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    DESIGN, SYNTHESIS AND ASSEMBLY OF SYNTHETIC NUCLEIC ACIDS
    2.
    发明申请
    DESIGN, SYNTHESIS AND ASSEMBLY OF SYNTHETIC NUCLEIC ACIDS 审中-公开
    合成核酸的设计，合成和组装

    公开(公告)号：US20130196864A1

    公开(公告)日：2013-08-01

    申请号：US13763529

    申请日：2013-02-08

    申请人： Sridhar Govindarajan ,  Jeremy S. Minshull ,  Jon E. Ness

    发明人： Sridhar Govindarajan ,  Jeremy S. Minshull ,  Jon E. Ness

    IPC分类号： C12N15/10

    CPC分类号： C12N15/1027 ,  C12N15/1089 ,  C12Q1/6806 ,  G16B25/00

    摘要： Methods of synthesizing oligonucleotides with high coupling efficiency (>99.5%) are provided. Methods for purification of synthetic oligonucleotides are also provided. Instrumentation configurations for oligonucleotide synthesis are also provided. Methods of designing and synthesizing polynucleotides are also provided. Polynucleotide design is optimized for subsequent assembly from shorter oligonucleotides. Modifications of phosphoramidite chemistry to improve the subsequent assembly of polynucleotides are provided. The design process also incorporates codon biases into polynucleotides that favor expression in defined hosts. Design and assembly methods are also provided for the efficient synthesis of sets of polynucleotide variants. Software to automate the design and assembly process is also provided.

    摘要翻译： 提供了具有高耦合效率的寡核苷酸（> 99.5％）的方法。 还提供了纯化合成寡核苷酸的方法。 也提供寡核苷酸合成的仪器配置。 还提供了设计和合成多核苷酸的方法。 多核苷酸设计被优化用于从较短的寡核苷酸的后续装配。 提供亚磷酰胺化学改性以改进随后的多核苷酸组装。 设计过程还将密码子偏差结合到有利于在定义的宿主中表达的多核苷酸。 还提供了设计和组装方法以有效合成多组DNA变体组。 还提供了自动化设计和组装过程的软件。

    Design, synthesis and assembly of synthetic nucleic acids
    3.
    发明申请
    Design, synthesis and assembly of synthetic nucleic acids 审中-公开
    合成核酸的设计，合成和装配

    公开(公告)号：US20090317873A1

    公开(公告)日：2009-12-24

    申请号：US11579568

    申请日：2005-05-04

    申请人： Sridhar Govindarajan ,  Nicolay V. Kulikov ,  Jeremy S. Minshull ,  Jon E. Ness

    发明人： Sridhar Govindarajan ,  Nicolay V. Kulikov ,  Jeremy S. Minshull ,  Jon E. Ness

    IPC分类号： C12P19/34 ,  C12M1/00

    CPC分类号： C07H21/00

    摘要： Methods of synthesizing oligonucleotides with high coupling efficiency (>99.5%) are provided. Methods for purification of synthetic oligonucleotides are also provided. Instrumentation configurations for oligonucleotide synthesis are also provided. Methods of designing and synthesizing polynucleotides are also provided. Polynucleotide design is optimized for subsequent assembly from shorter oligonucleotides. Modifications of phosphoramidite chemistry to improve the subsequent assembly of polynucleotides are provided. The design process also incorporates codon biases into polynucleotides that favor expression in defined hosts. Design and assembly methods are also provided for the efficient synthesis of sets of polynucleotide variants. Software to automate the design and assembly process is also provided.

    摘要翻译： 提供了具有高耦合效率的寡核苷酸（> 99.5％）的方法。 还提供了纯化合成寡核苷酸的方法。 也提供寡核苷酸合成的仪器配置。 还提供了设计和合成多核苷酸的方法。 多核苷酸设计被优化用于从较短的寡核苷酸的后续装配。 提供亚磷酰胺化学改性以改进随后的多核苷酸组装。 设计过程还将密码子偏差结合到有利于在定义的宿主中表达的多核苷酸。 还提供了设计和组装方法以有效合成多组DNA变体组。 还提供了自动化设计和组装过程的软件。

    Design, synthesis and assembly of synthetic nucleic acids
    4.
    发明授权
    Design, synthesis and assembly of synthetic nucleic acids 有权
    合成核酸的设计，合成和装配

