the second subset; andc) retaining the nucleic acid fragments in the first subset from the mixture, thereby generating a pool of sequencing templates enriched for the type of modified base.2. The method of claim 1 , wherein the retaining comprises binding the type of modified base to an agent linked to an affinity tag.3. The method of claim 1 , wherein the type of modified base is a methylated cytosine.4. The method of claim 1 , wherein the type of modified base is a hydroxymethylated cytosine.5. The method of claim 1 , wherein the adapters are hairpin or stem-loop adapters that link 3′ and 5′ termini at each end of the nucleic acid fragments.6. The method of claim 5 , wherein the adapters added to a first end of the nucleic acid fragments in the first subset are different from the adapters added to a second end of the nucleic acid fragments in the first subset.7. The method of claim 1 , wherein the retaining comprises affinity purifying the nucleic acid fragments.8. ...

Подробнее
Номер записи: 9
20-04-2017 дата публикации

ISOLATION OF POLYMERASE-NUCLEIC ACID COMPLEXES

Номер: US20170107570A1
Автор: Bhamidipati Arunashree, Clark Tyson A., Korlach Jonas, Olivares Eric, Pham Thang, Travers Kevin
Принадлежит:

Compositions, methods and systems are provided for isolating DNA having a modified or unnatural base. Circular DNA fragments, each comprising a double stranded DNA central region and single stranded regions on the ends of the double stranded regions, are obtained. Some of the fragments have one or more modified or unnatural base. The DNA fragments are treated with a primer and a polymerase such that the polymerase extends the primer to copy at least one of the strand of the double stranded region. This results in rendering the other strand single stranded. A binding protein or antibody that is specific to the modified or unnatural base is then used to isolate strands containing the modified or unnatural bases. Methods for loading such complexes onto substrates and for single molecule sequencing of such complexes are also provided. 121.-. (canceled)22. A method for isolating DNA having a modified or unnatural base comprising:obtaining a library of circular DNA fragments each comprising a double stranded DNA central region and single stranded regions on the ends of the double stranded regions wherein at least some of the fragments comprise one or more modified or unnatural base;treating the DNA fragments with a primer and a polymerase under conditions where the polymerase extends the primer to copy at least a portion of one strand of the double stranded region so as to render the other strand of the double-stranded portion single stranded;using a binding protein or antibody that is specific to the one or more modified or unnatural base to isolate strands containing one or more modified or unnatural base from those that do not contain an unnatural or modified base.23. The method of wherein the one or more modified or unnatural base includes methyl-C claim 22 , hydroxymethyl-C claim 22 , or oxo-G.24. The method of wherein the one or more modified or unnatural base includes 5-methyl-C.25. The method of wherein the library of circular DNA fragments is produced by ligating ...

Подробнее
Номер записи: 10
30-04-2015 дата публикации

DELAYING REAL-TIME SEQUENCING

Номер: US20150118685A1
Автор: Clark Tyson A., Heiner Cheryl, Korlach Jonas, Miller Erik, Travers Kevin
Принадлежит:

Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced. 1. A method for delaying the sequencing of a sequence of interest in a single-molecule , real-time sequencing reaction comprising:simultaneously initiating a plurality of single-molecule, real-time sequencing reactions on a plurality of polymerase-template complexes, wherein each of the polymerase-template complexes comprises a polymerase enzyme and a nucleic acid template wherein the nucleic acid template comprises, in order, a priming region, a runway region, and an insert region comprising a sequence of interest, wherein the time from the initiation of the sequencing reactions to the time of sequencing the insert region is greater than about 30 seconds for a majority of the polymerase-template complexes.2. The method of wherein each priming region in each nucleic acid template in each of the polymerase-template complexes comprises a substantially identical sequence.3. The method of wherein each runway region in each nucleic acid template in each of the polymerase-template complexes comprises a substantially identical sequence.4. The method of wherein the template nucleic acid comprises a double-stranded region and a hairpin connecting the strands of the double-stranded region.5. The method of wherein the template nucleic acid comprises a double-stranded region and hairpins on each end of the double-stranded region connecting the two strands.6. The method of wherein the incorporation of nucleotide residues is detected using fluorescence.7. The method of wherein the incorporation of nucleotide residues is detected electronically or magnetically.8. The method of wherein the incorporation of nucleotide residues is detected by electrochemistry claim 1 , capacitance claim 1 , conductivity claim 1 , impedance claim 1 , ...

Подробнее
Номер записи: 11
12-05-2016 дата публикации

Methods and compositions for sequencing modified nucleic acids

Номер: US20160130646A1
Автор: Jonas Korlach, Stephen Turner, Tyson A. Clark
Принадлежит: Pacific Biosciences of California Inc

Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.

