公开(公告)号：WO2009017673A3

公开(公告)日：2009-02-05

申请号：PCT/US2008/009054

申请日：2008-07-25

Applicant: DNA TWOPOINTO INC. ,  NESS, Jon, E. ,  MINSHULL, Jeremy, S.

Inventor： NESS, Jon, E. ,  MINSHULL, Jeremy, S.

IPC: C40B50/06 ,  C12N15/00

Abstract: Provided herein are methods, compositions, kits, and vectors useful for molecular cloning of, for example, blunt-ended DNA molec using DNA topoisomerase. In certain embodiments, the methods comprise combining into a mixture a first polynucleotide, wherein first polynucleotide comprises an origin of replication, a selectable marker, two topoisomerase recognition sequences, and two nick agent recognition sequences, wherein each of said two topoisomerase recognition sequences is within 0-50 nucleotides of at least of the nicking agent recognition sequences and wherein each of said two nicking agent recognition sequences is nicked, with a sequence-specific topoisomerase and a second polynucleotide, wherein said second polynucleotide comprises a 5' hydroxyl on ea end of the polynucleotide; and transforming the mixture into a host organism, thereby cloning the second polynucleotide.

公开(公告)号：WO2008127213A3

公开(公告)日：2008-12-11

申请号：PCT/US0214866

申请日：2002-05-09

Applicant: MAXYGEN INC ,  MINSHULL JEREMY ,  GUSTAFSSON CLAES ,  GOVINDARAJAN SRIDAR ,  ROY AJOY

Inventor： MINSHULL JEREMY ,  GUSTAFSSON CLAES ,  GOVINDARAJAN SRIDAR ,  ROY AJOY

IPC: C12Q1/68

CPC classification number: G06F19/22 ,  B01J2219/007 ,  B01J2219/00722 ,  C12N15/1089 ,  C12Q1/6806 ,  C12Q2531/113

Abstract: The present invention provides novel in silico recombination techniques in which all or part of a nucleic acid recombination procedure is performed or modeled in a digital system. In particular, this invention relates to methods of designing oligonucleotides for regulated recombination that approximates linkage characteristics obtained from fragmentation-based recombination techniques, such as family-based recombination. The methods of this invention include adjusting overlap regions in pairs of overlapping oligonucleotide character strings to bias recombination towards a desired genetic linkage. This invention also provides systems, computer program products, and kits for practicing the methods of the invention.

Abstract translation: 本发明提供了新的计算机重组技术，其中在数字系统中执行或建模全部或部分核酸重组程序。 特别地，本发明涉及设计用于调节重组的寡核苷酸的方法，其近似由基于片段的重组技术获得的连锁特征，例如基于家族的重组。 本发明的方法包括调整重叠的寡核苷酸字符串对中的重叠区域以将重组偏向期望的遗传连锁。 本发明还提供了用于实施本发明的方法的系统，计算机程序产品和套件。

公开(公告)号：WO2007022260A3

公开(公告)日：2008-08-28

申请号：PCT/US2006031976

申请日：2006-08-15

Applicant: DNA 2 0 INC ,  GUSTAFSSON CLAES ,  GOVINDARAJAN SRIDHAR ,  NESS JON E ,  VILLALOBOS ALAN MARCO ,  MINSHULL JEREMY

Inventor： GUSTAFSSON CLAES ,  GOVINDARAJAN SRIDHAR ,  NESS JON E ,  VILLALOBOS ALAN MARCO ,  MINSHULL JEREMY

IPC: G06F7/00

CPC classification number: G06F19/26 ,  G06F19/18 ,  G06F19/20

Abstract: 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 of 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.

