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1. 发明授权

US06828098B2 Method of producing a DNA library using positional amplification based on the use of adaptors and nick translation 失效
标题翻译：基于使用适配器的位置扩增和切口平移来制备DNA文库的方法
公开(公告)号：US06828098B2
公开(公告)日：2004-12-07
申请号：US09860738
申请日：2001-05-18
申请人： John P. Langmore , Vladimir L. Makarov
发明人： John P. Langmore , Vladimir L. Makarov
IPC分类号： C12Q168
CPC分类号： C12N15/1093 , C12N15/10 , C12N15/1096 , C12P19/34 , C12Q1/6844 , C12Q1/6855 , C40B40/00 , C12Q2525/155 , C12Q2521/319 , C12Q2521/101 , C12Q2533/101 , C12Q2531/113 , C12Q2525/191
摘要： The disclosed invention relates to general and specific methods to use the Primer Extension/Nick Translation (PENT) reaction to create an amplifiable DNA strand, called a PENTAmer. A PENTAmers can be made for the purpose of amplifying a controlled length of DNA located at a controlled position within a DNA molecule, a process referred to as Positional Amplification by Nick Translation (PANT). In contrast to PCR, which amplifies DNA between two specific sequences, PANT can amplify DNA between two specific positions. PENTAmers can be created to amplify very large regions of DNA (up to 500,000 bp) as random mixtures (unordered positional libraries), or as molecules sorted according to position (ordered positional libraries). PANT is fast and economical, because PENTAmer preparation can be multiplexed. A single PENTAmer preparation can include very complex mixtures of DNA such as hundreds of large-insert clones, complete genomes, or cDNA libraries. Subsequent PCR amplification of the preparation using a single specific primer can positionally amplify contiguous regions along a specific clone, along a specific genomic region, or along a specific expressed sequence.
摘要翻译：所公开的发明涉及使用引物延伸/翻译（PENT）反应产生称为PENTAmer的可扩增DNA链的一般和具体方法。可以制备PENTAmers用于扩增位于DNA分子内的受控位置的受控长度的DNA，通过Nick Translation（PANT）称为位置扩增的过程。与PCR扩增两个特定序列之间的DNA相比，PANT可以在两个特定位置之间扩增DNA。可以创建PENTAmers作为随机混合物（无序位置文库）或根据位置（有序位置文库）分类的分子扩增非常大的DNA区域（高达500,000bp）。 PANT是快速和经济的，因为PENTAmer准备可以复用。单一的PENTAmer制剂可以包括非常复杂的DNA混合物，例如数百个大插入克隆，完整的基因组或cDNA文库。随后使用单一特异性引物进行PCR制备的PCR扩增可以沿着特定克隆，沿着特定基因组区域或沿特定表达序列位置扩增连续区域。

2. 发明授权

US06762022B2 Compositions and methods for analysis of nucleic acids 失效
标题翻译：用于分析核酸的组合物和方法
公开(公告)号：US06762022B2
公开(公告)日：2004-07-13
申请号：US09801346
申请日：2001-03-06
申请人： Vladimir L. Makarov , John P. Langmore
发明人： Vladimir L. Makarov , John P. Langmore
IPC分类号： C12Q168
CPC分类号： C12Q1/6855 , C12Q1/6869 , C12Q2521/301 , C12Q2521/319 , C12Q2531/113 , C12Q2531/119 , C12Q2525/313
摘要： Disclosed are a number of methods that can be used in a variety of embodiments, including, creation of a nucleic acid terminated at one or more selected bases, sequence analysis of nucleic acids, mapping of sequence motifs within a nucleic acid, positional mapping of nucleic acid clones, and analysis of telomeric regions. The methods utilize double-stranded templates, and in most aspects involve a strand replacement reaction initiated at one or more random or specific locations created in a nucleic acid molecule, and in certain aspects utilizing an oligonucleotide primer.
摘要翻译：公开了可以用于各种实施方案中的多种方法，包括在一个或多个选择的碱基上终止的核酸的产生，核酸的序列分析，核酸内的序列基序的映射，核酸的位置定位酸克隆和端粒区域分析。该方法利用双链模板，并且在大多数方面涉及在核酸分子中产生的一个或多个随机或特定位置处引发的链置换反应，并且在某些方面使用寡核苷酸引物。

3. 发明授权

US08440404B2 Methods and compositions for generating and amplifying DNA libraries for sensitive detection and analysis of DNA methylation 有权
标题翻译：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
IPC分类号： C12Q1/68 , C12P19/34
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。

