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    NUCLEIC ACID ADAPTORS AND USES THEREOF
    3.
    发明申请
    NUCLEIC ACID ADAPTORS AND USES THEREOF 有权
    核酸适配器及其用途

    公开(公告)号：US20130261027A1

    公开(公告)日：2013-10-03

    申请号：US13877203

    申请日：2011-09-29

    申请人： Bin Li ,  Zhoutao Chen ,  Tanya Biorac ,  Melvin Wei

    发明人： Bin Li ,  Zhoutao Chen ,  Tanya Biorac ,  Melvin Wei

    IPC分类号： C12N15/10

    CPC分类号： C12Q1/6876 ,  C12N9/1252 ,  C12N9/20 ,  C12N15/1093 ,  C12N15/64 ,  C12Q1/6806 ,  C12Q1/6832 ,  C12Y207/07007 ,  C12Y301/01003 ,  C12Q2521/131 ,  C12Q2525/191 ,  C12Q2527/107 ,  C12Q2537/163 ,  C12Q2563/179

    摘要： Provided herein are compositions, systems, methods, and kits for joining together the ends of one or more polynucleotides using at least one pair of blocking oligonucleotide adaptors. Blocking oligonucleotide adaptors can be used to reduce the formation of adaptor dimers or trimers (or higher-order concatemers) which can improve the yield of desirable polynucleotide-adaptor products in any recombinant nucleic acid workflow. Blocking oligonucleotide adaptors can comprise a double-stranded oligonucleotide adaptor (duplex) having an overhang cohesive portion that anneals with a blocking oligonucleotide which can be a separate single-stranded oligonucleotide. A blocking oligonucleotide, when annealed to an overhang portion, can prevent undesirable hybridization of the overhang portion to another nucleic acid, such as the overhang portion from another blocking oligonucleotide adaptor or a polynucleotide of interest.

    摘要翻译： 本文提供了使用至少一对封闭寡核苷酸衔接子将一个或多个多核苷酸的末端连接在一起的组合物，系统，方法和试剂盒。 阻断寡核苷酸衔接子可用于减少适配器二聚体或三聚体（或更高级并行物）的形成，其可以改善任何重组核酸工作流程中期望的多核苷酸 - 衔接子产物的产量。 阻断寡核苷酸衔接子可以包含具有悬伸粘性部分的双链寡核苷酸衔接子（双链体），其与可以是单独的单链寡核苷酸的封闭寡核苷酸退火。 当与突出部分退火时，封闭寡核苷酸可以防止突出部分与另一种核酸（例如来自另一种封闭寡核苷酸衔接子或感兴趣的多核苷酸的突出部分）的不期望的杂交。

    System and method for adaptive reagent control in nucleic acid sequencing
    4.
    发明申请
    System and method for adaptive reagent control in nucleic acid sequencing 审中-公开
    核酸测序中适应性试剂控制的系统和方法

    公开(公告)号：US20090053724A1

    公开(公告)日：2009-02-26

    申请号：US12215455

    申请日：2008-06-27

    申请人： George Thomas Roth ,  John Richard Nobile ,  Maithreyan Srinivasan ,  Zhoutao Chen ,  James Matthew Nealis ,  Xavier Victor Gomes

    发明人： George Thomas Roth ,  John Richard Nobile ,  Maithreyan Srinivasan ,  Zhoutao Chen ,  James Matthew Nealis ,  Xavier Victor Gomes

    IPC分类号： C12Q1/68 ,  C12Q1/00 ,  C12M1/36 ,  C12M1/34 ,  C12Q1/34

    CPC分类号： C12Q1/6869 ,  C12Q2565/301

    摘要： An embodiment of a method for adaptive reagent control is described that comprising a) introducing a first concentration of an enzyme reagent into a reaction environment with a reaction substrate, where the enzyme reagent and reaction substrate are constituent parts of a sequencing process; b) measuring a level of activity of the first concentration of the enzyme reagent in the reaction environment, where the level of activity comprises a measurable product of a reaction between the enzyme reagent and the reaction substrate; c) identifying an optimal concentration using the measured level of activity of the first concentration; and d) performing the sequencing process in the reaction environment using the optimal concentration of the enzyme reagent, where the sequencing process comprises an iterative series of sequencing reactions.