Abstract translation: 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图标描绘了该组序列元素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。

公开(公告)号：WO2005013090A3

公开(公告)日：2006-04-13

申请号：PCT/US2004024752

申请日：2004-07-30

Applicant: DNA TWOPOINTO INC ,  GUSTAFSSON CLAES ,  GOVINDARAJAN SRIDHAR ,  MINSHULL JEREMY STEPHEN

Inventor： GUSTAFSSON CLAES ,  GOVINDARAJAN SRIDHAR ,  MINSHULL JEREMY STEPHEN

IPC: C07K16/10 ,  C07K16/46 ,  G01N20060101 ,  G06F20060101 ,  G06F19/16 ,  G06F19/18 ,  G06F19/24 ,  G01N33/00 ,  G01N33/48

CPC classification number: G06F19/18 ,  C07K16/1027 ,  C07K16/461 ,  C07K2317/76 ,  G06F19/16 ,  G06F19/24

Abstract: Methods, computer systems, and computer program products for biopolymer engineering. A variant set for a biopolymer of interest is constructed by identifying, using a plurality of rules, a plurality of positions in the biopolymer of interest and, for each respective position in the plurality of positions, substitutions for the respective position. The plurality of positions and the substitutions for each respective position in the plurality of positions collectively define a biopolymer sequence space. A variant set comprising a plurality of variants of the biopolymer of interest is selected. A property of all or a portion of the variants in the variant set is measured. A sequence-activity relationship is modeled between (i) one or more substitutions at one or more positions of the biopolymer of interest represented by the variant set and (ii) the property measured for all or the portion of the variants in the variant set. The variant set is redefined to comprise variants that include substitutions in the plurality of positions that are selected based on a function of the sequence-activity relationship.

Abstract translation: 方法，计算机系统和生物聚合物工程的计算机程序产品。 通过使用多个规则来识别感兴趣的生物聚合物中的多个位置，并且对于多个位置中的每个相应位置，通过识别相应位置的替换来构建用于感兴趣的生物聚合物的变体。 多个位置中的各个位置的多个位置和替换共同限定生物聚合物序列空间。 选择包含感兴趣的生物聚合物的多个变体的变体组。 测量变体集中全部或部分变体的属性。 序列活性关系在（i）由变体组表示的感兴趣的生物聚合物的一个或多个位置处的一个或多个取代和（ii）针对变体集中的全部或部分变体测量的性质之间建模。 变体集被重新定义为包括在基于序列活动关系的函数选择的多个位置中的替换的变体。

公开(公告)号：WO2003068955A3

公开(公告)日：2003-08-21

申请号：PCT/IB2003/000348

申请日：2003-01-31

Applicant: PFIZER PRODUCTS INC. ,  STUTZMAN-ENGWALL, Kim, Jonelle ,  GUSTAFSSON, Claes, Eric, Daniel ,  KREBBER, Anke ,  RAILLARD, Sun, Ai ,  MINSHULL, Jeremy, Stephen ,  KIM, Seran ,  CHEN, Yan

Inventor： STUTZMAN-ENGWALL, Kim, Jonelle ,  GUSTAFSSON, Claes, Eric, Daniel ,  KREBBER, Anke ,  RAILLARD, Sun, Ai ,  MINSHULL, Jeremy, Stephen ,  KIM, Seran ,  CHEN, Yan

IPC: C12N1/21

Abstract: The present invention relates to polynucleotide comprising nucleotide sequences encoding an aveC gene product, which polynucleotide molecules can be used to alter the ratio or amount of class 2:1 avermectins produced in fermentation cultures of S. avermitis. The present invention further relates to vectors, host cells, and mutant strains of S. avermitis in which the aveC gene has been inactivated, or mutated so as to change the ratio or amount of class 2:1 avermectins produced.

公开(公告)号：WO0210750A2

公开(公告)日：2002-02-07

申请号：PCT/US0124182

申请日：2001-07-31

Applicant: MAXYGEN INC ,  MINSHULL JEREMY ,  DAVIS S CHRISTOPHER ,  WELCH MARK ,  RAILLARD SUN AI ,  VOGEL KURT ,  KREBBER CLAUS

Inventor： MINSHULL JEREMY ,  DAVIS S CHRISTOPHER ,  WELCH MARK ,  RAILLARD SUN AI ,  VOGEL KURT ,  KREBBER CLAUS

IPC: C12N9/12 ,  C12N15/10 ,  C12P19/34 ,  C12Q1/68 ,  G01N33/50

CPC classification number: C12N9/1252 ,  C12N15/1055 ,  C12P19/34 ,  C12Q1/6888

Abstract: Methods for sensing test stimuli using arrays of biopolymers are provided. Libraries of biopolymers, such nucleic acid variants, and expression products encoded by nucleic acid variants are provided. Reusable library arrays, and methods for their use are provided.