    公开(公告)号：US08825411B2

    公开(公告)日：2014-09-02

    申请号：US11579704

    申请日：2005-05-04

    申请人： Sridhar Govindarajan ,  Jeremy S. Minshull ,  Jon E. Ness

    发明人： Sridhar Govindarajan ,  Jeremy S. Minshull ,  Jon E. Ness

    IPC分类号： G06F19/00 ,  G06G7/48 ,  C40B30/00 ,  C12N15/10 ,  C12Q1/68 ,  G06F19/20

    CPC分类号： C12N15/1027 ,  C12N15/1089 ,  C12Q1/6806 ,  G06F19/20

    摘要： Methods of synthesizing oligonucleotides with high coupling efficiency (>99.5%) are provided. Methods for purification of synthetic oligonucleotides are also provided. Instrumentation configurations for oligonucleotide synthesis are also provided. Methods of designing and synthesizing polynucleotides are also provided. Polynucleotide design is optimized for subsequent assembly from shorter oligonucleotides. Modifications of phosphoramidite chemistry to improve the subsequent assembly of polynucleotides are provided. The design process also incorporates codon biases into polynucleotides that favor expression in defined hosts. Design and assembly methods are also provided for the efficient synthesis of sets of polynucleotide variants. Software to automate the design and assembly process is also provided.

    摘要翻译： 提供了具有高耦合效率的寡核苷酸（> 99.5％）的方法。 还提供了纯化合成寡核苷酸的方法。 也提供寡核苷酸合成的仪器配置。 还提供了设计和合成多核苷酸的方法。 多核苷酸设计被优化用于从较短的寡核苷酸的后续装配。 提供亚磷酰胺化学改性以改进随后的多核苷酸组装。 设计过程还将密码子偏差结合到有利于在定义的宿主中表达的多核苷酸。 还提供了设计和组装方法以有效合成多组DNA变体组。 还提供了自动化设计和组装过程的软件。

    Design, Synthesis and Assembly of Synthetic Nucleic Acids
    5.
    发明申请
    Design, Synthesis and Assembly of Synthetic Nucleic Acids 有权
    合成核酸的设计，合成和装配

    公开(公告)号：US20080300842A1

    公开(公告)日：2008-12-04

    申请号：US11579704

    申请日：2005-05-04

    申请人： Sridhar Govindarajan ,  Jeremy S. Minshull ,  Jon E. Ness

    发明人： Sridhar Govindarajan ,  Jeremy S. Minshull ,  Jon E. Ness

    IPC分类号： G06G7/48

    CPC分类号： C12N15/1027 ,  C12N15/1089 ,  C12Q1/6806 ,  G06F19/20

    摘要： Methods of synthesizing oligonucleotides with high coupling efficiency (>99.5%) are provided. Methods for purification of synthetic oligonucleotides are also provided. Instrumentation configurations for oligonucleotide synthesis are also provided. Methods of designing and synthesizing polynucleotides are also provided. Polynucleotide design is optimized for subsequent assembly from shorter oligonucleotides. Modifications of phosphoramidite chemistry to improve the subsequent assembly of polynucleotides are provided. The design process also incorporates codon biases into polynucleotides that favor expression in defined hosts. Design and assembly methods are also provided for the efficient synthesis of sets of polynucleotide variants. Software to automate the design and assembly process is also provided.

    摘要翻译： 提供了具有高耦合效率的寡核苷酸（> 99.5％）的方法。 还提供了纯化合成寡核苷酸的方法。 也提供寡核苷酸合成的仪器配置。 还提供了设计和合成多核苷酸的方法。 多核苷酸设计被优化用于从较短的寡核苷酸的后续装配。 提供亚磷酰胺化学改性以改进随后的多核苷酸组装。 设计过程还将密码子偏差结合到有利于在定义的宿主中表达的多核苷酸。 还提供了设计和组装方法以有效合成多组DNA变体组。 还提供了自动化设计和组装过程的软件。

    Systems and methods for designing and ordering polynucleotides
    6.
    发明授权
    Systems and methods for designing and ordering polynucleotides 有权
    用于设计和排序多核苷酸的系统和方法