Подробнее
Номер записи: 12
09-05-2019 дата публикации

Loading extended polymerase-nucleic acid complexes

Номер: US20190136313A1
Автор: Arunashree Bhamidipati, Eric Olivares, Jonas Korlach, Kevin Travers, Thang Pham, Tyson A. Clark
Принадлежит: Pacific Biosciences of California Inc

Compositions, methods and systems are provided for the loading of extended polymerase-nucleic acid complexes onto substrates. Primed polymerase-template complex comprising a polymerase enzyme and a circular nucleic acid template comprising a double stranded region connected at each end by a single-stranded hairpin region are provides in which the circular nucleic acid template comprises at least one reversible pause point. Nucleic acid synthesis is carried out such that a nascent strand is synthesized up to the reversible stop point producing an extended polymerase-template complex. The extended polymerase-template complex is then attached to a substrate. Such attached complexes can be used for single molecule sequencing in which the nucleic acid synthesis is re-initiated such that nucleic acid synthesis continues past the reversible stop point.

Подробнее
Номер записи: 13
25-05-2017 дата публикации

COMPOSITIONS AND METHODS FOR SELECTION OF NUCLEIC ACIDS

Номер: US20170145492A1
Автор: Clark Tyson A., Korlach Jonas, Pham Thang Tat, Tsai Yu-Chih, Turner Stephen
Принадлежит:

Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations. 140-. (canceled)41. A method for enrichment of a target region in a nucleic acid sample comprising:a) obtaining a nucleic acid sample comprising a mixture of double-stranded nucleic acid fragments, wherein a subset of fragments in the mixture comprises the target region;b) digesting the nucleic acid sample with a nuclease engineered to cleave a particular nucleotide sequence that is upstream of the target region;c) ligating a first stem-loop adapter to the ends of nucleic acid fragments that have been cleaved by the engineered nuclease in the digesting step; andd) enriching for double-stranded nucleic acid fragments ligated to the first stem loop adapter, thereby enriching for the target region in the nucleic acid sample.42. The method of claim 41 , wherein the mixture of double-stranded nucleic acid fragments in step (a) are protected from exonuclease degradation.43. The method of claim 42 , wherein the mixture of double-stranded nucleic acid fragments comprise terminal blocking groups that are not susceptible to exonuclease degradation.44. The method of claim 42 , wherein the mixture of double-stranded nucleic acid fragments comprises terminal second stem-loop adapters that are not susceptible to exonuclease degradation claim 42 , wherein the second stem-loop adapters on the mixture of double-stranded nucleic acid fragments are different from the first stem-loop adapter.45. The method of claim 44 , wherein a primer binding sequence is present within the second stem-loop adapter.4636. The ...

Подробнее
Номер записи: 14
02-06-2016 дата публикации

CLASSIFICATION OF NUCLEIC ACID TEMPLATES

Номер: US20160153038A1
Автор: Clark Tyson A., Flusberg Benjamin, Hanes Jeremiah, Heiner Cheryl, Jia Lei, Kislyuk Andrey, Korlach Jonas, Lee Jessica, Lyle John, Marks Patrick, Sorenson Jon, Tomaney Austin B., Travers Kevin, Turner Stephen, Vilfan Igor Drasko, WEBSTER Dale, Wegener Jeffrey
Принадлежит:

Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid. 171-. (canceled)72. A method of identifying a barcode , the method comprising:a) providing a sequencing template comprising a nucleic acid linked to a barcode, wherein the barcode consists of a nucleotide sequence comprising a base modification;b) subjecting the sequencing template to a single-molecule sequencing reaction;c) collecting reaction data in real time during the single-molecule sequencing reaction, wherein said reaction data comprises a sequence read for the sequencing template, and wherein the reaction data further comprises a kinetic change in the single-molecule sequencing reaction, wherein the kinetic change is indicative of the base modification in the nucleotide sequence of the barcode; andd) analyzing both the sequence read and the kinetic change in the reaction data to detect the nucleotide sequence of the barcode, thereby identifying the barcode in the sequencing template.73. The method of claim 72 , wherein the sequencing template comprises a first polynucleotide region and a second polynucleotide region complementary to the first polynucleotide region claim 72 , where the first polynucleotide region and the second polynucleotide region are on a single strand of the sequencing template.74. The method of claim 72 , wherein the sequencing template is subjected to a treatment to alter the modified base prior to the single-molecule sequencing reaction.75. The method of claim 72 , wherein the single-molecule sequencing reaction comprises a polymerase enzyme.76. The method of claim 72 , ...

Подробнее
Номер записи: 15
24-12-2020 дата публикации

COMPOSITIONS AND METHODS FOR SELECTION OF NUCLEIC ACIDS

Номер: US20200399690A1
Автор: Clark Tyson A., Korlach Jonas, Pham Thang Tat, Tsai Yu-Chih, Turner Stephen
Принадлежит:

Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations. 135.-. (canceled)36. A method for enrichment of a target region in a nucleic acid sample comprising:a. fragmenting the nucleic acid sample to generate a mixture of double-stranded fragments, where a minority of the double-stranded fragments in the mixture comprise the target region, and a majority of the double-stranded fragments in the mixture do not comprise the target region; andb. selectively degrading the majority of the double-stranded fragments in the mixture that do not comprise the target region in the presence of the minority of the double-stranded fragments that comprise the target region, wherein the minority of the double-stranded fragments that comprise the target region are protected from the degrading, thereby enriching the mixture for the double-stranded fragments that comprise the target region.37. The method of claim 36 , wherein type IIs restriction enzymes are used in the fragmenting to generate the double-stranded fragments claim 36 , wherein the minority of the double-stranded fragments comprising the target region have known overhang sequences at both ends.38360. The method of claim claim 36 , wherein ligation of two stem-loop adapters to the double-stranded fragments that comprise the target region protects them from being degraded.39. The method of claim 36 , further comprising exposing the double-stranded fragments that comprise the target region to a primer and polymerase enzyme to generate a polymerase complex claim 36 , and exposing the polymerase complex to a ...

