公开(公告)号：WO2009149218A2

公开(公告)日：2009-12-10

申请号：PCT/US2009/046185

申请日：2009-06-03

Applicant: CODON DEVICES, INC. ,  BAYNES, Brian ,  LIPOVSEK, Dasa ,  LIPPOW, Shaun

Inventor： BAYNES, Brian ,  LIPOVSEK, Dasa ,  LIPPOW, Shaun

IPC: C12N15/10 ,  G06F19/00

CPC classification number: C12N15/1093 ,  C40B30/02 ,  G06F19/16 ,  G06F19/18

Abstract: Aspects of the invention relate to variant proteins and methods for designing and using the same. In some embodiments, the invention relates to methods for determining a functional variant of a protein that is restricted by one or more known legal rights, such as patent rights. Functional variants according to this invention are free of such restrictions.

Abstract translation: 本发明的方面涉及变体蛋白及其设计和使用的方法。 在一些实施方案中，本发明涉及用于确定由一种或多种已知合法权利（例如专利权）限制的蛋白质的功能性变体的方法。 根据本发明的功能变体没有这样的限制。

公开(公告)号：WO2007123742A3

公开(公告)日：2008-02-28

申请号：PCT/US2007007988

申请日：2007-03-30

Applicant: CODON DEVICES INC ,  BAYNES BRIAN M ,  NESMITH KENNETH G ,  MARSISCHKY GERALD THOMAS ,  CAMACHO JENNIFER A

Inventor： BAYNES BRIAN M ,  NESMITH KENNETH G ,  MARSISCHKY GERALD THOMAS ,  CAMACHO JENNIFER A

IPC: C12Q1/68

CPC classification number: C12N15/64 ,  C12N15/10 ,  C12N15/66 ,  C12Q1/686 ,  C12Q2521/507

Abstract: Certain aspects of the present invention provide methods for increasing the fidelity of nucleic acid assembly reactions. Fidelity-optimized conditions may be used in certain embodiments. Nucleic acid binding proteins and/or recombinases (e.g., heat stable variants) may be used in some embodiments. A RecA protein (e.g., a heat stable RecA) may be included in some assembly reactions. Aspects of the invention also provide related kits, compositions, devices, and systems to increase the fidelity of multiplex nucleic acid assembly reaction.

Abstract translation: 本发明的某些方面提供了增加核酸装配反应的保真度的方法。 在某些实施例中可以使用保真度优化的条件。 在一些实施方案中可以使用核酸结合蛋白和/或重组酶（例如热稳定变体）。 RecA蛋白（例如，热稳定的RecA）可以包括在一些装配反应中。 本发明的方面还提供了相关的试剂盒，组合物，装置和系统，以增加多重核酸装配反应的保真度。

公开(公告)号：WO2007136736A2

公开(公告)日：2007-11-29

申请号：PCT/US2007/011886

申请日：2007-05-18

Applicant: CODON DEVICES, INC. ,  CHURCH, George ,  CERRINA, Francisco ,  BAYNES, Brian, M. ,  PITCHER, Edmund, R.

Inventor： CHURCH, George ,  CERRINA, Francisco ,  BAYNES, Brian, M. ,  PITCHER, Edmund, R.

IPC: C12Q1/68

CPC classification number: C12Q1/6874 ,  C12Q2537/143 ,  C12Q2531/113

Abstract: Methods of sorting oligonucleotide sequences are provided. The methods include determining the sequences of oligonucleotides and selectively isolating one or more that are determined to have the desired sequence. Methods of nucleic acid preparation are also disclosed.

Abstract translation: 提供了分选寡核苷酸序列的方法。 所述方法包括确定寡核苷酸的序列并选择性分离被确定为具有所需序列的一个或多个。 还公开了核酸制备方法。

公开(公告)号：WO2007087347A2

公开(公告)日：2007-08-02

申请号：PCT/US2007/001888

申请日：2007-01-24

Applicant: CODON DEVICES, INC. ,  JACOBSON, Joseph, M. ,  ENDY, Drew ,  PITCHER, Edmund, R.

Inventor： JACOBSON, Joseph, M. ,  ENDY, Drew ,  PITCHER, Edmund, R.

CPC classification number: G06Q50/22 ,  G06F19/18 ,  G06F19/28

Abstract: A system and method for aiding in the design of molecular constructs is provided. A feature set associated with a molecular building block in a construct may be determined, wherein the feature set may comprise data indicative of third party rights that restrict use of the molecular segment or the lack of such rights. The method may include steps of defining a molecular structure for use in the construct; searching a database including a plurality of molecular structures and a plurality of rights, each right of the plurality of rights associated with each of the plurality of molecular structures; and displaying rights associated with the defined molecular structures in response to the search of said database. The system may include a library aggregating a plurality of intellectual property rights relating to fabricating biological constructs; a licensing module licensing the intellectual property rights required to make the specific construct for a fee; an accounts receivable module receiving the fee from a potential maker of the specific construct; and an accounts payable module distributing remuneration to the holders of the intellectual property rights required to make the specific construct.