    摘要翻译： 描述了一种用于自适应试剂控制的方法的实施方案，其包括：a）将酶试剂的第一浓度与反应底物引入反应环境，其中酶试剂和反应底物是测序过程的组成部分; b）测量反应环境中酶试剂的第一浓度的活性水平，其中活性水平包括酶试剂和反应底物之间的反应的可测量的产物; c）使用所测量的第一浓度的活性水平鉴定最佳浓度; 和d）使用酶试剂的最佳浓度在反应环境中进行测序过程，其中测序过程包括迭代的一系列测序反应。

    Paired end sequencing
    5.
    发明申请
    Paired end sequencing 审中-公开
    配对测序

    公开(公告)号：US20090233291A1

    公开(公告)日：2009-09-17

    申请号：US12322119

    申请日：2009-01-28

    申请人： Zhoutao Chen ,  Brian Christopher Godwin ,  Gianni Calogero Ferreri ,  David Roderick Riches

    发明人： Zhoutao Chen ,  Brian Christopher Godwin ,  Gianni Calogero Ferreri ,  David Roderick Riches

    IPC分类号： C12Q1/68

    CPC分类号： C12Q1/6809 ,  C12Q1/6869 ,  C12Q2531/125 ,  C12Q2521/125 ,  C12Q2565/518 ,  C12Q2563/131 ,  C12Q2521/301 ,  C12Q2521/319 ,  C12Q2521/507 ,  C12Q2521/313 ,  C12Q2525/307 ,  C12Q2525/191 ,  C12Q2539/103 ,  C12Q2525/155

    摘要： An embodiment of a method for obtaining a DNA construct comprising two end regions of a target nucleic acid in an in vitro reaction is described that comprises the steps of: fragmenting a large nucleic acid molecule to produce a target nucleic acid molecule; ligating a recombination adaptor element to each end of the target nucleic acid molecule to produce an adapted target nucleic acid molecule; exposing the adapted target nucleic acid to a site specific recombinase to produce a circular nucleic acid product and a linear nucleic acid product from the adapted target nucleic acid, wherein the circular nucleic acid product comprises the target nucleic acid molecule; and fragmenting the circular nucleic acid product to produce a template nucleic acid molecule comprising a sequence region from each end of the target nucleic acid molecule.

    摘要翻译： 描述了在体外反应中获得包含靶核酸的两个末端区域的DNA构建体的方法的实施方案，其包括以下步骤：将大核酸分子片段化以产生靶核酸分子; 将重组衔接子元件连接到靶核酸分子的每个末端以产生适应的靶核酸分子; 将适配的靶核酸暴露于位点特异性重组酶以产生来自适应的靶核酸的环状核酸产物和线性核酸产物，其中所述环状核酸产物包含靶核酸分子; 并将环状核酸产物片段化以产生包含靶核酸分子每端的序列区的模板核酸分子。

    Nucleic acid adaptors and uses thereof
    7.
    发明授权
    Nucleic acid adaptors and uses thereof 有权
    核酸适配器及其用途

    公开(公告)号：US09540637B2

    公开(公告)日：2017-01-10

    申请号：US13877203

    申请日：2011-09-29

    申请人： Bin Li ,  Zhoutao Chen ,  Tanya Biorac ,  Melvin Shiwade Wei

    发明人： Bin Li ,  Zhoutao Chen ,  Tanya Biorac ,  Melvin Shiwade Wei

    IPC分类号： C12Q1/68 ,  C12P19/34 ,  C12N15/10

    CPC分类号： C12Q1/6876 ,  C12N9/1252 ,  C12N9/20 ,  C12N15/1093 ,  C12N15/64 ,  C12Q1/6806 ,  C12Q1/6832 ,  C12Y207/07007 ,  C12Y301/01003 ,  C12Q2521/131 ,  C12Q2525/191 ,  C12Q2527/107 ,  C12Q2537/163 ,  C12Q2563/179

