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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Patent number: 11542529Abstract: 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: GrantFiled: February 24, 2020Date of Patent: January 3, 2023Assignee: Codex DNA, Inc.Inventors: Lei Young, Hamilton O. Smith, Daniel Glenn Gibson
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Publication number: 20220364134Abstract: 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: July 29, 2022Publication date: November 17, 2022Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
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Patent number: 11408020Abstract: 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: April 18, 2019Date of Patent: August 9, 2022Assignee: Codex DNA, Inc.Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
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Publication number: 20210254046Abstract: 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: ApplicationFiled: March 12, 2021Publication date: August 19, 2021Inventors: Clyde A. Hutchison, 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
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Patent number: 11085037Abstract: 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: GrantFiled: March 22, 2017Date of Patent: August 10, 2021Assignee: Codex DNA, Inc.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
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Patent number: 10818378Abstract: 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: GrantFiled: February 24, 2016Date of Patent: October 27, 2020Assignee: Codex DNA, Inc.Inventors: Clyde A. Hutchison, III, Michael G. Montague, Hamilton O. Smith
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Publication number: 20200190539Abstract: 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: ApplicationFiled: February 24, 2020Publication date: June 18, 2020Inventors: Lei Young, Hamilton O. Smith, Daniel Glenn Gibson
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Patent number: 10626429Abstract: 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: July 31, 2019Date of Patent: April 21, 2020Assignee: SGI-DNA, Inc.Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
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Patent number: 10577629Abstract: 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: GrantFiled: December 20, 2016Date of Patent: March 3, 2020Assignee: SGI-DNA, Inc.Inventors: Lei Young, Hamilton O. Smith, Daniel Glenn Gibson
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Publication number: 20190376103Abstract: 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: July 31, 2019Publication date: December 12, 2019Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
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Publication number: 20190241921Abstract: 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: April 18, 2019Publication date: August 8, 2019Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
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Patent number: 10266865Abstract: 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: March 2, 2015Date of Patent: April 23, 2019Assignee: Synthetic Genomics, Inc.Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
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Publication number: 20180340165Abstract: 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: ApplicationFiled: August 6, 2018Publication date: November 29, 2018Inventors: J. Craig Venter, Hamilton O. Smith, Clyde A. Hutchison, III, Daniel G. Gibson
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Patent number: 10041060Abstract: 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: GrantFiled: December 6, 2006Date of Patent: August 7, 2018Assignee: Synthetic Genomics, Inc.Inventors: J. Craig Venter, Hamilton O. Smith, Clyde A. Hutchison, III, Daniel G. Gibson
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Publication number: 20180119132Abstract: 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: ApplicationFiled: March 22, 2017Publication date: May 3, 2018Inventors: 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
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Publication number: 20170233764Abstract: 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: ApplicationFiled: December 20, 2016Publication date: August 17, 2017Inventors: Lei Young, Hamilton O. Smith, Daniel Glenn Gibson
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Patent number: 9593329Abstract: 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: GrantFiled: October 7, 2008Date of Patent: March 14, 2017Assignee: 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
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Patent number: 9534251Abstract: 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: GrantFiled: March 30, 2010Date of Patent: January 3, 2017Assignee: Synthetic Genomics, Inc.Inventors: Lei Young, Hamilton O. Smith, Daniel Glenn Gibson
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Patent number: 9434974Abstract: 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: GrantFiled: December 22, 2006Date of Patent: September 6, 2016Assignee: Synthetic Genomics, Inc.Inventors: John I. Glass, Lei Young, Carole Lartigue, Nacyra Assad-Garcia, Hamilton O. Smith, Clyde A. Hutchison, J. Craig Venter
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Publication number: 20160177338Abstract: 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: February 29, 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