Подробнее
Номер записи: 16
27-12-2016 дата публикации

Compositions and methods for selection of nucleic acids

Номер: US9528107B2
Автор: Jonas Korlach, Stephen Turner, Thang Tat Pham, Tyson A. Clark, Yu-Chih Tsai
Принадлежит: Pacific Biosciences of California Inc

Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.

Подробнее
Номер записи: 17
03-10-2013 дата публикации

Methods and composition for sequencing modified nucleic acids

Номер: CA2867489A1
Автор: Jonas Korlach, Stephen Turner, Tyson A. Clark
Принадлежит: Pacific Biosciences of California Inc

Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, a basic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.

Подробнее
Номер записи: 18
25-09-2018 дата публикации

Delaying real-time sequencing

Номер: US10081836B2
Автор: Cheryl Heiner, Erik Miller, Jonas Korlach, Kevin Travers, Tyson A. Clark
Принадлежит: Pacific Biosciences of California Inc

Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.

Подробнее
Номер записи: 19
25-02-2014 дата публикации

Isolation of polymerase-nucleic acid complexes

Номер: US8658364B2
Автор: Arunashree Bhamidipati, Eric Olivares, Jonas Korlach, Kevin Travers, Thang Pham, Tyson A. Clark
Принадлежит: Pacific Biosciences of California Inc

Compositions, methods and systems are provided for the isolation of polymerase-nucleic acid complexes. Complexes can be separated from free enzyme by using hook molecules to target single stranded regions on the nucleic acid. Active complexes can be isolated from mixtures having both active and inactive complexes by initiating nucleic acid synthesis so as to open up a portion of a double stranded region rendering that region single stranded. Hook molecules are targeted to bind the sequences that are thus exposed. The hook molecules bound to active polymerase-nucleic acid complex are isolated, and the active polymerase-nucleic acid complexes released.

Подробнее
Номер записи: 20
28-07-2011 дата публикации

Classification of nucleic acid templates

Номер: US20110183320A1
Автор: Andrey Kislyuk, Austin B. Tomaney, Benjamin Flusberg, Cheryl Heiner, Dale Webster, Igor Vilfan, Jeffrey Wegener, Jeremiah Hanes, Jessica Lee, John Lyle, Jon Sorenson, Jonas Korlach, Joseph Puglisi, Kevin Travers, LEI Jia, Patrick Marks, Stephen Turner, Tyson A. Clark
Принадлежит: Pacific Biosciences of California Inc

Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.

Подробнее
Номер записи: 21
28-11-2023 дата публикации

Methods for isolating nucleic acids

Номер: US11827934B2
Автор: Arunashree Bhamidipati, Eric Olivares, Jonas Korlach, Kevin Travers, Thang Pham, Tyson A. Clark
Принадлежит: Pacific Biosciences of California Inc

Compositions, methods and systems are provided for isolating nucleic acids. A polymerase-nucleic acid complex can be formed by mixing a polymerase enzyme comprising strand displacement activity and a mixture of double stranded nucleic acids. Nucleic acid synthesis can then be initiated by the polymerase enzyme to produce a nascent strand complementary to the first strand, thereby displacing a portion of the second strand. After halting or reducing the rate of nucleic acid synthesis, a hybridizing a hook oligonucleotide can be used hybridize to the nucleic acid through a capture region on the hook oligonucleotide that is complementary to the displaced portion of the second strand. The nucleic acid can then be isolated from the mixture of nucleic acids using the hook oligonucleotide.

Подробнее
Номер записи: 22
01-02-2024 дата публикации

Delaying real-time sequencing

Номер: US20240035085A1
Автор: Cheryl Heiner, Erik Miller, Jonas Korlach, Kevin Travers, Tyson A. Clark
Принадлежит: Pacific Biosciences of California Inc

Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.

Подробнее
Номер записи: 23
25-10-2016 дата публикации

Isolation of polymerase-nucleic acid complexes

Номер: US09475054B2
Автор: Arunashree Bhamidipati, Eric Olivares, Jonas Korlach, Kevin Travers, Thang Pham, Tyson A. Clark
Принадлежит: Pacific Biosciences of California Inc

Compositions, methods and systems are provided for the isolation of polymerase-nucleic acid complexes. Complexes can be separated from free enzyme by using hook molecules to target single stranded regions on the nucleic acid. Hook oligonucleotides are used to capture polymerase nucleic acid complexes where the nucleic acids comprise circular nucleic acids having a double stranded central region with hairpin regions on each end. Methods for loading such complexes onto substrates and for single molecule sequencing of such complexes are also provided.

Подробнее
Номер записи: 24