    摘要： Provided herein are compositions, systems, methods, and kits for joining together the ends of one or more polynucleotides using at least one pair of blocking oligonucleotide adaptors. Blocking oligonucleotide adaptors can be used to reduce the formation of adaptor dimers or trimers (or higher-order concatemers) which can improve the yield of desirable polynucleotide-adaptor products in any recombinant nucleic acid workflow. Blocking oligonucleotide adaptors can comprise a double-stranded oligonucleotide adaptor (duplex) having an overhang cohesive portion that anneals with a blocking oligonucleotide which can be a separate single-stranded oligonucleotide. A blocking oligonucleotide, when annealed to an overhang portion, can prevent undesirable hybridization of the overhang portion to another nucleic acid, such as the overhang portion from another blocking oligonucleotide adaptor or a polynucleotide of interest.

    摘要翻译： 本文提供了使用至少一对封闭寡核苷酸衔接子将一个或多个多核苷酸的末端连接在一起的组合物，系统，方法和试剂盒。 阻断寡核苷酸衔接子可用于减少适配器二聚体或三聚体（或更高级并行物）的形成，其可以改善任何重组核酸工作流程中期望的多核苷酸 - 衔接子产物的产量。 阻断寡核苷酸衔接子可以包含具有悬伸粘性部分的双链寡核苷酸衔接子（双链体），其与可以是单独的单链寡核苷酸的封闭寡核苷酸退火。 当与突出部分退火时，封闭寡核苷酸可以防止突出部分与另一种核酸（例如来自另一种封闭寡核苷酸衔接子或感兴趣的多核苷酸的突出部分）的不期望的杂交。

    Bi-directional sequencing compositions and methods
    8.
    发明授权
    Bi-directional sequencing compositions and methods 有权
    双向测序组合物和方法

    公开(公告)号：US09139874B2

    公开(公告)日：2015-09-22

    申请号：US13543521

    申请日：2012-07-06

    申请人： Jason Myers ,  Zhoutao Chen ,  Devin Dressman ,  Theo Nikiforov

    发明人： Jason Myers ,  Zhoutao Chen ,  Devin Dressman ,  Theo Nikiforov

    IPC分类号： C12P19/34 ,  C12Q1/68

    CPC分类号： C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6869 ,  C12Q2521/307 ,  C12Q2521/325 ,  C12Q2525/125 ,  C12Q2535/119 ,  C12Q2565/518

    摘要： In some embodiments, methods for obtaining sequence information from a nucleic acid template linked to a support include hybridizing a first primer to a template strand linked to a support, sequencing a portion of the nucleic acid template, thereby forming an extended first primer product that is complementary to a portion of the nucleic acid template. In some embodiments, the method further includes introducing a nick into a portion of the template strand that is hybridized to the extended first primer product, degrading a portion of the template strand from the nick using a degrading agent, where a portion of the extended first primer remains hybridized to an undegraded portion of the template strand, and sequencing at least some of the single-stranded portion of the extended first primer by synthesis.

    摘要翻译： 在一些实施方案中，从与支持物连接的核酸模板获得序列信息的方法包括将第一引物与连接于载体的模板链杂交，对核酸模板的一部分进行测序，从而形成延伸的第一引物产物， 与核酸模板的一部分互补。 在一些实施方案中，所述方法还包括将切口引入与延伸的第一引物产物杂交的模板链的一部分中，使用降解剂将模板链的一部分从切口中降解，其中延伸的第一底物 引物保留与模板链的未降解部分杂交，并通过合成测序延伸的第一引物的至少一些单链部分。