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).

  • Publication number: 20200190539
    Abstract: The present invention relates, e.g., to 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 contacting the two DNA molecules in a reaction mixture with (a) a non-processive 5? exonuclease; (b) a single stranded DNA binding protein (SSB) which accelerates nucleic acid annealing; (c) a non strand-displacing DNA polymerase; and (d) a ligase, under conditions effective to join the two DNA molecules to form an intact double stranded DNA molecule, in which a single copy of the region of sequence identity is retained. The method allows the joining of a number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes.
    Type: Application
    Filed: February 24, 2020
    Publication date: June 18, 2020
    Inventors: Lei Young, Hamilton O. Smith, Daniel Glenn Gibson
  • Patent number: 10626429
    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.
    Type: Grant
    Filed: July 31, 2019
    Date of Patent: April 21, 2020
    Assignee: SGI-DNA, Inc.
    Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
  • Patent number: 10577629
    Abstract: The present invention relates, e.g., to 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 contacting the two DNA molecules in a reaction mixture with (a) a non-processive 5? exonuclease; (b) a single stranded DNA binding protein (SSB) which accelerates nucleic acid annealing; (c) a non strand-displacing DNA polymerase; and (d) a ligase, under conditions effective to join the two DNA molecules to form an intact double stranded DNA molecule, in which a single copy of the region of sequence identity is retained. The method allows the joining of a number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes.
    Type: Grant
    Filed: December 20, 2016
    Date of Patent: March 3, 2020
    Assignee: SGI-DNA, Inc.
    Inventors: Lei Young, Hamilton O. Smith, Daniel Glenn Gibson
  • Publication number: 20190376103
    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.
    Type: Application
    Filed: July 31, 2019
    Publication date: December 12, 2019
    Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
  • Publication number: 20190241921
    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.
    Type: Application
    Filed: April 18, 2019
    Publication date: August 8, 2019
    Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
  • Patent number: 10266865
    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.
    Type: Grant
    Filed: March 2, 2015
    Date of Patent: April 23, 2019
    Assignee: Synthetic Genomics, Inc.
    Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
  • Publication number: 20180340165
    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.
    Type: Application
    Filed: August 6, 2018
    Publication date: November 29, 2018
    Inventors: J. Craig Venter, Hamilton O. Smith, Clyde A. Hutchison, III, Daniel G. Gibson
  • Patent number: 10041060
    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. Rational methods may be used to design the synthetic genome (e.g., to establish a minimal genome and/or to optimize the function of genes within a genome, such as by mutating or rearranging the order of the genes). Synthetic genomes of the invention may be introduced into vesicles (e.g., bacterial cells from which part or all of the resident genome has been removed, or synthetic vesicles) to generate synthetic cells.
    Type: Grant
    Filed: December 6, 2006
    Date of Patent: August 7, 2018
    Assignee: Synthetic Genomics, Inc.
    Inventors: J. Craig Venter, Hamilton O. Smith, Clyde A. Hutchison, III, Daniel G. Gibson
  • Publication number: 20180119132
    Abstract: Methods for generating synthetic genomes, for example synthetic genomes having desired properties or viable genomes of reduced size, are disclosed. Also disclosed are synthetic genomes produced by the methods disclosed herein and synthetic cells containing the synthetic genomes disclosed herein.
    Type: Application
    Filed: March 22, 2017
    Publication date: May 3, 2018
    Inventors: Clyde A. Hutchison, III, Ray-Yuan Chuang, Vladimir N. Noskov, Bogumil J. Karas, Kim S. Wise, Hamilton O. Smith, John I. Glass, Chuck Merryman, Daniel G. Gibson, J. Craig Venter, Krishna Kannan, Lin Ding
  • Publication number: 20170233764
    Abstract: The present invention relates, e.g., to 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 contacting the two DNA molecules in a reaction mixture with (a) a non-processive 5? exonuclease; (b) a single stranded DNA binding protein (SSB) which accelerates nucleic acid annealing; (c) a non strand-displacing DNA polymerase; and (d) a ligase, under conditions effective to join the two DNA molecules to form an intact double stranded DNA molecule, in which a single copy of the region of sequence identity is retained. The method allows the joining of a number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes.
