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1. 发明申请

WO2013123220A1 METHOD FOR RELATIVE QUANTIFICATION OF NUCLEIC ACID SEQUENCE, EXPRESSION, OR COPY CHANGES, USING COMBINED NUCLEASE, LIGATION, AND POLYMERASE REACTIONS 审中-公开
标题翻译：使用组合核酸酶，引物和聚合酶反应的核酸序列，表达或复制变化相对定量的方法
公开(公告)号：WO2013123220A1
公开(公告)日：2013-08-22
申请号：PCT/US2013/026180
申请日：2013-02-14
申请人： CORNELL UNIVERSITY , BARANY, Francis , SPIER, Eugene , MIR, Alain
发明人： BARANY, Francis , SPIER, Eugene , MIR, Alain
IPC分类号： C12Q1/68
CPC分类号： G01N33/5308 , C12Q1/6806 , C12Q1/6813 , C12Q1/6851 , C12Q1/6853 , C12Q1/6855 , C12Q2521/501 , C12Q2525/00 , C12Q2525/301 , C12Q2533/107 , C12Q2521/319 , C12Q2525/113 , C12Q2525/161 , C12Q2565/101 , C12Q2565/514 , C12Q2521/301
摘要： The present invention is directed to methods for identifying the presence of one or more target nucleotide sequences in a sample that involve a nuclease-ligation reaction. In some embodiments, the ligation products formed in the nuclease-ligation process of the present invention are subsequently amplified using a polymerase chain reaction. The ligated product sequences or extension products thereof are detected, and the presence of one or more target nucleotide sequences in the sample is identified based on the detection.
摘要翻译：本发明涉及用于鉴定涉及核酸酶连接反应的样品中一种或多种靶核苷酸序列的存在的方法。在一些实施方案中，随后使用聚合酶链式反应扩增在本发明的核酸酶连接方法中形成的连接产物。检测连接的产物序列或其延伸产物，并且基于检测鉴定样品中一个或多个靶核苷酸序列的存在。

2. 发明申请

WO2014160199A1 METHOD FOR RELATIVE QUANTIFICATION OF CHANGES IN DNA METHYLATION, USING COMBINED NUCLEASE, LIGATION, AND POLYMERASE REACTIONS 审中-公开
标题翻译：使用组合核酸酶，引物和聚合酶反应相关量化DNA甲基化变化的方法
公开(公告)号：WO2014160199A1
公开(公告)日：2014-10-02
申请号：PCT/US2014/026027
申请日：2014-03-13
申请人： CORNELL UNIVERSITY , BARANY, Francis , SPIER, Eugene
发明人： BARANY, Francis , SPIER, Eugene
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/683 , C12Q1/6858 , C12Q1/6886 , C12Q2600/154 , C12Q2521/331 , C12Q2521/501 , C12Q2525/191
摘要： The present invention is directed to methods for identifying the presence of one or more methylated or unmethylated target nucleotide sequences in a sample that involve a nuclease-ligation reaction. In some embodiments, the ligation products formed in the nuclease-ligation process of the present invention are subsequently amplified using a polymerase chain reaction. The ligated product sequences or extension products thereof are detected, and the presence of one or more methylated or unmethylated target nucleotide sequences in the sample is identified based on the detection.
摘要翻译：本发明涉及用于鉴定涉及核酸酶连接反应的样品中一种或多种甲基化或非甲基化靶核苷酸序列的存在的方法。在一些实施方案中，随后使用聚合酶链式反应扩增在本发明的核酸酶连接方法中形成的连接产物。检测连接的产物序列或其延伸产物，并且基于检测鉴定样品中一个或多个甲基化或未甲基化的靶核苷酸序列的存在。