    公开(公告)号：US07805252B2

    公开(公告)日：2010-09-28

    申请号：US11207151

    申请日：2005-08-16

    申请人： Claes Gustafsson ,  Sridhar Govindarajan ,  Jon E. Ness ,  Alan Marco Villalobos ,  Jeremy Minshull

    发明人： Claes Gustafsson ,  Sridhar Govindarajan ,  Jon E. Ness ,  Alan Marco Villalobos ,  Jeremy Minshull

    IPC分类号： G06F7/00

    CPC分类号： G06F19/26 ,  G06F19/18 ,  G06F19/20

    摘要： Computer systems, computer program products and methods for designing oligonucleotides are provided. A set of sequence elements is defined. Each sequence element represents an amino acid sequence segment or a nucleic acid sequence segment. The set of sequence elements collectively represent a design nucleic acid sequence. The set of sequence elements are displayed as a plurality icons in a linear or a near linear arrangement such that each respective icon in the plurality of icons uniquely represents a corresponding sequence element in the set of sequence elements. In this representation, neighboring icons in the plurality of icons represent neighboring sequence elements in the set of sequence elements. Each respective icon in the plurality of icons depicts a directional property for the corresponding sequence element in the set of sequence elements. An oligonucleotide selection module is used to identify oligonucleotides in the design nucleic acid sequence.

    摘要翻译： 提供计算机系统，计算机程序产品和设计寡核苷酸的方法。 定义了一组序列元素。 每个序列元件代表氨基酸序列片段或核酸序列片段。 序列元件的集合统称为设计核酸序列。 序列元素的集合被显示为线性或近似线性布置的多个图标，使得多个图标中的每个相应图标唯一地表示序列元素集合中的相应序列元素。 在该表示中，多个图标中的相邻图标表示该组序列元素中的相邻序列元素。 多个图标中的每个相应的图标描绘了序列元素集合中相应的序列元素的方向属性。 寡核苷酸选择模块用于鉴定设计核酸序列中的寡核苷酸。

    Methods, compositions and kits for one-step DNA cloning using DNA topoisomerase
    8.
    发明授权
    Methods, compositions and kits for one-step DNA cloning using DNA topoisomerase 有权
    使用DNA拓扑异构酶进行一步DNA克隆的方法，组合物和试剂盒

    公开(公告)号：US08323930B2

    公开(公告)日：2012-12-04

    申请号：US12178506

    申请日：2008-07-23

    申请人： Jon E. Ness ,  Jeremy S. Minshull

    发明人： Jon E. Ness ,  Jeremy S. Minshull

    IPC分类号： C12P19/34 ,  C12Q1/68

    CPC分类号： C12N15/66 ,  C12N9/90 ,  C12N15/10 ,  C12N15/64

    摘要： Provided are methods, compositions, and kits for molecular cloning of DNA using DNA topoisomerase. The methods comprise (I) combining into a mixture (A) a first polynucleotide, comprising an origin of replication, a selectable marker, two topoisomerase recognition sequences, and two nicking agent recognition sequences, each of the topoisomerase recognition sequences being within 50 nucleotides of at least one of the nicking agent recognition sequences and each of two nicking agent recognition sequences being nicked, with (B) a sequence-specific topoisomerase and (C) a second polynucleotide, having a 5′ hydroxyl on each end; and (II) transforming the mixture into a host organism, thereby cloning the second polynucleotide. Formation or purification of a DNA-protein adduct prior to the addition of the second polynucleotide is not required. Also provided are vector sequences to facilitate performance of the methods and methods for modifying a vector of interest to render it useful in the disclosed methods.

    摘要翻译： 提供了使用DNA拓扑异构酶分子克隆DNA的方法，组合物和试剂盒。 方法包括（I）将混合物（A）组合成包含复制起点的第一多核苷酸，选择性标记，两个拓扑异构酶识别序列和两个切口识别序列，每个拓扑异构酶识别序列在50个核苷酸内 具有（B）序列特异性拓扑异构酶的切割剂识别序列和两个切口剂识别序列中的至少一个，（C）第二多核苷酸，每个末端具有5'羟基; 和（II）将混合物转化为宿主生物体，从而克隆第二多核苷酸。 不需要在加入第二个多核苷酸之前形成或纯化DNA-蛋白质加合物。 还提供了用于促进用于修饰感兴趣的载体以使其在所公开的方法中有用的方法和方法的性能的载体序列。