公开(公告)号：US20150240280A1

公开(公告)日：2015-08-27

申请号：US14636082

申请日：2015-03-02

Applicant: Synthetic Genomics, Inc.

Inventor： Daniel G. Gibson ,  Hamilton O. Smith ,  Clyde A. Hutchison ,  Lei Young ,  J. Craig Venter

IPC: C12P19/34 ,  C12N15/66

CPC classification number: C12P19/34 ,  C12N15/10 ,  C12N15/1027 ,  C12N15/64 ,  C12N15/66

Abstract: The present invention relates to methods of joining two or more double-stranded (ds) or single-stranded (ss) DNA molecules of interest in vitro, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule of each pair share a region of sequence identity. The method allows the joining of a large number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest. Kits for performing the method are also disclosed. The methods of joining DNA molecules may be used to generate combinatorial libraries useful to generate, for example, optimal protein expression through codon optimization, gene optimization, and pathway optimization.

Abstract translation: 本发明涉及在体外连接两个或多个目的双链（ds）或单链（ss）DNA分子的方法，其中第一DNA分子的远端区域和第二DNA分子的近端区域 每对共享序列同一性区域。 该方法允许以预定顺序和取向连接大量DNA片段，而不使用限制酶。 其可以用于例如合成产生的感兴趣的基因或基因组的亚片段。 还公开了用于执行该方法的套件。 连接DNA分子的方法可用于产生组合文库，其可用于产生例如通过密码子优化，基因优化和途径优化的最佳蛋白质表达。

公开(公告)号：US20190241921A1

公开(公告)日：2019-08-08

申请号：US16388722

申请日：2019-04-18

Applicant: Synthetic Genomics, Inc.

Inventor： Daniel G. Gibson ,  Hamilton O. Smith ,  Clyde A. Hutchison ,  Lei Young ,  J. Craig Venter

IPC: C12P19/34 ,  C12N15/66 ,  C12N15/10 ,  C12N15/64

CPC classification number: C12P19/34 ,  C12N15/10 ,  C12N15/1027 ,  C12N15/64 ,  C12N15/66

Abstract: The present invention relates to methods of joining two or more double-stranded (ds) or single-stranded (ss) DNA molecules of interest in vitro, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule of each pair share a region of sequence identity. The method allows the joining of a large number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest. Kits for performing the method are also disclosed. The methods of joining DNA molecules may be used to generate combinatorial libraries useful to generate, for example, optimal protein expression through codon optimization, gene optimization, and pathway optimization.

公开(公告)号：US10266865B2

公开(公告)日：2019-04-23

申请号：US14636082

申请日：2015-03-02

Applicant: Synthetic Genomics, Inc.

Inventor： Daniel G. Gibson ,  Hamilton O. Smith ,  Clyde A. Hutchison ,  Lei Young ,  J. Craig Venter

IPC: C12P19/34 ,  C12N15/10 ,  C12N15/64 ,  C12N15/66

Abstract: The present invention relates to methods of joining two or more double-stranded (ds) or single-stranded (ss) DNA molecules of interest in vitro, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule of each pair share a region of sequence identity. The method allows the joining of a large number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest. Kits for performing the method are also disclosed. The methods of joining DNA molecules may be used to generate combinatorial libraries useful to generate, for example, optimal protein expression through codon optimization, gene optimization, and pathway optimization.

公开(公告)号：US20160177322A1

公开(公告)日：2016-06-23

申请号：US15051463

申请日：2016-02-23

Applicant: Synthetic Genomics, Inc.

Inventor： Gwynedd A. Benders ,  John I. Glass ,  Clyde A. Hutchison, III ,  Carole Lartigue ,  Sanjay Vashee ,  Mikkel A. Algire ,  Hamilton O. Smith ,  Charles E. Merryman ,  Vladimir N. Noskov ,  Ray-Yuan Chuang ,  Daniel G. Gibson ,  J. Craig Venter

IPC: C12N15/81 ,  C12N15/10

CPC classification number: C12N15/81 ,  C12N15/10 ,  C12N15/102 ,  C12N15/1031 ,  C12N15/1079 ,  C12N15/1093

Abstract: Compositions and methods are disclosed herein for cloning a synthetic or a semi-synthetic donor genome in a heterologous host cell. In one embodiment, the donor genome can be further modified within a host cell. Modified or unmodified genomes can be further isolated from the host cell and transferred to a recipient cell. Methods disclosed herein can be used to alter donor genomes from intractable donor cells in more tractable host cells.

