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1. 发明申请

WO2011008232A3 BIOSYNTHETIC ROUTES TO LONG-CHAIN a, w-HYDROXY ACIDS, DIACIDS AND THEIR CONVERSION TO OLIGOMERS AND POLYMERS 审中-公开
公开(公告)号：WO2011008232A3
公开(公告)日：2011-01-20
申请号：PCT/US2010/001362
申请日：2010-05-06
申请人： DNA 2.0 INC. , POLYTECHNIC INSTITUTE OF NEW YORK UNIVERSITY , GROSS, Richard, A. , LU, Wenhua , NESS, Jon , MINSHULL, Jeremy
发明人： GROSS, Richard, A. , LU, Wenhua , NESS, Jon , MINSHULL, Jeremy
IPC分类号： C12P7/64 , C12P1/02
摘要： A substantially pure Candida host cell for the production of a α-carboxyl-ω- hydroxy fatty acid having a carbon chain length in the range from C6 to C22, a α,ω- dicarboxylic fatty acid having a carbon chain length in the range from C6 to C22, or mixtures thereof, is provided. The Candida host cell is characterized by a first genetic modification class and a second genetic modification class. The first genetic modification class comprises one or more genetic modifications that disrupt the peroxisomal β-oxidation pathway. The second genetic modification class comprises one or more genetic modifications that collectively or individually disrupt at least one gene selected from the group consisting of a CYP52A type cytochrome P450 and a fatty alcohol oxidase.

2. 发明申请

WO2007022260A2 SYSTEMS AND METHODS FOR DESIGNING AND ORDERING POLYNUCLEOTIDES 审中-公开
标题翻译：用于设计和订购多核苷酸的系统和方法
公开(公告)号：WO2007022260A2
公开(公告)日：2007-02-22
申请号：PCT/US2006/031976
申请日：2006-08-15
申请人： DNA 2.0 INC. , GUSTAFSSON, Claes , GOVINDARAJAN, Sridhar , NESS, Jon, E. , VILLALOBOS, Alan, Marco , MINSHULL, Jeremy
发明人： GUSTAFSSON, Claes , GOVINDARAJAN, Sridhar , NESS, Jon, E. , VILLALOBOS, Alan, Marco , MINSHULL, Jeremy
IPC分类号： G06F19/00
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 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.
摘要翻译：提供了用于设计寡核苷酸的计算机系统，计算机程序产品和方法。定义了一组序列元素。每个序列元件代表氨基酸序列区段或核酸序列区段。该组序列元件共同表示设计核酸序列。该组序列元素以线性或近似线性排列显示为多个图标，使得多个图标中的每个相应图标唯一地表示该组序列元素中的对应序列元素。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的对应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。

3. 发明申请

WO2011008231A2 BIOTRANSFORMATION USING GENETICALLY MODIFIED CANDIDA 审中-公开
标题翻译：生物转化使用基因修饰的坎迪达
公开(公告)号：WO2011008231A2
公开(公告)日：2011-01-20
申请号：PCT/US2010/001361
申请日：2010-05-06
申请人： DNA 2.0 INC. , NESS, Jon , MINSHULL, Jeremy
发明人： NESS, Jon , MINSHULL, Jeremy
IPC分类号： C12P7/64 , C12N1/19 , C12N15/74
CPC分类号： C12P7/6409 , C12N9/0006 , C12N15/815 , C12P7/6427 , C12P7/6436 , C12P7/649 , Y02E50/13
摘要： A substantially pure Candida host cell is provided for the biotransformation of a substrate to a product wherein the host cell is characterized by a first genetic modification class that comprises one or more genetic modifications that collectively or individually disrupt at least one alcohol dehydrogenase gene in the substantially pure Candida host cell.
摘要翻译：提供了基本上纯的念珠菌宿主细胞用于将底物生物转化为产物，其中宿主细胞的特征在于第一遗传修饰类别，其包含一个或多个遗传因子在基本上纯的假丝酵母属宿主细胞中共同或单独破坏至少一种醇脱氢酶基因的修饰。

