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1. 发明授权

US08999674B2 Methods and apparatus for single molecule sequencing using energy transfer detection 有权
标题翻译：使用能量转移检测的单分子测序的方法和装置
公开(公告)号：US08999674B2
公开(公告)日：2015-04-07
申请号：US13562159
申请日：2012-07-30
申请人： Joseph Beechem , Theo Nikiforov , Vi-En Choong , Xinzhan Peng , Guobin Luo , Cheng-Yao Chen , Michael Previte
发明人： Joseph Beechem , Theo Nikiforov , Vi-En Choong , Xinzhan Peng , Guobin Luo , Cheng-Yao Chen , Michael Previte
IPC分类号： C12P19/34 , C12N9/12 , C07H19/20
CPC分类号： C12Q1/6869 , C07H19/20 , C12N9/1241 , C12N9/1252 , C12N9/96 , C12Q1/6818 , C12Y207/07 , C12Y207/07007 , G01N21/6428 , G01N33/582 , G01N2021/6432
摘要： Provided herein are systems and methods for nucleotide incorporation reactions. The systems comprise polymerases having altered nucleotide incorporation kinetics and are linked to an energy transfer donor moiety, and nucleotide molecules linked with at least one energy transfer acceptor moiety. The donor and acceptor moieties undergo energy transfer when the polymerase and nucleotide are proximal to each other during nucleotide binding and/or nucleotide incorporation. As the donor and acceptor moieties undergo energy transfer, they generate an energy transfer signal which can be associated with nucleotide binding or incorporation. Detecting a time sequence of the generated signals, or the change in the signals, can be used to determine the order of the incorporated nucleotides, and can therefore be used to deduce the sequence of the target molecule.
摘要翻译：本文提供了用于核苷酸掺入反应的系统和方法。该系统包含具有改变的核苷酸掺入动力学并且与能量转移供体部分连接的聚合酶，以及与至少一个能量转移受体部分连接的核苷酸分子。当核苷酸结合和/或核苷酸掺入期间聚合酶和核苷酸彼此接近时，供体和受体部分进行能量转移。当供体和受体部分进行能量转移时，它们产生可与核苷酸结合或掺入相关联的能量转移信号。检测所产生的信号的时间序列或信号的变化可用于确定掺入的核苷酸的顺序，因此可用于推导靶分子的序列。

2. 发明申请

US20100255487A1 METHODS AND APPARATUS FOR SINGLE MOLECULE SEQUENCING USING ENERGY TRANSFER DETECTION 审中-公开
标题翻译：使用能量转移检测的单分子序列的方法和装置
公开(公告)号：US20100255487A1
公开(公告)日：2010-10-07
申请号：US12748168
申请日：2010-03-26
申请人： JOSEPH BEECHEM , THEO NIKIFOROV , Vi-En Choong , Xinzhan Peng , Guobin Luo , Cheng-Yao Chen , Michael Previte
发明人： JOSEPH BEECHEM , THEO NIKIFOROV , Vi-En Choong , Xinzhan Peng , Guobin Luo , Cheng-Yao Chen , Michael Previte
IPC分类号： C12Q1/68 , C12N9/10
CPC分类号： C12Q1/6869 , C07H19/20 , C12N9/1241 , C12N9/1252 , C12N9/96 , C12Q1/6818 , C12Y207/07 , C12Y207/07007 , G01N21/6428 , G01N33/582 , G01N2021/6432
摘要： Provided herein are systems and methods for nucleotide incorporation reactions. The systems comprise polymerases having altered nucleotide incorporation kinetics and are linked to an energy transfer donor moiety, and nucleotide molecules linked with at least one energy transfer acceptor moiety. The donor and acceptor moieties undergo energy transfer when the polymerase and nucleotide are proximal to each other during nucleotide binding and/or nucleotide incorporation. As the donor and acceptor moieties undergo energy transfer, they generate an energy transfer signal which can be associated with nucleotide binding or incorporation. Detecting a time sequence of the generated signals, or the change in the signals, can be used to determine the order of the incorporated nucleotides, and can therefore be used to deduce the sequence of the target molecule.
摘要翻译：本文提供了用于核苷酸掺入反应的系统和方法。该系统包含具有改变的核苷酸掺入动力学并且与能量转移供体部分连接的聚合酶，以及与至少一个能量转移受体部分连接的核苷酸分子。当核苷酸结合和/或核苷酸掺入期间聚合酶和核苷酸彼此接近时，供体和受体部分进行能量转移。当供体和受体部分进行能量转移时，它们产生可与核苷酸结合或掺入相关联的能量转移信号。检测所产生的信号的时间序列或信号的变化可用于确定掺入的核苷酸的顺序，因此可用于推导靶分子的序列。

