公开(公告)号：US10370706B1

公开(公告)日：2019-08-06

申请号：US16111590

申请日：2018-08-24

申请人： Shuichi Hoshika ,  Nicole A Leal ,  Steven A Benner

发明人： Shuichi Hoshika ,  Nicole A Leal ,  Steven A Benner

IPC分类号： C12Q1/68 ,  C12N15/11 ,  C12P19/34 ,  C07H21/00 ,  C12Q1/6853 ,  C12Q1/686

摘要： This invention covers a new molecular recognition system, where duplexes of DNA-like molecules comprise segments built from nucleotides that carry only a small pyrimidine-like analog, and where the segments pair by pyrimidine analog:pyrimidine analog “skinny” pairing. This pairing retains hydrogen bonding complementarity. Further, this invention relates to processes for preparing those duplexes, and processes that use such duplexes as primer:template complexes for reactions catalyzed by DNA polymerases.

公开(公告)号：US20110319298A1

公开(公告)日：2011-12-29

申请号：US12311982

申请日：2009-04-21

申请人： Steven A. Benner ,  Shuichi Hoshika ,  Nicole Leal

发明人： Steven A. Benner ,  Shuichi Hoshika ,  Nicole Leal

IPC分类号： C40B50/06 ,  C07H21/00

CPC分类号： C12Q1/6855 ,  C12Q1/6853 ,  C12Q1/6858 ,  C12Q2521/301 ,  C12Q2525/121 ,  C12Q2525/179 ,  C12Q2525/186 ,  C12Q2525/191 ,  C12Q2525/204 ,  C12Q2535/122 ,  C12Q2535/125 ,  C12Q2563/131

摘要： This patent application claims processes and compositions of matter that enable the discovery of single nucleotide polymorphisms (SNPs) that distinguish the genomes of two individual organisms in the same species, as well as that distinguish the paternal and maternal genetic inheritance of a single individual, as well as distinguish the genomes of cells in special tissues (e.g. cancer tissues) within an individual from the genomes of the standard cells in the same individuals, as well as the SNPs that are discovered using these processes and compositions. Two steps are essential to the invention disclosed in this application. The first step provides four sets of primers, which are designated “T-extendable”, “A-extendable”, “C-extendable”, and “G-extendable”. These primers, when targeted against a reference genome as a template, add (respectively) T, A, C, and G to their 3′-ends in a template-directed primer extension reaction. The second step presents these four primer sets, separately, to a sample of the target genome DNA under conditions where they bind to their complementary segments within the target DNA. Once bound, members of each primer set serve as primers for a template-directed primer extension reaction using the target genome as the template. If the template from the target genome presents the same templating nucleotide for the first nucleotide added in the extension reaction as the reference genome, then the T-extendable, A-extendable, C-extendable, and G-extendable primers will be extended (respectively) by T, A, C, and G. If, however, the template from the target genome presents a nucleotide different from the reference genome, then the T-extendable, A-extendable, C-extendable, and G-extendable primers will be extended (respectively) by not T, not A, not C, and not G (referred to here as “3N” or “3”, to indicate the other three nucleotides, where which of the other three is understood by context). In these cases, the primers have discovered a SNP, a difference between the target and reference genomes. Then, the T-extendable, A-extendable, C-extendable, and G-extendable primers that add (respectively) not-T, not-A, not-C, and not-G are separated or made otherwise physically distinct (through, for example, the use of irreversible terminators, such as 2′,3′-dideoxynucleosides) from those that added T, A, C, and G (respectively). Those that added T, A, C, and G (respectively) did not discover a SNP, and are discarded. The primers that added “not-T”, “not-A”, “not-C”, and “not-G” discovered a SNP, and presented in a mixture enriched (relative to those primers that did not discover a SNP) in a useful deliverable. Following these steps, the SNPs discoveries are realized by sequencing the extracted species. The information obtained from this sequencing allows the identification of the locus of the SNP in the in silico genome.

公开(公告)号：US10059737B1

公开(公告)日：2018-08-28

申请号：US15461073

申请日：2017-03-16

申请人： Steven A Benner ,  Shuichi Hoshika

发明人： Steven A Benner ,  Shuichi Hoshika

IPC分类号： C07H21/04

CPC分类号： C07H21/04

摘要： This invention is for a new molecular recognition system, where DNA-like molecules comprising segments built from nucleotides that carry only a small which comprises process by which one molecule interacts with a specific second molecule, or by which a portion of a single molecule interacts specifically with another portion of the same molecule. Further, this invention relates to molecular recognition that follows simple rules. Further, this invention relates to molecular systems that are linear biopolymers that are analogs of DNA and RNA, in that they are built from a small set of building blocks that are linked together by phosphate groups, where the building blocks comprise a sugar (ribose, 2′-deoxyribose, or an analog) attached to a heterocycle. The molecular recognition that they display differs from that displayed by DNA and RNA, in that the rules governing molecular recognition break the rules of size complementarity followed in molecular recognition displayed between and within strands of DNA and RNA.

公开(公告)号：US10829511B1

公开(公告)日：2020-11-10

申请号：US16530600

申请日：2019-08-02

申请人： Steven A Benner ,  Shuichi Hoshika

发明人： Steven A Benner ,  Shuichi Hoshika

IPC分类号： C07H21/04

摘要： This invention covers oligonucleotide analogs that fold in part by having a segment of consecutive pyrimidine analogs form pyrimidine analog:pyrimidine analog pairs with another a segment of consecutive pyrimidine analogs segment, and where the segments pair by pyrimidine analog:pyrimidine analog “skinny” pairing. This pairing retains hydrogen bonding complementarity seen in standard DNA.