4. 发明申请

WO2009148616A2 SYSTEMS AND METHODS FOR DETERMINING PROPERTIES THAT AFFECT AN EXPRESSION PROPERTY VALUE OF POLYNUCLEOTIDES IN AN EXPRESSION SYSTEM 审中-公开
标题翻译：用于确定在表达系统中影响多核苷酸的表达性质的性质的系统和方法
公开(公告)号：WO2009148616A2
公开(公告)日：2009-12-10
申请号：PCT/US2009/003412
申请日：2009-06-05
申请人： DNA 2.0 INC. , WELCH, Mark , GUSTAFSSON, Claes
发明人： WELCH, Mark , GUSTAFSSON, Claes
IPC分类号： C40B30/02 , C40B60/12
CPC分类号： C12N15/67 , G06F19/20 , G06F19/22
摘要： A method of designing a polynucleotide sequence encoding a polypeptide sequence of a predetermined polypeptide is provided. A frequency lookup table corresponding to an expression system is obtained. The table comprises a plurality of sequence elements and a plurality of frequency ranges, each frequency range for a corresponding sequence element. Each frequency range is a range of frequencies with which a corresponding sequence element can occur in a polynucleotide. The polynucleotide sequence is defined using the frequency lookup table by determining, for each respective sequence element in the frequency lookup table, whether the respective sequence element encodes a portion of the polypeptide sequence. When the respective sequence element encodes a portion of the polypeptide sequence, the sequence element is incorporated into the polynucleotide at a frequency of occurrence that is within the frequency range specified for the respective sequence element in the lookup table.
摘要翻译：提供了设计编码预定多肽的多肽序列的多核苷酸序列的方法。获得与表达式系统对应的频率查找表。该表包括多个序列元素和多个频率范围，每个频率范围用于相应的序列元素。每个频率范围是在多核苷酸中可以发生相应序列元件的频率范围。使用频率查找表来定义多核苷酸序列，对于频率查找表中的每个相应序列元件，确定各个序列元件是否编码多肽序列的一部分。当各个序列元件编码多肽序列的一部分时，序列元件以在查找表中对于相应序列元件指定的频率范围内的发生频率被并入多核苷酸。

5. 发明申请

WO2010047733A2 MODIFIED PROLYL ENDOPEPTIDASES FOR THE TREATMENT OF DISEASES CAUSED BY IMMUNE RESPONSES TO DIETARY PROTEINS 审中-公开
标题翻译：改良的PRLYL内肽酶治疗由免疫应答引起的疾病对膳食蛋白质的影响
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
申请人： DNA 2.0 INC. , KHOSLA, Chaitan , EHREN, Jennifer , MINSHULL, Jeremy , GOVINDARAJAN, Sridhar
发明人： KHOSLA, Chaitan , EHREN, Jennifer , MINSHULL, Jeremy , GOVINDARAJAN, Sridhar
IPC分类号： C12N9/50
CPC分类号： C12N9/52
摘要： 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.
摘要翻译：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。

6. 发明申请

US20160032295A1 METHODS, COMPOSITIONS AND KITS FOR A ONE-STEP DNA CLONING SYSTEM 审中-公开
标题翻译：用于一步DNA克隆系统的方法，组合物和试剂盒
公开(公告)号：US20160032295A1
公开(公告)日：2016-02-04
申请号：US14881004
申请日：2015-10-12
申请人： DNA 2.0, Inc.
发明人： Jeremy Minshull , Jon Ness
IPC分类号： C12N15/64
CPC分类号： C12N15/64 , C12N15/66
摘要： Methods and kits for joining three or more polynucleotides to form a product polynucleotide are provided. Such a method includes forming a reaction mixture comprising (i) a vector fragment whose ends have four base overhangs resulting from cleavage of a vector with a first type IIs enzyme, (ii) a first insert nucleic acid with a four base overhang at one end resulting from cleavage by the first type IIs enzyme and a three base overhang at the other end resulting from cleavage by the second type IIs enzyme; and (iii) a second insert nucleic acid with a four base overhang at one end resulting from cleavage by the first type IIs enzyme and a three base overhang at the other end resulting from cleavage by the second type IIs enzyme, and (iv) a ligase. The four base overhangs of the vector ligate with the four base overhangs of the first and second inserts and the three base overhangs of the first and second inserts ligate with each other or three base overhangs of a spacer nucleic acid resulting from cleavage with the second type IIs enzyme to form a product polynucleotide in which the first and second insert nucleic acids are joined to the vector fragment.
摘要翻译：提供了用于连接三个或更多个多核苷酸以形成产物多核苷酸的方法和试剂盒。这种方法包括形成反应混合物，其包含（i）载体片段，其末端具有由第一类型IIs酶切割载体产生的四个碱基突出端，（ii）在一端具有四个碱基突出端的第一插入核酸由第一类型IIs酶的切割引起，另一端的三碱基突出端由第二种II型酶切割而产生; 和（iii）第二插入核酸，其一端具有四碱基突出端，其由第一类型IIs酶切割，另一端由三碱基突出端引起，由第二类型II酶切割，以及（iv）连接酶载体的四个碱基突出部分与第一和第二插入物的四个基本突出部连接，并且第一和第二插入物的三个基部突出端彼此连接或由与第二种类型的切割产生的间隔核心的三个底部突出端连接 IIs酶以形成其中第一和第二插入核酸与载体片段连接的产物多核苷酸。