3. 发明授权

US08632975B2 Nucleotide transient binding for sequencing methods 有权
标题翻译：测序方法的核苷酸瞬变结合
公开(公告)号：US08632975B2
公开(公告)日：2014-01-21
申请号：US12790760
申请日：2010-05-28
申请人： Peter B. Vander Horn , Cheng-Yao Chen , Guobin Luo , Michael Previte , Jamshid Temirov , Theo Nikiforov , Zhaohui Zhou , Hongye Sun , Yufang Wang , Stefanie Yukiko Nishimura , Hongyi Wang , Marian Peris , Barnett B. Rosenblum , Michael Phelan
发明人： Peter B. Vander Horn , Cheng-Yao Chen , Guobin Luo , Michael Previte , Jamshid Temirov , Theo Nikiforov , Zhaohui Zhou , Hongye Sun , Yufang Wang , Stefanie Yukiko Nishimura , Hongyi Wang , Marian Peris , Barnett B. Rosenblum , Michael Phelan
IPC分类号： C12Q1/68
CPC分类号： C12N9/1252 , C12Q1/68 , C12Q1/6804 , C12Q1/6818 , C12Q1/6827 , C12Q1/6869 , C12Q1/6872 , C12Y207/07007 , G01N2500/00 , C12Q2565/632 , C12Q2563/137 , C12Q2563/107 , C12Q2565/30 , C12Q2537/157
摘要： Provided herein are compositions and systems for use in polymerase-dependent, nucleotide transient-binding methods. The methods are useful for deducing the sequence of a template nucleic acid molecule and single nucleotide polymorphism (SNP) analyses. The methods rely on the fact that the polymerase transient-binding time for a complementary nucleotide is longer compared to that of a non-complementary nucleotide. The labeled nucleotides transiently-binds the polymerase in a template-dependent manner, but does not incorporate. The methods are conducted under any reaction condition that permits transient binding of a complementary or non-complementary nucleotide to a polymerase, and inhibits nucleotide incorporation.
摘要翻译：本文提供了用于聚合酶依赖性核苷酸瞬变结合方法的组合物和系统。该方法可用于推导模板核酸分子和单核苷酸多态性（SNP）分析的序列。该方法依赖于与非互补核苷酸相比，互补核苷酸的聚合酶瞬时结合时间更长的事实。标记的核苷酸以模板依赖的方式瞬时结合聚合酶，但不包括在内。所述方法在允许互补或非互补核苷酸与聚合酶短暂结合并且抑制核苷酸掺入的任何反应条件下进行。