公开(公告)号：US20090270601A1

公开(公告)日：2009-10-29

申请号：US12386595

申请日：2009-04-21

申请人： Steven Albert Benner ,  Shuichi Hoshika ,  Nicole Aurora Leal

发明人： Steven Albert Benner ,  Shuichi Hoshika ,  Nicole Aurora Leal

IPC分类号： C12P19/34 ,  C07H21/04

CPC分类号： C12P19/34 ,  C12Q1/6809 ,  C12Q2533/101 ,  C12Q2525/117

摘要： This application claims processes and compositions that enable discovery of single nucleotide polymorphisms (SNPs) and other sequence variation that follows two essentially identical sequences, one a reference, the other a target, as well as SNPs discovered using these processes and compositions. The inventive process comprises preparation of four sets of primers, “T-extendable”, “A-extendable”, “C-extendable”, and “G-extendable”. These primers, when templated on a reference genome, add (respectively) T, A, C, and G to their 3′-ends. The invention also comprises a step where these primer sets are separately bound to complementary sequences on target DNA and, once bound, prime extension reactions using target DNA as the template. If the target DNA directs incorporation of the same nucleotide as the reference DNA, then the T-, A-, C-, and G-extendable primers are extended (respectively) by T, A, C, and G. The architecture of the process distinguishes products from these extensions from products derived if not T, not A, not C and not G (“3N” or “3”, to indicate the other three nucleotides) are not added. Thus, this process discovers differences between the target and reference DNA in the site queried by the primer extension reaction. The distinction makes the two kinds of products either separable or differentially extendable. This distinction is used to disregard products that added T, A, C, and G and to identify the sequence(s) of primers that added not-T, not-A, not-C, and not-G. Further and optionally, information from these sequences identifies loci of the SNPs in an in silico genome.

摘要翻译： 本申请要求能够发现单核苷酸多态性（SNP）和遵循两个基本相同的序列的其他序列变异的方法和组合物，一个是参考，另一个靶标，以及使用这些方法和组合物发现的SNP。 本发明方法包括制备四组引物“T可延伸”，“可扩展”，“可扩展”和“可扩展”。 当在参照基因组上模板时，这些引物将T，A，C和G（分别）添加到它们的3'末端。 本发明还包括一个步骤，其中这些引物组分别与靶DNA上的互补序列结合，并且一旦结合，使用靶DNA作为模板进行初始延伸反应。 如果目标DNA引导与参考DNA相同的核苷酸引入，则T，A，C和G分别扩增T，A，C和G可延伸的引物。 过程将产品从这些扩展区分出来的产品，如果不是T，而不是A，而不是C而不是G（“3N”或“3”，表示其他三个核苷酸）。 因此，该过程发现由引物延伸反应查询的位点中的靶标和参照DNA之间的差异。 这种区别使得两种产品可分离或差异扩展。 这种区别用于忽视添加T，A，C和G的产物，并鉴定未添加-T，而不是A，非-C和非-G的引物序列。 进一步和任选地，来自这些序列的信息识别计算机基因组中SNP的位点。

公开(公告)号：US08871469B1

公开(公告)日：2014-10-28

申请号：US12229159

申请日：2008-08-20

申请人： Steven Albert Benner ,  Shuichi Hoshika ,  Fei Chen

发明人： Steven Albert Benner ,  Shuichi Hoshika ,  Fei Chen

IPC分类号： C12P19/34 ,  C07H21/04

CPC分类号： C12Q1/6853 ,  C07H21/04 ,  C12Q1/6848 ,  C12Q1/6876 ,  C12Q2525/117 ,  C12Q2600/16 ,  C12Q2531/113 ,  C12Q2527/107 ,  C12Q2525/185 ,  C12Q2537/143 ,  C12Q2525/101

摘要： This invention concerns self-avoiding molecular recognition systems (SAMRS), compositions that bind to natural DNA and RNA, but do not bind to compositions at sites that incorporate other SAMRS components, and processes dependent on them. Their utility is shown by discoveries that DNA polymerases accept these compositions as primers and templates, where standard triphosphates are added to primers containing SAMRS components, and added opposite to SAMRS components in the template. A critical mass of data are provided in 16 examples to provide first-generation heuristic rules to permit design of SAMRS sequences can be used as primers and templates that are accepted by DNA polymerases. The presently preferred primers are at least 12 nucleotide units in length, and more preferably between 15 and 30 nucleotides in length. Also preferred are chimeric primers that have standard nucleotides in their 5′-segments, and SAMRS nucleotides in their 3′-segments, and in multiplexed priming.

摘要翻译： 本发明涉及自回避分子识别系统（SAMRS），与天然DNA和RNA结合但不结合其他SAMRS组分的位点的组合物以及依赖于它们的方法的组合物。 通过发现DNA聚合酶接受这些组合物作为引物和模板，其中将标准三磷酸加入到含有SAMRS组分的引物中，并与模板中的SAMRS组分相反地添加，发现其实用性。 在16个例子中提供了大量数据，以提供第一代启发式规则，以允许SAMRS序列的设计可以用作DNA聚合酶所接受的引物和模板。 目前优选的引物长度为至少12个核苷酸单位，更优选长度为15至30个核苷酸。 还优选的是在其5'-节段中具有标准核苷酸的嵌合引物，以及它们的3'-区段中的SAMRS核苷酸以及多重引发。