Abstract translation: 提供了用于帮助设计分子构建体的系统和方法。 可以确定与构建体中的分子构建块相关联的特征集，其中该特征集可以包括指示限制分子段的使用或缺乏这种权利的第三方权利的数据。 该方法可以包括定义用于构建体中的分子结构的步骤; 搜索包括多个分子结构和多个权利的数据库，与所述多个分子结构中的每一个相关的所述多个权利中的每一个权利; 以及响应于对所述数据库的搜索而显示与所定义的分子结构相关联的权利。 该系统可以包括集合涉及制造生物构建体的多个知识产权的库; 一个授权模块，授权收取特定结构所需的知识产权; 应收账款模块，从特定建筑的潜在制造商处收取费用; 以及向制作特定结构所需的知识产权持有人分配报酬的应付账款模块。

公开(公告)号：WO2008127283A2

公开(公告)日：2008-10-23

申请号：PCT/US2007021473

申请日：2007-10-06

Applicant: CODON DEVICES INC ,  JACOBSON JOSEPH M ,  CHURCH GEORGE ,  BAYNES BRIAN M

Inventor： JACOBSON JOSEPH M ,  CHURCH GEORGE ,  BAYNES BRIAN M

CPC classification number: C12N15/10 ,  C12N15/1093 ,  C12N15/52

Abstract: Certain aspects of the present invention provide methods for designing and engineering metabolic pathways. Aspects of the invention also provide metabolic pathway components and cells containing engineered metabolic pathways. Certain aspects of the invention provide medical, pharmaceutical, industrial, agricultural, environmental, and other Nuses for engineered metabolic pathways of the invention.

Abstract translation: 本发明的某些方面提供了用于设计和工程化代谢途径的方法。 本发明的方面还提供含有工程化代谢途径的代谢途径成分和细胞。 本发明的某些方面为本发明的工程代谢途径提供医学，制药，工业，农业，环境和其它用途。

公开(公告)号：WO2008024319A3

公开(公告)日：2008-04-10

申请号：PCT/US2007018437

申请日：2007-08-20

Applicant: CODON DEVICES INC ,  MUIR CRAIG DOUGLAS ,  EMIG CHRISTOPHER J

Inventor： MUIR CRAIG DOUGLAS ,  EMIG CHRISTOPHER J

IPC: B01J19/00 ,  B01L3/00 ,  C12Q1/68

CPC classification number: B01L3/5027 ,  B01J19/0046 ,  B01J2219/00286 ,  B01J2219/00317 ,  B01J2219/00423 ,  B01J2219/00585 ,  B01J2219/0059 ,  B01J2219/00722 ,  B01J2219/00912 ,  B01L3/502753 ,  B01L7/52 ,  B01L2200/10 ,  B01L2300/0816 ,  B01L2300/0838 ,  B01L2400/0421 ,  B01L2400/0487

Abstract: Certain aspects of the present invention provide devices and methods for assembling nucleic acid molecules on micro fluidic devices, e.g. via extension and/or ligation reactions. The invention also provides systems comprising one or more acoustic liquid handlers, one or more microfluidic devices, and/or one or more robotic liquid handlers for automating a nucleic acid assembly- procedure. The microdevice may comprise the following components: a sipper, or means for transferring reagents (310); a main channel (315); a splitter, or means for transferring reagents (320), sample wells for storage of reagents or buffers (330, 335, 340), separation or concentration channels (350, 355) and sample or reaction wells (360, 365) e.g. a thermocycler.

Abstract translation: 本发明的某些方面提供了用于在微流体装置上装配核酸分子的装置和方法，例如， 通过延伸和/或连接反应。 本发明还提供包括一个或多个声学液体处理器，一个或多个微流体装置和/或用于使核酸组装过程自动化的一个或多个机器人液体处理器的系统。 微型装置可以包括以下部件：吸嘴或用于转移试剂的装置（310）; 主渠道（315）; 分离器或用于转移试剂（320）的装置，用于储存试剂或缓冲液（330,335,340），分离或浓缩通道（350,355）和样品或反应孔（360,365）的样品孔。 一个热循环仪

公开(公告)号：WO2007120624A3

公开(公告)日：2008-04-03

申请号：PCT/US2007008785

申请日：2007-04-10

Applicant: CODON DEVICES INC ,  STRACK-LOGUE BETTINA ,  BLAKE WILLIAM J ,  BAYNES BRIAN M

Inventor： STRACK-LOGUE BETTINA ,  BLAKE WILLIAM J ,  BAYNES BRIAN M

IPC: C12N15/66

CPC classification number: C12N15/66 ,  C12N15/10 ,  C12N15/64

Abstract: Certain aspects of the present invention provide methods for increasing the efficiency of nucleic acid assembly reactions by using concerted assembly to covalently connect a plurality of nucleic acid fragments in a single procedure. Aspects of the invention also provide kits, compositions, devices, and systems for designing and assembling nucleic acid products using concerted assembly procedures.