Abstract translation: 提供使用生物聚合物阵列感测测试刺激的方法。 提供了生物聚合物，核酸变体和由核酸变体编码的表达产物的文库。 提供了可重用库数组及其使用方法。

公开(公告)号：WO0004190A9

公开(公告)日：2000-08-10

申请号：PCT/US9915972

申请日：1999-07-15

Applicant: MAXYGEN INC ,  DEL CARDAYRE STEPHEN ,  TOBIN MATTHEW ,  STEMMER WILLEM P C ,  NESS JON E ,  MINSHULL JEREMY ,  PATTEN PHILLIP A ,  SUBRAMANIAN VENKITESWATAN ,  CASTLE LINDA A ,  KREBBER CLAUS M ,  BASS STEVE ,  ZHANG YING XIN ,  COX TONY ,  HUISMAN GJALT ,  YUAN LING ,  AFFHOLTER JOSEPH A

Inventor： DEL CARDAYRE STEPHEN ,  TOBIN MATTHEW ,  STEMMER WILLEM P C ,  NESS JON E ,  MINSHULL JEREMY ,  PATTEN PHILLIP A ,  SUBRAMANIAN VENKITESWATAN ,  CASTLE LINDA A ,  KREBBER CLAUS M ,  BASS STEVE ,  ZHANG YING-XIN ,  COX TONY ,  HUISMAN GJALT ,  YUAN LING ,  AFFHOLTER JOSEPH A

IPC: A01H5/00 ,  A01K67/027 ,  C07K14/245 ,  C12N15/09 ,  C12N15/10 ,  C12N15/82 ,  C12P17/16 ,  C12Q1/68 ,  C12N15/00

CPC classification number: C12N15/102 ,  C07K14/245 ,  C12N15/1027 ,  C12N15/8271 ,  C12N15/8273 ,  C12N15/8279 ,  C12P17/162 ,  C12Q1/68 ,  C12Q1/6811 ,  C12Q1/6827 ,  C12R1/465

Abstract: The invention provides methods employing iterative cycles of recombination and selection/screening for evolution of whole cells and organisms toward acquisition of desired properties. Examples of such properties include enhanced recombinogenicity, genome copy number, and capacity for expression and/or secretion of proteins and secondary metabolites.

Abstract translation: 本发明提供了采用迭代循环重组和选择/筛选全细胞和生物体以获得所需性质的方法的方法。 这些性质的实例包括增加的重组原性，基因组拷贝数以及蛋白质和次级代谢物的表达和/或分泌能力。

公开(公告)号：WO2010047733A3

公开(公告)日：2010-09-16

申请号：PCT/US2009003172

申请日：2009-05-22

Applicant: DNA 2 0 INC ,  KHOSLA CHAITAN ,  EHREN JENNIFER ,  MINSHULL JEREMY ,  GOVINDARAJAN SRIDHAR

Inventor： KHOSLA CHAITAN ,  EHREN JENNIFER ,  MINSHULL JEREMY ,  GOVINDARAJAN SRIDHAR

IPC: C12N9/48

CPC classification number: C12N9/52

Abstract: Provided are prolyl endopeptidases that have been produced by alteration of the amino acid sequence of a naturally occurring prolyl endopeptidase, thereby enhancing the proteolysis by said prolyl endopeptidase of one or more peptides produced by the digestion of gluten. Further provided are prolyl endopeptidase in which enhanced proteolysis results from the improved activity of the modified prolyl endopeptidase under conditions inside the human alimentary canal, or from increased resistance of the modified prolyl endopeptidase to digestion by one or more digestive enzymes in the human alimentary canal.