Abstract translation: 本文公开了在异源宿主细胞中克隆合成或半合成供体基因组的组合物和方法。 在一个实施方案中，可以在宿主细胞内进一步修饰供体基因组。 修饰或未修饰的基因组可以进一步从宿主细胞中分离并转移到受体细胞。 本文公开的方法可用于在更容易处理的宿主细胞中改变来自难治性供体细胞的供体基因组。

公开(公告)号：US09206435B2

公开(公告)日：2015-12-08

申请号：US14015070

申请日：2013-08-30

Applicant: Synthetic Genomics, Inc.

Inventor： Bogumil J. Karas ,  Hutchison Clyde A., III ,  Hamilton O. Smith ,  Yo Suzuki

IPC: C12N15/81 ,  C12N15/87

CPC classification number: C12N15/81 ,  C12N15/87

Abstract: The presently disclosed invention relates to methods of transferring large nucleic acid molecules or a genome from one cell (the donor) into heterologous host cells in the presence of a crowding agent. The method allows for greater ease and efficiency of transfer of genetic material. Introduction of the donor genetic material into the recipient host cells also allows for manipulation of the donor nucleic acid molecule or genome within the host cells. Methods disclosed herein can be used to alter donor genomes from intractable donor cells in more tractable host cells.

Abstract translation: 本公开的本发明涉及在拥挤剂存在下将大核酸分子或基因组从一个细胞（供体）转移到异源宿主细胞中的方法。 该方法允许遗传物质的转移更容易和有效。 将供体遗传物质引入受体宿主细胞还允许操纵宿主细胞内的供体核酸分子或基因组。 本文公开的方法可用于在更容易处理的宿主细胞中改变来自难治性供体细胞的供体基因组。

公开(公告)号：US20130295645A1

公开(公告)日：2013-11-07

申请号：US13864108

申请日：2013-04-16

Applicant: Synthetic Genomics, Inc.

Inventor： Daniel Glenn Gibson ,  Hamilton O. Smith

IPC: C12N9/12

CPC classification number: C12N9/1252 ,  C12N15/10 ,  C12N15/102 ,  C12N15/1031 ,  C12N15/64 ,  C12N15/66 ,  C12P19/34

Abstract: The present invention relates to an in vitro method, using isolated protein reagents, for joining two double-stranded (ds) DNA molecules of interest, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule share a region of sequence identity. The method allows the joining of a number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest.

Abstract translation: 本发明涉及一种使用分离的蛋白质试剂连接两个感兴趣的双链（ds）DNA分子的体外方法，其中第一DNA分子的远端区域和第二DNA分子的近端区域共享一个区域 的序列同一性。 该方法允许以预定的顺序和取向连接多个DNA片段，而不使用限制酶。 其可以用于例如合成产生的感兴趣的基因或基因组的亚片段。

公开(公告)号：US20180340165A1

公开(公告)日：2018-11-29

申请号：US16056343

申请日：2018-08-06

Applicant: Synthetic Genomics, Inc.

Inventor： J. Craig Venter ,  Hamilton O. Smith ,  Clyde A. Hutchison, III ,  Daniel G. Gibson

IPC: C12N15/10 ,  C12N15/66

Abstract: Methods are provided for constructing a synthetic genome, comprising generating and assembling nucleic acid cassettes comprising portions of the genome, wherein at least one of the nucleic acid cassettes is constructed from nucleic acid components that have been chemically synthesized, or from copies of the chemically synthesized nucleic acid components. In one embodiment, the entire synthetic genome is constructed from nucleic acid components that have been chemically synthesized, or from copies of the chemically synthesized nucleic acid components. Synthetic genomes or synthetic cells may be used for a variety of purposes, including the generation of synthetic fuels, such as hydrogen or ethanol.

公开(公告)号：US20160168579A1

公开(公告)日：2016-06-16

申请号：US15052781

申请日：2016-02-24

Applicant: SYNTHETIC GENOMICS, INC.