7. 发明授权

US10253321B2 Methods, compositions and kits for a one-step DNA cloning system 有权
公开(公告)号：US10253321B2
公开(公告)日：2019-04-09
申请号：US14881004
申请日：2015-10-12
申请人： DNA 2.0, Inc.
发明人： Jeremy Minshull , Jon Ness
IPC分类号： C12Q1/68 , C07H21/00 , C12P19/34 , C12N15/64 , C12N15/66
摘要： Methods and kits for joining three or more polynucleotides to form a product polynucleotide are provided. Such a method includes forming a reaction mixture comprising (i) a vector fragment whose ends have four base overhangs resulting from cleavage of a vector with a first type IIs enzyme, (ii) a first insert nucleic acid with a four base overhang at one end resulting from cleavage by the first type IIs enzyme and a three base overhang at the other end resulting from cleavage by the second type IIs enzyme; and (iii) a second insert nucleic acid with a four base overhang at one end resulting from cleavage by the first type IIs enzyme and a three base overhang at the other end resulting from cleavage by the second type IIs enzyme, and (iv) a ligase. The four base overhangs of the vector ligate with the four base overhangs of the first and second inserts and the three base overhangs of the first and second inserts ligate with each other or three base overhangs of a spacer nucleic acid resulting from cleavage with the second type IIs enzyme to form a product polynucleotide in which the first and second insert nucleic acids are joined to the vector fragment.

8. 发明公开

EP1934865A2 SYSTEMS AND METHODS FOR DESIGNING AND ORDERING POLYNUCLEOTIDES 审中-公开
标题翻译：系统和设计方法和多核苷酸的规则
公开(公告)号：EP1934865A2
公开(公告)日：2008-06-25
申请号：EP06813483.2
申请日：2006-08-15
申请人： DNA 2.0 Inc.
发明人： GUSTAFSSON, Claes , GOVINDARAJAN, Sridhar , NESS, Jon, E. , VILLALOBOS, Alan, Marco , MINSHULL, Jeremy
IPC分类号： G06F19/00
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 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.

9. 发明公开

EP2294407A2 SYSTEMS AND METHODS FOR DETERMINING PROPERTIES THAT AFFECT AN EXPRESSION PROPERTY VALUE OF POLYNUCLEOTIDES IN AN EXPRESSION SYSTEM 有权转让
标题翻译：系统和方法用于确定性能 - 影响多核苷酸的表达特性数值在表达系统
公开(公告)号：EP2294407A2
公开(公告)日：2011-03-16
申请号：EP09758779.4
申请日：2009-06-05
申请人： DNA 2.0 Inc.
发明人： WELCH, Mark , GUSTAFSSON, Claes
IPC分类号： G01N33/48 , C12Q1/68
CPC分类号： C12N15/67 , G06F19/20 , G06F19/22
摘要： A method of designing a polynucleotide sequence encoding a polypeptide sequence of a predetermined polypeptide is provided. A frequency lookup table corresponding to an expression system is obtained. The table comprises a plurality of sequence elements and a plurality of frequency ranges, each frequency range for a corresponding sequence element. Each frequency range is a range of frequencies with which a corresponding sequence element can occur in a polynucleotide. The polynucleotide sequence is defined using the frequency lookup table by determining, for each respective sequence element in the frequency lookup table, whether the respective sequence element encodes a portion of the polypeptide sequence. When the respective sequence element encodes a portion of the polypeptide sequence, the sequence element is incorporated into the polynucleotide at a frequency of occurrence that is within the frequency range specified for the respective sequence element in the lookup table.

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