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1.发明授权公开(公告)号：US08399199B2
公开(公告)日：2013-03-19
申请号：US13286937
申请日：2011-11-01
CPC分类号： C12Q1/6853 , C12N15/1068 , C12P19/34 , C12Q1/6855 , C12Q1/686 , C12Q1/6865 , C12Q2525/301 , C12Q2525/119 , C12Q2521/301 , C12Q2525/191 , C12Q2521/501
摘要： The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.
摘要翻译： 本发明涉及使用茎环寡核苷酸制备DNA分子，例如文库。 在具体实施方案中，本发明采用单一反应混合物和条件。 特别地，在制备分子期间，至少部分反向回文被去除以促进分子的扩增。 因此，在具体实施方案中，DNA分子适合于扩增，并且不受回文的存在的阻碍。
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2.发明授权公开(公告)号：US08409804B2
公开(公告)日：2013-04-02
申请号：US11367046
申请日：2006-03-02
CPC分类号： C12N15/1065 , C12N15/1003 , C12N15/1093 , C12Q1/6846 , C12Q1/6886 , C12Q2537/164 , C12Q2527/107
摘要： The present invention concerns isolation, library preparation and selective amplification from a compositionally heterogeneous pool of DNA fragments of a fraction of molecules, such as those originating from promoter CpG islands and characterized by a high GC content. In particular, the process utilizes a heat-induced segregation of DNA molecules into GC-poor, single-stranded molecule fractions and GC-rich, double-stranded molecule fractions, with subsequent enzymatic conversion of the GC-rich, double-stranded DNA molecules into a library, and, optionally, amplification. In specific embodiments, the isolation process is used to generate promoter-enriched genomic and methylome libraries for research and diagnostic applications, for example.
摘要翻译： 本发明涉及分离，文库制备和从部分分子的DNA片段的组成不均一聚集体（例如源自启动子CpG岛的那些DNA片段）的选择性扩增，并且特征在于高GC含量。 特别地，该方法利用热分解DNA分子到GC-不良的单链分子级分和富含GC的双链分子级分，随后富含GC的双链DNA分子的酶转化 进入文库，可选地，扩增。 在具体实施方案中，例如，分离过程用于产生用于研究和诊断应用的富含启动子的基因组和甲基化文库。
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3.发明申请COMPOSITIONS AND METHODS FOR PROCESSING AND AMPLIFICATION OF DNA, INCLUDING USING MULTIPLE ENZYMES IN A SINGLE REACTION 有权用于加工和放大DNA的组合物和方法，包括在单反应中使用多种酶公开(公告)号：US20110081685A1
公开(公告)日：2011-04-07
申请号：US12892359
申请日：2010-09-28
CPC分类号： C12Q1/6853 , C12N15/1068 , C12P19/34 , C12Q1/6855 , C12Q1/686 , C12Q1/6865 , C12Q2525/301 , C12Q2525/119 , C12Q2521/301 , C12Q2525/191 , C12Q2521/501
摘要： The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.
摘要翻译： 本发明涉及使用茎环寡核苷酸制备DNA分子，例如文库。 在具体实施方案中，本发明采用单一反应混合物和条件。 特别地，在制备分子期间，至少部分反向回文被去除以促进分子的扩增。 因此，在具体实施方案中，DNA分子适合于扩增，并且不受回文的存在的阻碍。
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公开(公告)号：US08071312B2
公开(公告)日：2011-12-06
申请号：US12892359
申请日：2010-09-28
CPC分类号： C12Q1/6853 , C12N15/1068 , C12P19/34 , C12Q1/6855 , C12Q1/686 , C12Q1/6865 , C12Q2525/301 , C12Q2525/119 , C12Q2521/301 , C12Q2525/191 , C12Q2521/501
摘要： The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.