3. 发明申请

WO2013022807A1 METHODS AND COMPOSITIONS FOR DETECTION OF NUCLEIC ACIDS USING 5'-NUCLEASE CLEAVAGE AND AMPLIFICATION 审中-公开
标题翻译：检测使用5'-核酸酶清除和放大的核酸的方法和组合物
公开(公告)号：WO2013022807A1
公开(公告)日：2013-02-14
申请号：PCT/US2012/049672
申请日：2012-08-05
申请人： UNITAQ BIO , SPIER, Eugene
发明人： SPIER, Eugene
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6858 , C12Q1/686 , C12Q2525/301 , C12Q2521/319 , C12Q2525/161 , C12Q2525/186 , C12Q2535/125 , C12Q2563/107 , C12Q2563/113 , C12Q2565/1015
摘要： In some embodiments, methods and compositions are provided to improve the efficiency of 5'nuclease cleavage during PCR by incorporating a short, typically single base, overlap of sequence between the 3' end of a digestion-driving primer and the 5' portion of a probe. A similar overlap can also be used when the primer has an additional 5' portion and spacer between its 5' and 3' ends, such that it can form a unimolecular circular configuration when annealed to the amplicon. In some embodiments, an amplicon forms an intramolecular hairpin structure so that 5' end of a stem overlaps with the 3' end of a digestion-driving primer, when the latter anneals to the amplicon. The amplification reactions can be conducted in solution or with surface-bound primer and/or probes. In some embodiments, methods and compositions are provided to increase the specificity of mutation (allele) specific PCR using blocking oligos cleavable by 5'nuclease reaction.
摘要翻译：在一些实施方案中，提供了方法和组合物，以通过在消化驱动引物的3'末端和5'部分之间引入短的（通常为单碱基）序列的重叠来提高PCR期间5'核酸酶切割的效率探测。当引物在其5'和3'末端之间具有另外的5'部分和间隔物时，也可以使用类似的重叠，使得当与扩增子退火时，它可以形成单分子环形构型。在一些实施方案中，扩增子形成分子内发夹结构，使得当尾端与扩增子退火时，茎的5'末端与消化驱动引物的3'末端重叠。扩增反应可以在溶液中或与表面结合的引物和/或探针进行。在一些实施方案中，提供了方法和组合物，以通过使用可通过5'nuclease反应切割的封闭寡核苷酸来增加突变（等位基因）特异性PCR的特异性。

4. 发明申请

WO2011100057A2 METHODS AND COMPOSITIONS FOR UNIVERSAL DETECTION OF NUCLEIC ACIDS 审中-公开
标题翻译：通常检测核酸的方法和组合物
公开(公告)号：WO2011100057A2
公开(公告)日：2011-08-18
申请号：PCT/US2011/000243
申请日：2011-02-09
申请人： SPIER, Eugene
发明人： SPIER, Eugene
IPC分类号： C12Q1/68 , C12N15/11 , G01N33/52
CPC分类号： C12Q1/6853 , C12N2310/141 , C12Q1/686 , C12Q2565/107 , C12Q2525/301 , C12Q2525/155 , C12Q2565/1015
摘要： Provided are methods and compositions for detecting the presence or amount of one or more target nucleic acids in a sample. Methods of the present invention include linking universal nucleic acid segments into a single molecule in a linking reaction dependent on a target nucleic acid of interest. A variety of universal segment linking strategies are provided, including preamplification by polymerase chain reaction, ligation- based strategies, reverse transcription and linear polymerase extension. Linking the universal segments into a single molecule generates a tagged target nucleic acid which is detected in a manner dependent on an intramolecular interaction between one universal segment and a second portion of the tagged target nucleic acid. In certain embodiments, the intramolecular interaction includes the formation of a hairpin having a stem between a universal segment at one end of the tagged target nucleic acid and a second universal segment at the opposite end of the tagged target nucleic acid. A variety of detection formats are provided, including solution-phase and surface-based formats. The methods and compositions are well-suited for highly multiplexed nucleic acid detection, and are applicable for the detection of any target nucleic acid of interest in both research and clinical settings.
摘要翻译：提供了用于检测样品中一种或多种靶核酸的存在或量的方法和组合物。本发明的方法包括将通用核酸片段连接在依赖目的靶核酸的连接反应中的单个分子中。提供了多种通用片段连接策略，包括通过聚合酶链反应进行预扩增，基于连接的策略，逆转录和线性聚合酶扩增。将通用片段连接成单个分子产生标记的靶核酸，其以取决于标记的靶核酸的一个通用片段和第二部分之间的分子内相互作用的方式检测。在某些实施方案中，分子内相互作用包括在标记的靶核酸的一端的通用片段与标记的靶核酸的相对端的第二通用片段之间形成具有茎的发夹。提供了各种检测格式，包括溶液相和基于表面的格式。所述方法和组合物非常适用于高度多重化的核酸检测，并且适用于在研究和临床环境中检测目标靶核酸。

