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1. 发明授权

US08257954B2 Generation of modified polymerases for improved accuracy in single molecule sequencing 有权
标题翻译：修饰聚合酶的生成，提高了单分子测序的准确性
公开(公告)号：US08257954B2
公开(公告)日：2012-09-04
申请号：US12384112
申请日：2009-03-30
申请人： Sonya Clark , Arek Bibillo , Paul Peluso , Fred Christians , Molly He , Insil Park , Harold Lee , Keith Bjornson , Lei Jia , Robin Emig
发明人： Sonya Clark , Arek Bibillo , Paul Peluso , Fred Christians , Molly He , Insil Park , Harold Lee , Keith Bjornson , Lei Jia , Robin Emig
IPC分类号： C12N9/12 , C12P19/34
CPC分类号： C12N9/1252 , C12Q1/6844 , C12Q1/6869 , C12Q2521/101
摘要： Provided are compositions comprising modified recombinant polymerases that exhibit branching fractions that are less than the branching fractions of the polymerases from which they were derived, or branching fractions that are less than about 25% for a phosphate-labeled nucleotide analog. Also provided are compositions comprising modified recombinant polymerases that exhibit closed polymerase/DNA complexes with increased stability relative to the parental polymerases. Also provided are compositions comprising modified recombinant polymerases that exhibit decreased rate constants relative to the parental polymerases. Provided are methods for generating polymerases with the aforementioned phenotypes. Provided are methods of using such polymerases to make a DNA or to sequence a DNA template.
摘要翻译：提供了包含修饰的重组聚合酶的组合物，其表现出小于其衍生自其的聚合酶的支化部分的支化部分，或对于磷酸酯标记的核苷酸类似物的支化部分小于约25％。还提供了包含修饰的重组聚合酶的组合物，其表现出相对于亲本聚合酶具有增加的稳定性的闭合的聚合酶/ DNA复合物。还提供了包含修饰的重组聚合酶的组合物，其相对于亲本聚合酶表现出降低的速率常数。提供了产生具有上述表型的聚合酶的方法。提供使用这种聚合酶制备DNA或顺序DNA模板的方法。

2. 发明授权

US09353412B2 Conformational probes and methods for sequencing nucleic acids 有权
标题翻译：构象探针和核酸测序方法
公开(公告)号：US09353412B2
公开(公告)日：2016-05-31
申请号：US13162325
申请日：2011-06-16
申请人： Molly He , Cheng-Yao Chen , Eric Kool , Mostafa Ronaghi , Michael Previte , Rigo Pantoja
发明人： Molly He , Cheng-Yao Chen , Eric Kool , Mostafa Ronaghi , Michael Previte , Rigo Pantoja
IPC分类号： C12P19/34 , C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6806 , C12Q1/6818 , C12Q2565/133 , C12Q2563/125 , C12Q2525/101 , C12Q2565/1015
摘要： This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.
摘要翻译：本公开提供了确定核酸模板的核苷酸序列的方法。该方法可以包括以下步骤：使构象标记的聚合酶和至少四种不同的核苷酸物种在其中所述构象标记的聚合酶催化核苷酸物种的顺序加入以形成核酸模板的核酸补体的条件下接触，其中每个不同核苷酸类型的顺序加入从所述构象标记的聚合酶产生构象信号变化，并且其中所述构象信号变化的速率或持续时间对于每个不同的核苷酸种类是可区分的; 在条件下检测来自构象标记的聚合酶的信号的一系列变化; 并确定信号变化的速率或时间，从而确定核酸模板的核苷酸序列。

3. 发明授权

US08133672B2 Two slow-step polymerase enzyme systems and methods 有权
标题翻译：两个慢步聚合酶系统和方法
公开(公告)号：US08133672B2
公开(公告)日：2012-03-13
申请号：US12414191
申请日：2009-03-30
申请人： Keith Bjornson , Harold Lee , Jonas Korlach , Stephen Turner , Arek Bibillo , Fred Christians , Robin Emig , Molly He , Insil Park , Lei Jia , Andrei Fedorov , John Lyle
发明人： Keith Bjornson , Harold Lee , Jonas Korlach , Stephen Turner , Arek Bibillo , Fred Christians , Robin Emig , Molly He , Insil Park , Lei Jia , Andrei Fedorov , John Lyle
IPC分类号： C12Q1/68 , C12P19/34 , C07H21/02 , C07H21/04
CPC分类号： C12Q1/6869 , C12Q1/6874 , C12Q2527/125 , C12Q2527/119 , C12Q2527/101 , C12Q2565/1015 , C12Q2527/137 , C12Q2521/101
摘要： Compositions, kits, methods and systems for nucleotide sequencing comprising producing polymerase reactions that exhibit two kinetically observable steps within an observable phase of the polymerase reaction. Two slow step systems can be produced, for example, by selecting the appropriate polymerase enzyme, polymerase reaction conditions including cofactors, and polymerase reaction substrates including the primed template and nucleotides.
摘要翻译：用于核苷酸测序的组合物，试剂盒，方法和系统，其包括产生聚合酶反应，其在聚合酶反应的可观察期内显示两个动力学可观察步骤。可以通过例如选择合适的聚合酶，包括辅因子的聚合酶反应条件和包括引发的模板和核苷酸的聚合酶反应底物来产生两个缓慢的步骤系统。