Inventor： Clyde A. Hutchison ,  Michael G. Montague ,  Hamilton O. Smith

IPC: C12N15/64 ,  G06F17/30

CPC classification number: C12N15/64 ,  C12Q1/6806 ,  G06F16/86 ,  C12Q2563/185

Abstract: Methods and apparatus are disclosed herein for encoding human readable text conveying a non-genetic message into nucleic acid sequences with a substantially reduced probability of biological impact and decoding such text from nucleic acid sequences. In one embodiment, each symbol of a symbol set of human readable symbols uniquely maps to a respective codon identifier. Mapping may ensure that each symbol will not map to a codon identifier that generates an amino acid residue which has a single-letter abbreviation that is the equivalent to the respective symbol. Synthetic nucleic acid sequences comprising such human readable text, and recombinant or synthetic cells comprising such sequences are provided, as well as methods of identifying cells, organisms, or samples containing such sequences.

Abstract translation: 本文公开的方法和装置用于编码将非遗传信息输送到核酸序列中的人类可读文本，其中生物影响的概率显着降低，并且从核酸序列解码该文本。 在一个实施例中，人类可读符号的符号集合的每个符号唯一映射到相应的密码子标识符。 映射可以确保每个符号不会映射到生成具有等同于相应符号的单字母缩写的氨基酸残基的密码子标识符。 提供了包含这种人类可读文本的合成核酸序列，以及包含此类序列的重组或合成细胞，以及鉴定包含该序列的细胞，生物体或样品的方法。

公开(公告)号：US20150344837A1

公开(公告)日：2015-12-03

申请号：US14733743

申请日：2015-06-08

Applicant: Synthetic Genomics, Inc.

Inventor： John I. Glass ,  Hamilton O. Smith ,  Clyde A. Hutchison lll ,  Nina Y. Alperovich ,  Nacyra Assad-Garcia

IPC: C12N1/20 ,  C12R1/35 ,  C07K14/30 ,  C12N9/16

CPC classification number: C12N1/20 ,  C07K14/195 ,  C07K14/30 ,  C12N9/16 ,  C12P3/00 ,  C12P7/06 ,  C12R1/35 ,  C12Y301/04046 ,  Y02E50/17

Abstract: The present invention relates, e.g., to a minimal set of protein-coding genes which provides the information required for replication of a free-living organism in a rich bacterial culture medium, wherein (1) the gene set does not comprise the 100 genes listed in Table 2; and/or wherein (2) the gene set comprises the 382 protein-coding genes listed in Table 3 and, optionally, one of more of: a set of three genes encoding ABC transporters for phosphate import (genes MG410, MG411 and MG412; or genes MG289, MG290 and MG291); the lipoprotein-encoding gene MG185 or MG260; and/or the glycerophosphoryl diester phosphodiesterase gene MG293 or MG385.

Abstract translation: 本发明涉及例如提供在富细菌培养基中复制自由活体的所需信息的蛋白质编码基因的最小集合，其中（1）基因组不包括所列出的100个基因 在表2中; 和/或其中（2）基因组包含表3中列出的382个蛋白质编码基因，以及任选地，一组编码ABC转运蛋白的三个基因（基因MG410，MG411和MG412;或 基因MG289，MG290和MG291）; 编码脂蛋白的基因MG185或MG260; 和/或甘油磷酸二酯磷酸二酯酶基因MG293或MG385。

公开(公告)号：US20140179001A1

公开(公告)日：2014-06-26

申请号：US14015070

申请日：2013-08-30

Applicant: Synthetic Genomics, Inc.

Inventor： Bogumil J. Karas ,  Hutchison Clyde A., III ,  Hamilton O. Smith ,  Yo Suzuki

IPC: C12N15/81

CPC classification number: C12N15/81 ,  C12N15/87

Abstract: The presently disclosed invention relates to methods of transferring large nucleic acid molecules or a genome from one cell (the donor) into heterologous host cells in the presence of a crowding agent. The method allows for greater ease and efficiency of transfer of genetic material. Introduction of the donor genetic material into the recipient host cells also allows for manipulation of the donor nucleic acid molecule or genome within the host cells. Methods disclosed herein can be used to alter donor genomes from intractable donor cells in more tractable host cells.

Abstract translation: 本公开的本发明涉及在拥挤剂存在下将大核酸分子或基因组从一个细胞（供体）转移到异源宿主细胞中的方法。 该方法允许遗传物质的转移更容易和有效。 将供体遗传物质引入受体宿主细胞还允许操纵宿主细胞内的供体核酸分子或基因组。 本文公开的方法可以用于在更容易处理的宿主细胞中改变来自难治性供体细胞的供体基因组。