5. 发明申请

WO2008083259A1 SYSTEMS AND METHODS FOR DETECTING NUCLEIC ACIDS 审中-公开
标题翻译：用于检测核酸的系统和方法
公开(公告)号：WO2008083259A1
公开(公告)日：2008-07-10
申请号：PCT/US2007/089007
申请日：2007-12-28
申请人： APPLERA CORPORATION , AIVAZACHVILI, Vissarion , SCABOO, Kristian , SPIER, Eugene
发明人： AIVAZACHVILI, Vissarion , SCABOO, Kristian , SPIER, Eugene
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6823 , C12Q1/6825 , C12Q1/6827 , C12Q2531/113 , C12Q2521/307 , C12Q2525/161 , C12Q2525/301 , C12Q2565/607 , C12Q2565/519 , C12Q2521/301 , C12Q2561/109
摘要： A method and kit for detecting a target nucleic acid in a sample is described. The sample to be analyzed may include a primer which hybridizes to at least a portion of the target nucleic acid, a probe having a first region which hybridizes to at least a portion of the target nucleic acid and a second region having a detectable label, a polymerase which extends the hybridized primer and an enzyme comprising exonuclease activity that can cleave the hybridized hybridization probe to thereby generate a labeled probe fragment. At least one portion of the hybridization probe hybridizes to another portion of the hybridization probe to thereby form a folded structure. The method can involve melting the sample, reducing the temperature of the sample to allow primer and probe to each hybridize to at least a portion of single stranded target nucleic acid in the sample, elongating the primer and releasing the labeled probe fragment. The sample can be contacted with a solid support comprising surface bound capture probes which hybridize to the labeled probe fragments. The label can then be detected.
摘要翻译：描述了用于检测样品中靶核酸的方法和试剂盒。要分析的样品可以包括与靶核酸的至少一部分杂交的引物，具有与靶核酸的至少一部分杂交的第一区的探针和具有可检测标记的第二区，扩增杂交引物的聚合酶和包含外切核酸酶活性的酶，其可以切割杂交的杂交探针，从而产生标记的探针片段。至少一部分杂交探针与杂交探针的另一部分杂交，从而形成折叠结构。该方法可以包括熔化样品，降低样品的温度以使引物和探针各自与样品中的至少一部分单链靶核酸杂交，延长引物并释放标记的探针片段。样品可以与包含与标记的探针片段杂交的表面结合捕获探针的固体支持物接触。然后可以检测标签。

6. 发明申请

WO2011106460A2 METHODS FOR FLIP-STRAND IMMOBILIZING AND SEQUENCING NUCLEIC ACIDS 审中-公开
标题翻译：用于螺旋状态固定和测序核酸的方法
公开(公告)号：WO2011106460A2
公开(公告)日：2011-09-01
申请号：PCT/US2011/025964
申请日：2011-02-23
申请人： LIFE TECHNOLOGIES CORPORATION , MCKERNAN, Kevin , BLANCHARD, Alan , ZON, Gerald , LAO, Kai , STRAUS, Neil , SPIER, Eugene , CHEN, Caifu
发明人： MCKERNAN, Kevin , BLANCHARD, Alan , ZON, Gerald , LAO, Kai , STRAUS, Neil , SPIER, Eugene , CHEN, Caifu
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6834 , C12Q1/6869 , C12Q2521/301 , C12Q2521/501 , C12Q2525/301 , C12Q2565/518 , C12Q2563/149 , C12Q2525/125 , C12Q2525/119 , C12Q2537/119 , C12Q2525/155
摘要： Provided herein are compositions, materials, methods and kits for immobilizing a template polynucleotide in a first orientation, and immobilizing a complementary sequence of the template polynucleotide in an orientation that is flipped compared to the orientation of the template polynucleotide. Provided herein are adaptive oligonucleotides that can be used in various nucleic acid manipulations to generate immobilized complement polynucleotides that are flipped in orientation compared to the orientation of the immobilized template polynucleotides.
摘要翻译：本文提供了用于将模板多核苷酸固定在第一取向中的组合物，材料，方法和试剂盒，并且与模板多核苷酸的取向相比，将模板多核苷酸的互补序列固定在翻转的取向中。本文提供的适应性寡核苷酸可用于各种核酸操作以产生与固定的模板多核苷酸的取向相比翻转的固定的补体多核苷酸。