4. 发明申请

US20110189659A1 Generation of modified polymerases for improved accuracy in single molecule sequencing 有权
标题翻译：修饰聚合酶的生成，提高了单分子测序的准确性
公开(公告)号：US20110189659A1
公开(公告)日：2011-08-04
申请号：US12924701
申请日：2010-09-30
申请人： Sonya Clark , Arek Bibillo , Paul Peluso , Fred Christians , Molly He , Insil Park , Harold Lee , Keith Bjornson , Lei Jia , Robin Emig
发明人： Sonya Clark , Arek Bibillo , Paul Peluso , Fred Christians , Molly He , Insil Park , Harold Lee , Keith Bjornson , Lei Jia , Robin Emig
IPC分类号： C12N9/12 , C12Q1/68 , C12N11/00 , C12P19/34
CPC分类号： C12N9/12 , C12N11/00 , C12P19/34 , C12Q1/68
摘要： Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions and/or heterologous or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include reduced reaction rates at one or more steps of the polymerase kinetic cycle, increased closed polymerase/DNA complex stability, enhanced metal ion coordination, reduced exonuclease activity, decreased branching fractions, and the like. Polymerases that exhibit branching fractions that are less than the branching fractions of the polymerases from which they were derived, or branching fractions that are less than about 25% for a phosphate-labeled nucleotide analog, are also provided. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.
摘要翻译：提供了包含重组DNA聚合酶的组合物，其包括氨基酸取代，插入，缺失和/或异源或外源特征，其在聚合酶上赋予改进的性质以用于增强的单分子测序。这种性质可以包括聚合酶动力学循环的一个或多个步骤的降低的反应速率，增加的闭合聚合酶/ DNA复合物稳定性，增强的金属离子配位，减少的核酸外切酶活性，降低的支化部分等。还提供了表现出低于其衍生的聚合酶的支化级分的支化级分的聚合酶，或者对于磷酸酯标记的核苷酸类似物的支化级分小于约25％。还提供了编码具有上述表型的聚合酶的核酸，以及使用这种聚合酶制备DNA或顺序DNA模板的方法。

5. 发明申请

US20100112645A1 Generation of modified polymerases for improved accuracy in single molecule sequencing 有权
标题翻译：修饰聚合酶的生成，提高了单分子测序的准确性
公开(公告)号：US20100112645A1
公开(公告)日：2010-05-06
申请号：US12384112
申请日：2009-03-30
申请人： Sonya Clark , Arek Bibillo , Paul Peluso , Fred Christians , Molly He , Insil Park , Harold Lee , Keith Bjornson , Lei Jia , Robin Emig
发明人： Sonya Clark , Arek Bibillo , Paul Peluso , Fred Christians , Molly He , Insil Park , Harold Lee , Keith Bjornson , Lei Jia , Robin Emig
IPC分类号： C12P19/34 , C12N9/12 , C12N11/00
CPC分类号： C12N9/1252 , C12Q1/6844 , C12Q1/6869 , C12Q2521/101
摘要： Provided are compositions comprising modified recombinant polymerases that exhibit branching fractions that are less than the branching fractions of the polymerases from which they were derived, or branching fractions that are less than about 25% for a phosphate-labeled nucleotide analog. Also provided are compositions comprising modified recombinant polymerases that exhibit closed polymerase/DNA complexes with increased stability relative to the parental polymerases. Also provided are compositions comprising modified recombinant polymerases that exhibit decreased rate constants relative to the parental polymerases. Provided are methods for generating polymerases with the aforementioned phenotypes. Provided are methods of using such polymerases to make a DNA or to sequence a DNA template.
摘要翻译：提供了包含修饰的重组聚合酶的组合物，其表现出小于其衍生自其的聚合酶的支化部分的支化部分，或对于磷酸酯标记的核苷酸类似物的支化部分小于约25％。还提供了包含修饰的重组聚合酶的组合物，其表现出相对于亲本聚合酶具有增加的稳定性的闭合的聚合酶/ DNA复合物。还提供了包含修饰的重组聚合酶的组合物，其相对于亲本聚合酶表现出降低的速率常数。提供了产生具有上述表型的聚合酶的方法。提供使用这种聚合酶制备DNA或顺序DNA模板的方法。