    Type: Application
    Filed: December 20, 2016
    Publication date: August 17, 2017
    Inventors: Lei Young, Hamilton O. Smith, Daniel Glenn Gibson
  • Patent number: 9593329
    Abstract: A method to assemble any desired nucleic acid molecule by combining cassettes in vitro to form assemblies which are further combined in vivo, or by assembling large numbers of DNA fragments by recombination in a yeast culture to obtain desired DNA molecules of substantial size is described.
    Type: Grant
    Filed: October 7, 2008
    Date of Patent: March 14, 2017
    Assignee: Synthetic Genomics, Inc.
    Inventors: Daniel G. Gibson, Lei Young, John I. Glass, Gwynedd A. Benders, J. Craig Venter, Clyde A. Hutchison, III, Hamilton O. Smith
  • Patent number: 9534251
    Abstract: The present invention relates, e.g., to 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 contacting the two DNA molecules in a reaction mixture with (a) a non-processive 5? exonuclease; (b) a single stranded DNA binding protein (SSB) which accelerates nucleic acid annealing; (c) a non strand-displacing DNA polymerase; and (d) a ligase, under conditions effective to join the two DNA molecules to form an intact double stranded DNA molecule, in which a single copy of the region of sequence identity is retained. The method allows the joining of a number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes.
    Type: Grant
    Filed: March 30, 2010
    Date of Patent: January 3, 2017
    Assignee: Synthetic Genomics, Inc.
    Inventors: Lei Young, Hamilton O. Smith, Daniel Glenn Gibson
  • Patent number: 9434974
    Abstract: A method is provided for introducing a genome into a cell or cell-like system. The introduced genome may occur in nature, be manmade with or without automation, or may be a hybrid of naturally occurring and manmade materials. The genome is obtained outside of a cell with minimal damage. Materials such as a proteins, RNAs, polycations, nucleoid condensation proteins, or gene translation systems may accompany the genome. The genome is installed into a naturally occurring cell or into a manmade cell-like system. A cell-like system or synthetic cell resulting from the practice of the provided method may be designed and used to yield gene-expression products, such as desired proteins. By enabling the synthesis of cells or cell-like systems comprising a wide variety of genomes, accompanying materials and membrane types, the provided method makes possible a broader field of experimentation and bioengineering than has been available using prior art methods.
    Type: Grant
    Filed: December 22, 2006
    Date of Patent: September 6, 2016
    Assignee: Synthetic Genomics, Inc.
    Inventors: John I. Glass, Lei Young, Carole Lartigue, Nacyra Assad-Garcia, Hamilton O. Smith, Clyde A. Hutchison, J. Craig Venter
  • Publication number: 20160177338
    Abstract: 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: Application
    Filed: February 29, 2016
    Publication date: June 23, 2016
    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
  • Publication number: 20160177322
    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.
    Type: Application
    Filed: February 23, 2016
    Publication date: June 23, 2016
    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
  • Publication number: 20160168579
    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.
    Type: Application
    Filed: February 24, 2016
    Publication date: June 16, 2016
    Inventors: Clyde A. Hutchison, Michael G. Montague, Hamilton O. Smith
  • Patent number: 9273310
    Abstract: 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: Grant
    Filed: March 5, 2010
    Date of Patent: March 1, 2016
    Assignee: 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
  • Patent number: 9267132
    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.
    Type: Grant
    Filed: May 19, 2010
    Date of Patent: February 23, 2016
    Assignee: 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
  • Patent number: 9206435
    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.
    Type: Grant
    Filed: August 30, 2013
    Date of Patent: December 8, 2015
    Assignee: Synthetic Genomics, Inc.
    Inventors: Bogumil J. Karas, Hutchison Clyde A., III, Hamilton O. Smith, Yo Suzuki
  • Publication number: 20150344837
    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.
    Type: Application
    Filed: June 8, 2015
    Publication date: December 3, 2015
    Inventors: John I. Glass, Hamilton O. Smith, Clyde A. Hutchison lll, Nina Y. Alperovich, Nacyra Assad-Garcia