Abstract translation: 本发明的某些方面提供了通过使用协同组合以单一程序共价连接多个核酸片段来提高核酸装配反应效率的方法。 本发明的方面还提供了使用协调的组装方法设计和组装核酸产品的试剂盒，组合物，装置和系统。

公开(公告)号：WO2008027558A2

公开(公告)日：2008-03-06

申请号：PCT/US2007/019209

申请日：2007-08-31

Applicant: CODON DEVICES, INC. ,  BLAKE, William, J.

Inventor： BLAKE, William, J.

IPC: C12N15/09

CPC classification number: C12N15/66 ,  C12N15/10 ,  C12N15/64

Abstract: Certain aspects of the present invention provide methods for assembling nucleic acid molecules using iterative activation of one or more vector-encoded traits to progressively assemble a longer nucleic acid insert. Aspects of the invention also provide kits, compositions, devices, and systems for assembling synthetic nucleic acids using iterative activation of one or more vector-encoded traits.

Abstract translation: 本发明的某些方面提供了使用一种或多种载体编码性状的迭代激活来组装核酸分子以逐步组装更长的核酸插入物的方法。 本发明的各方面还提供了用于使用一种或多种载体编码性状的迭代激活来组装合成核酸的试剂盒，组合物，装置和系统。

公开(公告)号：WO2007136834A2

公开(公告)日：2007-11-29

申请号：PCT/US2007/012076

申请日：2007-05-19

Applicant: CODON DEVICES, INC. ,  BAYNES, Brian, M. ,  CHAPMAN, Brad ,  KAMENTSKY, Lee

Inventor： BAYNES, Brian, M. ,  CHAPMAN, Brad ,  KAMENTSKY, Lee

IPC: C12Q1/68

CPC classification number: C12N15/115 ,  C12N15/10 ,  C12N15/66 ,  C12Q1/6862 ,  C12Q2537/143 ,  C12Q2521/101

Abstract: Certain aspects of the present invention provide methods for assembling nucleic acid molecules. Some embodiments involve analyzing nucleic acid sequences and determining appropriate assembly strategies based on the presence or absence of sequence features that are known or predicted to interfere with extension-based and/or ligation-based assembly techniques. Aspects of the invention also provide kits, compositions, devices, and systems for assembling synthetic nucleic acids using polymerase-based techniques, ligase-based techniques, or combinations thereof.

Abstract translation: 本发明的某些方面提供了组装核酸分子的方法。 一些实施方案涉及分析核酸序列并基于已知或预测会干扰基于扩展和/或基于连接的组装技术的序列特征的存在或不存在来确定适当的组装策略。 本发明的各方面还提供了使用基于聚合酶的技术，基于连接酶的技术或其组合来组装合成核酸的试剂盒，组合物，装置和系统。

公开(公告)号：WO2007136833A2

公开(公告)日：2007-11-29

申请号：PCT/US2007012075

申请日：2007-05-19

Applicant: CODON DEVICES INC ,  CHURCH GEORGE ,  JACOBSON JOSEPH M ,  BAYNES BRIAN M

Inventor： CHURCH GEORGE ,  JACOBSON JOSEPH M ,  BAYNES BRIAN M

IPC: C12Q1/68 ,  C12N15/11 ,  C12N15/115

CPC classification number: C12N15/115 ,  C12N15/1048 ,  C12N15/111 ,  C12N2310/16 ,  C12N2320/10 ,  C12N2330/31

Abstract: Certain aspects of the present invention provide methods for assembling nucleic acid libraries that represent large numbers of sequence variants. Some embodiments involve generating libraries of RNA molecules that can be subjected to in vivo screens or selections to identify one or more aptamers. Certain aspects of the invention provide cells that transcribe one or more different aptamers (e.g., 10) that each bind to a different ligand and are each fused to a different reporter RNA.

Abstract translation: 本发明的某些方面提供组装代表大量序列变体的核酸文库的方法。 一些实施方案涉及产生可以经受体内筛选或选择以鉴定一种或多种适体的RNA分子的文库。 本发明的某些方面提供转录一种或多种不同适配体（例如，10）的细胞，其各自结合不同的配体并且各自与不同的报道RNA融合。