6. 发明申请

US20190040382A1 CONTIGUITY PRESERVING TRANSPOSITION 审中-公开
公开(公告)号：US20190040382A1
公开(公告)日：2019-02-07
申请号：US15519482
申请日：2015-10-16
申请人： Frank J. STEEMERS , Kevin L. GUNDERSON , Fan ZHANG , Jason Richard BETLEY , Niall Anthony GORMLEY , Wouter MEULEMAN , Jacqueline WEIR , Avgousta IOANNOU , Gareth JENKINS , Rosamond JACKSON , Natalie MORRELL , Dmitry K. POKHOLOK , Steven J. NORBERG , Molly HE , Amirali KIA , Igor GORYSHIN , Rigo PANTOJA , ILLUMINA CAMBRIDGE LIMITED
发明人： Frank J. Steemers , Kevin L. Gunderson , Fan Zhang , Jason Richard Betley , Niall Anthony Gormley , Wouter Meuleman , Jacqueline Weir , Avgousta Ioannou , Gareth Jenkins , Rosamond Jackson , Natalie Morrell , Dmitry K. Pokholok , Steven J. Norberg , Molly He , Amirali Kia , Igor Goryshin , Rigo Pantoja
IPC分类号： C12N15/10 , C12Q1/68
摘要： Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.

7. 发明申请

US20090286245A1 TWO SLOW-STEP POLYMERASE ENZYME SYSTEMS AND METHODS 有权
标题翻译：两个慢步聚合酶酶系统和方法
公开(公告)号：US20090286245A1
公开(公告)日：2009-11-19
申请号：US12414191
申请日：2009-03-30
申请人： Keith Bjornson , Harold Lee , Jonas Korlach , Stephen Turner , Arek Bibillo , Fred Christians , Robin Emig , Molly He , Insil Park , Lei Jia , Andrei Fedorov , John Lyle
发明人： Keith Bjornson , Harold Lee , Jonas Korlach , Stephen Turner , Arek Bibillo , Fred Christians , Robin Emig , Molly He , Insil Park , Lei Jia , Andrei Fedorov , John Lyle
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , C12Q1/6874 , C12Q2527/125 , C12Q2527/119 , C12Q2527/101 , C12Q2565/1015 , C12Q2527/137 , C12Q2521/101
摘要： Compositions, kits, methods and systems for nucleotide sequencing comprising producing polymerase reactions that exhibit two kinetically observable steps within an observable phase of the polymerase reaction. Two slow step systems can be produced, for example, by selecting the appropriate polymerase enzyme, polymerase reaction conditions including cofactors, and polymerase reaction substrates including the primed template and nucleotides.
摘要翻译：用于核苷酸测序的组合物，试剂盒，方法和系统，其包括产生聚合酶反应，其在聚合酶反应的可观察期内显示两个动力学可观察步骤。可以通过例如选择合适的聚合酶，包括辅因子的聚合酶反应条件和包括引发的模板和核苷酸的聚合酶反应底物来产生两个缓慢的步骤系统。