4. 发明申请

US20100330570A1 NUCLEOTIDE TRANSIENT BINDING FOR SEQUENCING METHODS 有权
标题翻译：用于测序方法的核心瞬态绑定
公开(公告)号：US20100330570A1
公开(公告)日：2010-12-30
申请号：US12790760
申请日：2010-05-28
申请人： Peter B. VANDER HORN , Cheng-Yao Chen , Guobin Luo , Michael Previte , Jamshid Temirov , Theo Nikiforov , Zhaohui Zhou , Hongye Sun , Yufang Wang , Stefanie Yukiko Nishimura , Hongyi Wang , Marian Peris , Barnett B. Rosenblum , Michael Phelan
发明人： Peter B. VANDER HORN , Cheng-Yao Chen , Guobin Luo , Michael Previte , Jamshid Temirov , Theo Nikiforov , Zhaohui Zhou , Hongye Sun , Yufang Wang , Stefanie Yukiko Nishimura , Hongyi Wang , Marian Peris , Barnett B. Rosenblum , Michael Phelan
IPC分类号： C12Q1/68 , C12N9/96
CPC分类号： C12N9/1252 , C12Q1/68 , C12Q1/6804 , C12Q1/6818 , C12Q1/6827 , C12Q1/6869 , C12Q1/6872 , C12Y207/07007 , G01N2500/00 , C12Q2565/632 , C12Q2563/137 , C12Q2563/107 , C12Q2565/30 , C12Q2537/157
摘要： Provided herein are compositions and systems for use in polymerase-dependent, nucleotide transient-binding methods. The methods are useful for deducing the sequence of a template nucleic acid molecule and single nucleotide polymorphism (SNP) analyses. The methods rely on the fact that the polymerase transient-binding time for a complementary nucleotide is longer compared to that of a non-complementary nucleotide. The labeled nucleotides transiently-binds the polymerase in a template-dependent manner, but does not incorporate. The methods are conducted under any reaction condition that permits transient binding of a complementary or non-complementary nucleotide to a polymerase, and inhibits nucleotide incorporation.
摘要翻译：本文提供了用于聚合酶依赖性核苷酸瞬变结合方法的组合物和系统。该方法可用于推导模板核酸分子和单核苷酸多态性（SNP）分析的序列。该方法依赖于与非互补核苷酸相比，互补核苷酸的聚合酶瞬时结合时间更长的事实。标记的核苷酸以模板依赖的方式瞬时结合聚合酶，但不包括在内。所述方法在允许互补或非互补核苷酸与聚合酶短暂结合并且抑制核苷酸掺入的任何反应条件下进行。

5. 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。

6. 发明授权

US11591629B2 Method and kit for template-independent nucleic acid synthesis 有权
公开(公告)号：US11591629B2
公开(公告)日：2023-02-28
申请号：US16725420
申请日：2019-12-23
申请人： Cheng-Yao Chen
发明人： Cheng-Yao Chen
IPC分类号： C12P19/34
摘要： A method for synthesizing a nucleic acid includes providing an initiator having a 3′ end having an unprotected hydroxyl group, providing a nucleic acid polymerase having at least a conservative catalytic polymerase domain of a family-B DNA polymerase, providing a nucleotide monomer, and exposing the initiator to the nucleotide monomer in the presence of the nucleic acid polymerase and a metal cofactor which is a bivalent cation, and in the absence of a template, such that the nucleotide monomer is incorporated to the initiator. The kit includes the initiator, the nucleic acid polymerase, and the nucleotide monomer, and is used according to the method.

7. 发明申请

US20140065675A1 NUCLEOTIDES AND PRIMERS WITH REMOVABLE BLOCKING GROUPS 有权
标题翻译：具有可移动阻塞组的核心和主体
公开(公告)号：US20140065675A1
公开(公告)日：2014-03-06
申请号：US13782066
申请日：2013-03-01
申请人： Cheng-Yao Chen , Gothami Padmabandu
发明人： Cheng-Yao Chen , Gothami Padmabandu
IPC分类号： C12P19/34
CPC分类号： C12P19/34 , C12Q1/6848 , C12Q2523/107 , C12Q2525/186 , C12Q2563/137 , C12Q2549/101
摘要： Provided herein is a method of amplifying nucleic acids using a plurality of modified nucleotides one or more of the nucleotides comprising a 3′ blocking group. Also provided is a method of amplifying nucleic acids using oligonucleotide primers one or both of the primers comprising a 3′ blocking group on one or more of the nucleotides of the primers.
摘要翻译：本文提供了使用多个修饰的核苷酸扩增核酸的方法，所述核苷酸包含3'阻断基团的一个或多个核苷酸。还提供了使用寡核苷酸引物扩增核酸的方法，所述引物在引物的一个或多个核苷酸上包含3'封闭基团的一个或两个引物。

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