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    NUCLEIC ACID SEQUENCE ANALYSIS
    5.
    发明申请
    NUCLEIC ACID SEQUENCE ANALYSIS 有权
    核酸序列分析

    公开(公告)号：US20120115736A1

    公开(公告)日：2012-05-10

    申请号：US13271889

    申请日：2011-10-12

    申请人： Keith Bjornson ,  Arek Bibillo ,  Fred Christians ,  Kevin Travers ,  Robin Emig ,  Stephen Turner

    发明人： Keith Bjornson ,  Arek Bibillo ,  Fred Christians ,  Kevin Travers ,  Robin Emig ,  Stephen Turner

    IPC分类号： C12Q1/68 ,  C40B20/00

    CPC分类号： C12Q1/6869 ,  C07K14/00 ,  C12Q1/6874 ,  C12Q2531/125 ,  C12Q2521/101

    摘要： Provided are methods for sequencing a nucleic acid with a sequencing enzyme, e.g., a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. In certain embodiments, a template is fixed to a surface through a template localizing moiety. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Also provided are methods for using data from analytical reactions wherein two different enzymes are employed, e.g., at a same or different reaction regions.

    摘要翻译： 提供了用测序酶（例如聚合酶或外切核酸酶）对核酸进行测序的方法。 测序酶可以任选地与第二个测序酶交换，其继续测序核酸。 在某些实施方案中，通过模板定位部分将模板固定在表面上。 模板定位部分可任选地与核酸退火和/或与测序酶缔合。 还提供了包含核酸和第一测序酶的组合物，其可以对核酸进行序列化并且任选与组合物中存在的第二测序酶交换。 提供其中将模板定位部分固定在表面上的组合物。 还提供了使用来自分析反应的数据的方法，其中使用两种不同的酶，例如在相同或不同的反应区域。

    Nucleic acid sequence analysis
    6.
    发明授权
    Nucleic acid sequence analysis 有权
    核酸序列分析

    公开(公告)号：US08921046B2

    公开(公告)日：2014-12-30

    申请号：US13271889

    申请日：2011-10-12

    申请人： Keith Bjornson ,  Arek Bibillo ,  Fred Christians ,  Kevin Travers ,  Robin Emig ,  Stephen Turner

    发明人： Keith Bjornson ,  Arek Bibillo ,  Fred Christians ,  Kevin Travers ,  Robin Emig ,  Stephen Turner

    IPC分类号： C12Q1/68 ,  C12P19/34 ,  C07H21/04

    CPC分类号： C12Q1/6869 ,  C07K14/00 ,  C12Q1/6874 ,  C12Q2531/125 ,  C12Q2521/101

    摘要： Provided are methods for sequencing a nucleic acid with a sequencing enzyme, e.g., a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. In certain embodiments, a template is fixed to a surface through a template localizing moiety. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Also provided are methods for using data from analytical reactions wherein two different enzymes are employed, e.g., at a same or different reaction regions.

    摘要翻译： 提供了用测序酶（例如聚合酶或外切核酸酶）对核酸进行测序的方法。 测序酶可以任选地与第二个测序酶交换，其继续测序核酸。 在某些实施方案中，通过模板定位部分将模板固定在表面上。 模板定位部分可任选地与核酸退火和/或与测序酶缔合。 还提供了包含核酸和第一测序酶的组合物，其可以对核酸进行序列化并且任选与组合物中存在的第二测序酶交换。 提供其中将模板定位部分固定在表面上的组合物。 还提供了使用来自分析反应的数据的方法，其中使用两种不同的酶，例如在相同或不同的反应区域。

    Generation of modified polymerases for improved accuracy in single molecule sequencing
    8.
    发明授权
    Generation of modified polymerases for improved accuracy in single molecule sequencing 有权
    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。

    IMMOBILIZED NUCLEIC ACID COMPLEXES FOR SEQUENCE ANALYSIS
    9.
    发明申请
    IMMOBILIZED NUCLEIC ACID COMPLEXES FOR SEQUENCE ANALYSIS 有权
    用于序列分析的固定核酸复合物

    公开(公告)号：US20100075328A1

    公开(公告)日：2010-03-25

    申请号：US12562690

    申请日：2009-09-18

    申请人： KEITH BJORNSON ,  Arek Bibillo ,  Fred Christians ,  Kevin Travers ,  Robin Emig

    发明人： KEITH BJORNSON ,  Arek Bibillo ,  Fred Christians ,  Kevin Travers ,  Robin Emig

    IPC分类号： C12Q1/68

    CPC分类号： C12Q1/6874 ,  C12Q2531/125

    摘要： Provided are methods for sequencing a nucleic acid that include fixing a template to a surface through a template localizing moiety and sequencing the nucleic acid with a sequencing enzyme, e.g. a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid fixed to a surface via a template localizing moiety, and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Compositions for sequencing reactions are provided. Also provided are sequencing systems comprising reaction regions in which or near which template localizing moieties are immobilized.

    摘要翻译： 提供了用于对核酸进行测序的方法，其包括通过模板定位部分将模板固定到表面，并用测序酶（例如）测序核酸。 聚合酶或外切核酸酶。 测序酶可以任选地与第二个测序酶交换，其继续测序核酸。 模板定位部分可任选地与核酸退火和/或与测序酶缔合。 还提供了包含通过模板定位部分固定在表面上的核酸的组合物和可以使序列核酸并任选地与组合物中存在的第二测序酶交换的第一测序酶。 提供其中将模板定位部分固定在表面上的组合物。 提供了测序反应的组合物。 还提供了包含反应区的测序系统，其中固定有定位部分的模板定位部分。

    Generation of modified polymerases for improved accuracy in single molecule sequencing
    10.
    发明申请
    Generation of modified polymerases for improved accuracy in single molecule sequencing 有权
    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。