Patents by Inventor Hamilton O. Smith
Hamilton O. Smith has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20160177322Abstract: 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.Type: ApplicationFiled: February 23, 2016Publication date: June 23, 2016Inventors: 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
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Publication number: 20160168579Abstract: 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.Type: ApplicationFiled: February 24, 2016Publication date: June 16, 2016Inventors: Clyde A. Hutchison, Michael G. Montague, Hamilton O. Smith
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Patent number: 9273310Abstract: Compositions and methods are disclosed herein for cloning a 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.Type: GrantFiled: March 5, 2010Date of Patent: March 1, 2016Assignee: Synthetic Genomics, Inc.Inventors: 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
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Patent number: 9267132Abstract: 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.Type: GrantFiled: May 19, 2010Date of Patent: February 23, 2016Assignee: Synthetic Genomics, Inc.Inventors: Gwynedd A. Benders, John I. Glass, Clyde A. Hutchison, 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
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Patent number: 9206435Abstract: 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.Type: GrantFiled: August 30, 2013Date of Patent: December 8, 2015Assignee: Synthetic Genomics, Inc.Inventors: Bogumil J. Karas, Hutchison Clyde A., III, Hamilton O. Smith, Yo Suzuki
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Publication number: 20150344837Abstract: 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.Type: ApplicationFiled: June 8, 2015Publication date: December 3, 2015Inventors: John I. Glass, Hamilton O. Smith, Clyde A. Hutchison lll, Nina Y. Alperovich, Nacyra Assad-Garcia
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Publication number: 20150240280Abstract: 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.Type: ApplicationFiled: March 2, 2015Publication date: August 27, 2015Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
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Patent number: 8968999Abstract: 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.Type: GrantFiled: February 13, 2009Date of Patent: March 3, 2015Assignee: Synthetic Genomics, Inc.Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
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Patent number: 8859744Abstract: A recombinant cyanobacterium comprising an oxygen-tolerant, hydrogen-evolving hydrogenase, kit, and methods of use.Type: GrantFiled: October 16, 2007Date of Patent: October 14, 2014Assignee: Synthetic Genomics, Inc.Inventors: Qing Xu, Hamilton O. Smith
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Publication number: 20140179001Abstract: 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.Type: ApplicationFiled: August 30, 2013Publication date: June 26, 2014Applicant: Synthetic Genomics, Inc.Inventors: Bogumil J. Karas, Hutchison Clyde A., III, Hamilton O. Smith, Yo Suzuki
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Publication number: 20130295645Abstract: 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.Type: ApplicationFiled: April 16, 2013Publication date: November 7, 2013Inventors: Daniel Glenn Gibson, Hamilton O. Smith
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Patent number: 8497069Abstract: The present invention relates, e.g., to a method for amplifying a small number of copies (e.g. a single copy) of a single-stranded circular DNA molecule (e.g. having a size of about 5-6 kb) by an isothermal rolling circle mechanism, using random or partially random primers and a F29-type DNA polymerase. The method, which can also be used for amplifying DNAs by non-rolling types of multiple displacement amplification, comprises incubating the reaction components in a small volume, e.g. about 10 ?l or less, such as about 0.6 ?l or less. The degree of amplification can be about 109 fold, or higher. A method for cell-free cloning of DNA, using the rolling circle amplification method of the invention, is described.Type: GrantFiled: May 1, 2006Date of Patent: July 30, 2013Assignee: Synthetic Genomics, Inc.Inventors: Clyde A. Hutchison, III, Hamilton O. Smith
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Patent number: 8435736Abstract: 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.Type: GrantFiled: June 22, 2010Date of Patent: May 7, 2013Assignee: Synthetic Genomics, Inc.Inventors: Daniel Glenn Gibson, Hamilton O. Smith
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Publication number: 20120053087Abstract: 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.Type: ApplicationFiled: February 25, 2011Publication date: March 1, 2012Applicant: Synthetic Genomics, Inc.Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
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Publication number: 20110269119Abstract: 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.Type: ApplicationFiled: October 29, 2010Publication date: November 3, 2011Applicant: Synthetic Genomics, Inc.Inventors: Clyde A. Hutchison, Michael G. Montague, Hamilton O. Smith
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Publication number: 20110053272Abstract: Compositions and methods are disclosed herein for cloning a 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.Type: ApplicationFiled: March 5, 2010Publication date: March 3, 2011Inventors: 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
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Publication number: 20110053273Abstract: 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.Type: ApplicationFiled: May 19, 2010Publication date: March 3, 2011Applicant: Synthetic Genomics, Inc.Inventors: Gwynedd A. Benders, John I. Glass, Clyde A. Hutchison, 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
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Publication number: 20100311126Abstract: The present invention relates, e.g., 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, comprising (a) chewing back the DNA molecules with an enzyme having an exonuclease activity, to yield single-stranded overhanging portions of each DNA molecule which contain a sufficient length of the region of sequence identity to hybridize specifically to each other; (b) specifically annealing the single-stranded overhangs; and (c) repairing single-stranded gaps in the annealed DNA molecules and sealing the nicks thus formed (ligating the nicked DNA molecules). The region of sequence identity generally comprises at least 20 non-palindromic nucleotides (nt), e.g., at least about 40 non-palindromic nt.Type: ApplicationFiled: June 22, 2010Publication date: December 9, 2010Inventors: Daniel Glenn GIBSON, Hamilton O. SMITH
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Publication number: 20100291651Abstract: A recombinant cyanobacterium comprising an oxygen-tolerant, hydrogen-evolving hydrogenase, kit, and methods of use.Type: ApplicationFiled: October 16, 2007Publication date: November 18, 2010Inventors: Qing Xu, Hamilton O. Smith
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Patent number: 7776532Abstract: The present invention relates, e.g., 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, comprising (a) chewing back the DNA molecules with an enzyme having an exonuclease activity, to yield single-stranded overhanging portions of each DNA molecule which contain a sufficient length of the region of sequence identity to hybridize specifically to each other; (b) specifically annealing the single-stranded overhangs; and (c) repairing single-stranded gaps in the annealed DNA molecules and sealing the nicks thus formed (ligating the nicked DNA molecules). The region of sequence identity generally comprises at least 20 non-palindromic nucleotides (nt), e.g., at least about 40 non-palindromic nt.Type: GrantFiled: August 11, 2006Date of Patent: August 17, 2010Assignee: Synthetic Genomics, Inc.Inventors: Daniel Glenn Gibson, Hamilton O. Smith