7. 发明申请

WO2007101075A3 DOUBLE-LIGATION METHOD FOR HAPLOTYPE AND LARGE-SCALE POLYMORPHISM DETECTION 审中-公开
公开(公告)号：WO2007101075A3
公开(公告)日：2007-09-07
申请号：PCT/US2007/062607
申请日：2007-02-22
申请人： APPLERA CORPORATION , SPIER, Eugene
发明人： SPIER, Eugene
IPC分类号： C12Q1/68
摘要： The present teachings provide methods, compositions, and kits for querying the identity of a target polynucleotide strand comprising. In some embodiments, the present teachings provide a method comprising forming a reaction complex comprising the target polynucleotide strand hybridized to an upstream probe, a middle probe, and a downstream probe, wherein the middle probe comprises, A) a first target specific portion, B) a second target specific portion, C) a non-target specific portion, wherein the non-target specific portion is located between the first target specific portion and the second target specific portion, wherein the downstream probe comprises a 5' end that is adjacent with the 3' end of the middle probe, wherein the upstream probe comprises a 3' end that is adjacent with the 5' end of the middle probe; ligating the upstream probe to the middle probe and the middle probe to the downstream probe to form a ligation product; detecting the ligation product; and, determining the identity of the target polynucleotide strand.

8. 发明授权

EP2814986B1 METHOD FOR RELATIVE QUANTIFICATION OF NUCLEIC ACID SEQUENCE, EXPRESSION, OR COPY CHANGES, USING COMBINED NUCLEASE, LIGATION, AND POLYMERASE REACTIONS 有权
标题翻译：用于核酸序列，表达或复制变化的相对定量的方法，使用组合核酸酶，连接和聚合酶反应
公开(公告)号：EP2814986B1
公开(公告)日：2017-10-25
申请号：EP13749841.6
申请日：2013-02-14
申请人： Cornell University
发明人： BARANY, Francis , SPIER, Eugene , MIR, Alain
IPC分类号： C12Q1/68
CPC分类号： G01N33/5308 , C12Q1/6806 , C12Q1/6813 , C12Q1/6851 , C12Q1/6853 , C12Q1/6855 , C12Q2521/501 , C12Q2525/00 , C12Q2525/301 , C12Q2533/107 , C12Q2521/319 , C12Q2525/113 , C12Q2525/161 , C12Q2565/101 , C12Q2565/514 , C12Q2521/301
摘要： The present invention is directed to methods for identifying the presence of one or more target nucleotide sequences in a sample that involve a nuclease-ligation reaction. In some embodiments, the ligation products formed in the nuclease-ligation process of the present invention are subsequently amplified using a polymerase chain reaction. The ligated product sequences or extension products thereof are detected, and the presence of one or more target nucleotide sequences in the sample is identified based on the detection.

9. 发明公开

EP2814986A1 METHOD FOR RELATIVE QUANTIFICATION OF NUCLEIC ACID SEQUENCE, EXPRESSION, OR COPY CHANGES, USING COMBINED NUCLEASE, LIGATION, AND POLYMERASE REACTIONS 有权
标题翻译：相对定量方法基于组合的核酸酶，连接和聚合酶反应的核酸表达或COPY变化
公开(公告)号：EP2814986A1
公开(公告)日：2014-12-24
申请号：EP13749841.6
申请日：2013-02-14
申请人： Cornell University
发明人： BARANY, Francis , SPIER, Eugene , MIR, Alain
IPC分类号： C12Q1/68
CPC分类号： G01N33/5308 , C12Q1/6806 , C12Q1/6813 , C12Q1/6851 , C12Q1/6853 , C12Q1/6855 , C12Q2521/501 , C12Q2525/00 , C12Q2525/301 , C12Q2533/107 , C12Q2521/319 , C12Q2525/113 , C12Q2525/161 , C12Q2565/101 , C12Q2565/514 , C12Q2521/301
摘要： The present invention is directed to methods for identifying the presence of one or more target nucleotide sequences in a sample that involve a nuclease-ligation reaction. In some embodiments, the ligation products formed in the nuclease-ligation process of the present invention are subsequently amplified using a polymerase chain reaction. The ligated product sequences or extension products thereof are detected, and the presence of one or more target nucleotide sequences in the sample is identified based on the detection.

10. 发明授权

EP2971172B1 METHOD FOR RELATIVE QUANTIFICATION OF CHANGES IN DNA METHYLATION, USING COMBINED NUCLEASE, LIGATION, AND POLYMERASE REACTIONS 有权
公开(公告)号：EP2971172B1
公开(公告)日：2019-07-24
申请号：EP14773880.1
申请日：2014-03-13
申请人： Cornell University
发明人： BARANY, Francis , SPIER, Eugene
IPC分类号： C12Q1/6858 , C12Q1/683 , C12Q1/6886

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