4. 发明授权

US07803550B2 Methods of producing nucleic acid molecules comprising stem loop oligonucleotides 有权
标题翻译：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
申请人： Vladimir L. Makarov , Emmanuel Kamberov , Brendan J. Tarrier
发明人： Vladimir L. Makarov , Emmanuel Kamberov , Brendan J. Tarrier
IPC分类号： C12Q1/68 , C12P19/34
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。

5. 发明授权

US07655791B2 DNA amplification and sequencing using DNA molecules generated by random fragmentation 有权
标题翻译： 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：US07655791B2
公开(公告)日：2010-02-02
申请号：US10293048
申请日：2002-11-13
申请人： Vladimir L. Makarov , Irina Sleptsova , Emmanuel Kamberov , Eric Bruening
发明人： Vladimir L. Makarov , Irina Sleptsova , Emmanuel Kamberov , Eric Bruening
IPC分类号： C07H21/00 , C12P19/34
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。

6. 发明申请

US20100021973A1 COMPOSITIONS AND METHODS FOR PROCESSING AND AMPLIFICATION OF DNA, INCLUDING USING MULTIPLE ENZYMES IN A SINGLE REACTION 有权
标题翻译：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
申请人： Vladimir L. Makarov , Emmanuel Kamberov , Brendan J. Tarrier
发明人： Vladimir L. Makarov , Emmanuel Kamberov , Brendan J. Tarrier
IPC分类号： C12P19/34 , C07H21/04
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。

7. 发明授权

US06777187B2 Genome walking by selective amplification of nick-translate DNA library and amplification from complex mixtures of templates 有权
标题翻译：通过选择性扩增切口翻译DNA文库并从模板的复杂混合物中扩增的基因组
公开(公告)号：US06777187B2
公开(公告)日：2004-08-17
申请号：US09999018
申请日：2001-11-15
申请人： Vladimir L. Makarov , Emmanuel Kamberov , Irina Sleptsova
发明人： Vladimir L. Makarov , Emmanuel Kamberov , Irina Sleptsova
IPC分类号： C12Q168
CPC分类号： C12Q1/6869 , C12Q1/6876
摘要： Improved methods and reagents for chromosome walking of nucleic acid are discussed herein. A library of amplifiable nick translation molecules is generated, and a chromosome walk is initiated from a known sequence in the nucleic acid by producing at least one nick translate molecule, sequencing part of the nick translate molecule, and producing a second nick translate molecule by initiating the primer extension from the region of the obtained sequence of the prior nick translate molecule.
摘要翻译：本文讨论了用于核酸染色体行走的改进方法和试剂。产生可扩增切口平移分子的文库，通过产生至少一个切口平移分子，切割平移分子的测序部分，并通过引发产生第二切口平移分子，从核酸中的已知序列引发染色体步态来自所获得的先前切口平移分子序列的区域的引物延伸。

8. 发明授权

US08399199B2 Use of stem-loop oligonucleotides in the preparation of nucleic acid molecules 有权
标题翻译：茎环寡核苷酸在制备核酸分子中的应用
公开(公告)号：US08399199B2
公开(公告)日：2013-03-19
申请号：US13286937
申请日：2011-11-01
申请人： Vladimir L. Makarov , Emmanuel Kamberov , Brendan J. Tarrier
发明人： Vladimir L. Makarov , Emmanuel Kamberov , Brendan J. Tarrier
IPC分类号： C12Q1/68 , C12P19/34
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。

9. 发明申请

US20120142060A1 Compositions and Methods for Processing and Amplification of DNA, Including Using Multiple Enzymes in a Single Reaction 有权
标题翻译：用于处理和扩增DNA的组合物和方法，包括在单个反应中使用多种酶
公开(公告)号：US20120142060A1
公开(公告)日：2012-06-07
申请号：US13286937
申请日：2011-11-01
申请人： VLADIMIR L. MAKAROV , Emmanuel Kamberov , Brendan J. Tarrier
发明人： VLADIMIR L. MAKAROV , Emmanuel Kamberov , Brendan J. Tarrier
IPC分类号： C12P19/34
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。

10. 发明授权

US07718403B2 Amplification and analysis of whole genome and whole transcriptome libraries generated by a DNA polymerization process 有权
标题翻译：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
IPC分类号： C12Q1/68 , C12P19/34
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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