摘要翻译： 本发明涉及使用茎环寡核苷酸制备DNA分子，例如文库。 在具体实施方案中，本发明采用单一反应混合物和条件。 特别地，在制备分子期间，至少部分反向回文被去除，以促进分子的扩增。 因此，在具体实施方案中，DNA分子适合于扩增，并且不受回文的存在的阻碍。
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5.发明授权Methods and compositions for generating and amplifying DNA libraries for sensitive detection and analysis of DNA methylation 有权用于产生和扩增DNA文库以灵敏检测和分析DNA甲基化的方法和组合物公开(公告)号：US08440404B2
公开(公告)日：2013-05-14
申请号：US11071864
申请日：2005-03-03
申请人： Vladimir L. Makarov , Emmanuel Kamberov , Tong Sun , Jonathon H. Pinter , Brendan J. Tarrier , Eric E. Bruening , Takao Kurihara , Tim Tesmer , Joseph M'Mwirichia
发明人： Vladimir L. Makarov , Emmanuel Kamberov , Tong Sun , Jonathon H. Pinter , Brendan J. Tarrier , Eric E. Bruening , Takao Kurihara , Tim Tesmer , Joseph M'Mwirichia
CPC分类号： C12Q1/6869 , C12N15/1072 , C12Q1/6827 , C12Q1/6855 , C12Q2525/301 , C12Q2525/191 , C12Q2521/331 , C12Q2523/125
摘要： The present invention regards a variety of methods and compositions for obtaining epigenetic information, such as DNA methylation patterns, through the preparation, amplification and analysis of Methylome libraries. In particular, the method employs preparation of a DNA molecule by digesting the DNA molecule with at least one methylation-sensitive restriction enzyme; incorporating a nucleic acid molecule into at least some of the digested DNA molecules by either (1) incorporating at least one primer from a plurality of primers that have a 5′ constant sequence and a 3′ variable sequence, wherein the primers are substantially non-self-complementary and substantially non-complementary to other primers in the plurality; or (2) incorporating an oligonucleotide having an inverted repeat and a loop under conditions wherein the oligonucleotide becomes blunt-end ligated to one strand of the digested DNA molecule, followed by polymerization from a 3′ hydroxyl group present in a nick in the oligonucleotide-linked molecule; and amplifying one or more of the DNA molecules.
摘要翻译： 本发明涉及通过Methylome文库的制备，扩增和分析来获得表观遗传信息的各种方法和组合物，例如DNA甲基化模式。 特别地，该方法通过用至少一种甲基化敏感性限制酶消化DNA分子来制备DNA分子; 通过（1）从具有5'恒定序列和3'可变序列的多个引物掺入至少一个引物，将核酸分子掺入到至少一些消化的DNA分子中，其中所述引物基本上不含 与多个中的其它引物互补且基本上不互补; 或者（2）在其中寡核苷酸变得钝端连接到消化的DNA分子的一条链上，然后从存在于寡聚核苷酸的切口中的3'羟基聚合的条件下，引入具有反向重复和环的寡核苷酸， 连接分子 并扩增一个或多个DNA分子。
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6.发明授权Methods of producing nucleic acid molecules comprising stem loop oligonucleotides 有权产生包含茎环寡核苷酸的核酸分子的方法公开(公告)号：US07803550B2
公开(公告)日：2010-09-28
申请号：US12270850
申请日：2008-11-13
CPC分类号： C12Q1/6853 , C12N15/1068 , C12P19/34 , C12Q1/6855 , C12Q1/686 , C12Q1/6865 , C12Q2525/301 , C12Q2525/119 , C12Q2521/301 , C12Q2525/191 , C12Q2521/501
摘要： The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.
摘要翻译： 本发明涉及使用茎环寡核苷酸制备DNA分子，例如文库。 在具体实施方案中，本发明采用单一反应混合物和条件。 特别地，在制备分子期间，至少部分反向回文被去除以促进分子的扩增。 因此，在具体实施方案中，DNA分子适合于扩增，并且不受回文的存在的阻碍。
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7.发明申请COMPOSITIONS AND METHODS FOR PROCESSING AND AMPLIFICATION OF DNA, INCLUDING USING MULTIPLE ENZYMES IN A SINGLE REACTION 有权用于加工和放大DNA的组合物和方法，包括在单反应中使用多种酶公开(公告)号：US20100021973A1
公开(公告)日：2010-01-28
申请号：US12270850
申请日：2008-11-13
CPC分类号： C12Q1/6853 , C12N15/1068 , C12P19/34 , C12Q1/6855 , C12Q1/686 , C12Q1/6865 , C12Q2525/301 , C12Q2525/119 , C12Q2521/301 , C12Q2525/191 , C12Q2521/501
摘要： The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.