Abstract translation: 提供的是通过改变天然存在的脯氨酰内肽酶的氨基酸序列而产生的脯氨酰内肽酶，从而增强所述脯氨酰内肽酶对通过消化谷蛋白产生的一种或多种肽的蛋白水解。 进一步提供的是脯氨酰内肽酶，其中增强的蛋白水解来自改良的脯氨酰内肽酶在人消化道内的条件下的活性改善，或由于修饰的脯氨酰内肽酶对人消化道中的一种或多种消化酶消化而增加的抗性。

公开(公告)号：WO2010047733A2

公开(公告)日：2010-04-29

申请号：PCT/US2009/003172

申请日：2009-05-22

Applicant: DNA 2.0 INC. ,  KHOSLA, Chaitan ,  EHREN, Jennifer ,  MINSHULL, Jeremy ,  GOVINDARAJAN, Sridhar

Inventor： KHOSLA, Chaitan ,  EHREN, Jennifer ,  MINSHULL, Jeremy ,  GOVINDARAJAN, Sridhar

IPC: C12N9/50

CPC classification number: C12N9/52

Abstract: Provided are prolyl endopeptidases that have been produced by alteration of the amino acid sequence of a naturally occurring prolyl endopeptidase, thereby enhancing the proteolysis by said prolyl endopeptidase of one or more peptides produced by the digestion of gluten. Further provided are prolyl endopeptidase in which enhanced proteolysis results from the improved activity of the modified prolyl endopeptidase under conditions inside the human alimentary canal, or from increased resistance of the modified prolyl endopeptidase to digestion by one or more digestive enzymes in the human alimentary canal.

Abstract translation: 提供了通过改变天然存在的脯氨酰内肽酶的氨基酸序列而产生的脯氨酰内肽酶，从而增强所述脯氨酰内肽酶通过消化麸质产生的一种或多种肽的蛋白水解。 进一步提供了脯氨酰内肽酶，其中增强的蛋白水解是由于在人类消化道内部条件下修饰的脯氨酰内肽酶的活性改善或者由修饰的脯氨酰内肽酶对人类消化道中的一种或多种消化酶消化的抗性增加造成的。

公开(公告)号：WO2008127213A2

公开(公告)日：2008-10-23

申请号：PCT/US2002/014866

申请日：2002-05-09

Applicant: MAXYGEN, INC. ,  MINSHULL, Jeremy ,  GUSTAFSSON, Claes ,  GOVINDARAJAN, Sridar ,  ROY, Ajoy

Inventor： MINSHULL, Jeremy ,  GUSTAFSSON, Claes ,  GOVINDARAJAN, Sridar ,  ROY, Ajoy

IPC: C12Q1/68

CPC classification number: G06F19/22 ,  B01J2219/007 ,  B01J2219/00722 ,  C12N15/1089 ,  C12Q1/6806 ,  C12Q2531/113

Abstract: The present invention provides novel in silico recombination techniques in which all or part of a nucleic acid recombination procedure is performed or modeled in a digital system. In particular, this invention relates to methods of designing oligonucleotides for regulated recombination that approximates linkage characteristics obtained from fragmentation-based recombination techniques, such as family-based recombination. The methods of this invention include adjusting overlap regions in pairs of overlapping oligonucleotide character strings to bias recombination towards a desired genetic linkage. This invention also provides systems, computer program products, and kits for practicing the methods of the invention.

Abstract translation: 本发明提供新颖的计算机重组技术，其中全部或部分核酸重组程序在数字系统中进行或模拟。 具体而言，本发明涉及设计用于调控重组的寡核苷酸的方法，其接近从基于片段化的重组技术获得的连锁特征，例如基于家族的重组。 本发明的方法包括调整重叠的寡核苷酸字符串对中的重叠区域以偏向重要的遗传连锁。 本发明还提供用于实施本发明方法的系统，计算机程序产品和试剂盒。