Patents by Inventor Clyde A. Hutchison, III
Clyde A. Hutchison, III 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: 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: 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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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: 9481880Abstract: The presently disclosed invention relates to methods of installing a genome isolated from one species (the donor) into suitably prepared cells of a second species (the recipient). Introduction of the donor genetic material into the recipient host cell effectively converts the recipient host cell into a new cell that, as a result of the operation of the donated genetic material, is functionally classified as belonging to the genus and species of the donor genetic material.Type: GrantFiled: May 1, 2008Date of Patent: November 1, 2016Assignee: Synthetic Genomics, Inc.Inventors: John I. Glass, Nina Alperovich, Clyde A. Hutchison, III, Carole Lartigue, Charles E. Merryman, Sanjay Vashee, 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
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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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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: 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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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: 20110045592Abstract: The presently disclosed invention relates to methods of installing a genome isolated from one species (the donor) into suitably prepared cells of a second species (the recipient). Introduction of the donor genetic material into the recipient host cell effectively converts the recipient host cell into a new cell that, as a result of the operation of the donated genetic material, is functionally classified as belonging to the genus and species of the donor genetic material.Type: ApplicationFiled: May 1, 2008Publication date: February 24, 2011Inventors: John I. Glass, Nina Alperovich, Clyde A. Hutchison, III, Carole Lartigue, Charles E. Merryman, Sanjay Vashee, J. Craig Venter
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Publication number: 20090275086Abstract: 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: ApplicationFiled: October 7, 2008Publication date: November 5, 2009Applicant: 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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Publication number: 20090176280Abstract: 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: ApplicationFiled: May 1, 2006Publication date: July 9, 2009Applicant: The J. Craig Venter InstituteInventors: Clyde A. Hutchison III, Hamilton O. Smith
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Patent number: 6537773Abstract: The present invention provides the nucleotide sequence of the entire genome of Mycoplasma genitalium, SEQ ID NO:1. The present invention further provides the sequence information stored on computer readable media, and computer-based systems and methods which facilitate its use. In addition to the entire genomic sequence, the present invention identifies protein encoding fragments of the genome, and identifies, by position relative to two (2) genes known to flank the origin of replication, any regulatory elements which modulate the expression of the protein encoding fragments of the Mycoplasma genitalium genome.Type: GrantFiled: October 19, 1995Date of Patent: March 25, 2003Assignees: The Institute for Genomic Research, Johns Hopkins University, The University of North Carolina at Chapel HillInventors: Claire M. Fraser, Mark D. Adams, Jeannine D. Gocayne, Clyde A. Hutchison, III, Hamilton O. Smith, J. Craig Venter, Owen White