摘要翻译： 本发明涉及使用茎环寡核苷酸制备DNA分子，例如文库。 在具体实施方案中，本发明采用单一反应混合物和条件。 特别地，在制备分子期间，至少部分反向回文被去除以促进分子的扩增。 因此，在具体实施方案中，DNA分子适合于扩增，并且不受回文的存在的阻碍。
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8.发明授权Amplification and analysis of whole genome and whole transcriptome libraries generated by a DNA polymerization process 有权通过DNA聚合过程产生的全基因组和整个转录组文库的扩增和分析公开(公告)号：US07718403B2
公开(公告)日：2010-05-18
申请号：US10795667
申请日：2004-03-08
申请人： Emmanuel Kamberov , Tong Sun , Eric Bruening , Jonathon H. Pinter , Irina Sleptsova , Takao Kurihara , Vladimir L. Makarov
发明人： Emmanuel Kamberov , Tong Sun , Eric Bruening , Jonathon H. Pinter , Irina Sleptsova , Takao Kurihara , Vladimir L. Makarov
CPC分类号： C12N15/1093 , C12N15/10 , C12Q1/686 , C40B40/06 , C40B50/06 , C12Q2525/161 , C12Q2525/179 , C12Q2525/15
摘要： The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.
摘要翻译： 本发明涉及用于全基因组扩增和全转录组扩增的多种方法和组合物。 在本发明的特定方面，存在扩增包含文库产生步骤之后是文库扩增步骤的基因组的方法。 在具体实施方案中，文库产生步骤使用特异性引物混合物和DNA聚合酶，其中特异性引物混合物被设计为消除混合物内其它引物自我杂交和/或杂交的能力，但有效且频繁引发核酸模板。
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9.发明授权DNA amplification and sequencing using DNA molecules generated by random fragmentation 有权DNA扩增和使用随机碎裂产生的DNA分子进行测序公开(公告)号：US08815504B2
公开(公告)日：2014-08-26
申请号：US12697886
申请日：2010-02-01
CPC分类号： C12Q1/6855 , C12Q1/6844 , C12Q1/6846 , C12Q1/6869 , C12Q2531/113 , C12Q2525/191 , C12Q2521/301 , C12Q2523/107
摘要： The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3′ end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.
摘要翻译： 本发明涉及通过随机碎裂制备DNA分子或多个DNA分子的方法。 在一些实施方案中，本发明涉及通过随机断裂制备用于DNA测序的模板。 在具体实施方案中，随机碎裂包括化学断裂，机械破碎或酶促碎裂。 在进一步的具体实施方案中，通用序列附着于DNA片段的3'末端，例如通过连接衔接子序列或通过与末端脱氧核苷酸转移酶的均聚尾料连接。 在其它实施方案中，使用本发明的方法制备文库。
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公开(公告)号：US20130085083A1
公开(公告)日：2013-04-04
申请号：US13487637
申请日：2012-06-04
申请人： Emmanuel Kamberov , Tong Sun , Eric Bruening , Jonathon H. Pinter , Irina Sleptsova , Takao Kurihara , Vladimir L. Makarov
发明人： Emmanuel Kamberov , Tong Sun , Eric Bruening , Jonathon H. Pinter , Irina Sleptsova , Takao Kurihara , Vladimir L. Makarov
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6853 , C12N15/10 , C12N15/1093 , C12Q1/6806 , C12Q1/686 , C12Q1/6876 , C12Q2525/161 , C12Q2525/179 , C12Q2525/15
摘要： The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.
摘要翻译： 本发明涉及用于全基因组扩增和全转录组扩增的多种方法和组合物。 在本发明的特定方面，存在扩增包含文库产生步骤之后是文库扩增步骤的基因组的方法。 在具体实施方案中，文库产生步骤使用特异性引物混合物和DNA聚合酶，其中特异性引物混合物被设计为消除混合物内其它引物自我杂交和/或杂交的能力，但有效且频繁引发核酸模板。
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