8. 发明授权

US08420366B2 Generation of modified polymerases for improved accuracy in single molecule sequencing 有权
标题翻译：修饰聚合酶的生成，提高了单分子测序的准确性
公开(公告)号：US08420366B2
公开(公告)日：2013-04-16
申请号：US12924701
申请日：2010-09-30
申请人： Sonya Clark , Arek Bibillo , Paul Peluso , Fred Christians , Molly He , Insil Park , Harold Lee , Keith Bjornson , Lei Jia , Robin Emig
发明人： Sonya Clark , Arek Bibillo , Paul Peluso , Fred Christians , Molly He , Insil Park , Harold Lee , Keith Bjornson , Lei Jia , Robin Emig
IPC分类号： C12N9/12 , C12P19/34
CPC分类号： C12N9/12 , C12N11/00 , C12P19/34 , C12Q1/68
摘要： Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions and/or heterologous or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include reduced reaction rates at one or more steps of the polymerase kinetic cycle, increased closed polymerase/DNA complex stability, enhanced metal ion coordination, reduced exonuclease activity, decreased branching fractions, and the like. Polymerases that exhibit branching fractions that are less than the branching fractions of the polymerases from which they were derived, or branching fractions that are less than about 25% for a phosphate-labeled nucleotide analog, are also provided. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.
摘要翻译：提供了包含重组DNA聚合酶的组合物，其包括氨基酸取代，插入，缺失和/或异源或外源特征，其在聚合酶上赋予改进的性质以用于增强的单分子测序。这种性质可以包括聚合酶动力学循环的一个或多个步骤的降低的反应速率，增加的闭合聚合酶/ DNA复合物稳定性，增强的金属离子配位，减少的核酸外切酶活性，降低的支化部分等。还提供了表现出低于其衍生的聚合酶的支化级分的支化级分的聚合酶，或者对于磷酸酯标记的核苷酸类似物的支化级分小于约25％。还提供了编码具有上述表型的聚合酶的核酸，以及使用这种聚合酶制备DNA或顺序DNA模板的方法。

9. 发明申请

US20120034602A1 Recombinant Polymerases For Improved Single Molecule Sequencing 有权
标题翻译：用于改进单分子测序的重组聚合酶
公开(公告)号：US20120034602A1
公开(公告)日：2012-02-09
申请号：US13176697
申请日：2011-07-05
申请人： Robin Emig , Insil Park , Lei Jia , Arek Bibillo , Keith Bjornson , Molly He , Jeremiah Hanes , Harold Lee , Sonya Clark , Fred Christians , Paul Peluso , John Vieceli , Satwik Kamtekar , Erik Miller , Colleen Cutcliffe , Walter Lee
发明人： Robin Emig , Insil Park , Lei Jia , Arek Bibillo , Keith Bjornson , Molly He , Jeremiah Hanes , Harold Lee , Sonya Clark , Fred Christians , Paul Peluso , John Vieceli , Satwik Kamtekar , Erik Miller , Colleen Cutcliffe , Walter Lee
IPC分类号： C12N9/12 , C12Q1/68
CPC分类号： C12N9/1252 , C12N9/1241 , C12P19/34 , C12Q1/6869
摘要： Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.
摘要翻译：提供了包含重组DNA聚合酶的组合物，其包括赋予聚合酶修饰性质以增强单分子测序的氨基酸取代，插入，缺失和/或外源特征。这种性质可以包括增强的金属离子配位，降低的核酸外切酶活性，在聚合酶动力学循环的一个或多个步骤中降低的反应速率，降低的支化部分，改变的辅因子选择性，增加的产率，增加的热稳定性，增加的准确度，增加的速度，增加的读长度，等等。还提供了编码具有上述表型的聚合酶的核酸，以及使用这种聚合酶制备DNA或顺序DNA模板的方法。

10. 发明申请

US20110312529A1 CONFORMATIONAL PROBES AND METHODS FOR SEQUENCING NUCLEIC ACIDS 有权
标题翻译：用于测序核酸的合成探针和方法
公开(公告)号：US20110312529A1
公开(公告)日：2011-12-22
申请号：US13162325
申请日：2011-06-16
申请人： MOLLY HE , CHENG-YAO CHEN , ERIC KOOL , MOSTAFA RONAGHI , MICHAEL PREVITE , RIGO PANTOJA
发明人： MOLLY HE , CHENG-YAO CHEN , ERIC KOOL , MOSTAFA RONAGHI , MICHAEL PREVITE , RIGO PANTOJA
IPC分类号： C40B30/04 , C40B30/00
CPC分类号： C12Q1/6874 , C12Q1/6806 , C12Q1/6818 , C12Q2565/133 , C12Q2563/125 , C12Q2525/101 , C12Q2565/1015
摘要： This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.
摘要翻译：本公开提供了确定核酸模板的核苷酸序列的方法。该方法可以包括以下步骤：使构象标记的聚合酶和至少四种不同的核苷酸物种在其中所述构象标记的聚合酶催化核苷酸物种的顺序加入以形成核酸模板的核酸补体的条件下接触，其中每个不同核苷酸类型的顺序加入从所述构象标记的聚合酶产生构象信号变化，并且其中所述构象信号变化的速率或持续时间对于每个不同的核苷酸种类是可区分的; 在条件下检测来自构象标记的聚合酶的信号的一系列变化; 并确定信号变化的速率或时间，从而确定核酸模板的核苷酸序列。

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