Patents by Inventor John E. Gill

John E. Gill 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: 20240368658
    Abstract: The invention provides methods of synthesizing a product DNA molecule having a desired and/or defined sequence. The methods involve assembling oligonucleotide members of a library that contains less than 20,000 members that can be assembled into all possible DNA sequences using the methods provided herein. Also disclosed are kits containing a library of 20,000 or less oligonucleotide members, where the oligonucleotide members in the library can be assembled into every possible polynucleotide sequence. Further disclosed are oligonucleotide libraries having less than 20,000 defined locations and having an oligonucleotide library member at each location, and the oligonucleotide library members can be assembled into every possible polynucleotide sequence.
    Type: Application
    Filed: July 10, 2024
    Publication date: November 7, 2024
    Applicant: Telesis Bio Inc.
    Inventors: Krishna Kannan, John E Gill, Lixia Fu, Daniel G Gibson
  • Publication number: 20240287581
    Abstract: The invention provides methods of assembling a DNA molecule having a desired sequence. The methods involve contacting a DNA ligase with a plurality of short oligonucleotides to be assembled and performing the ligase chain reaction to thereby generate a set of polynucleotides. Oligonucleotides in the plurality overlap with and are complementary to a sequence of at least one other oligonucleotide in the plurality, and at least 50% of the oligonucleotides in the plurality are 6-30 nucleotides in length. The set of polynucleotides produced are contacted with a DNA polymerase and dNTPs in a mixture to join the set of polynucleotides and thereby create a DNA molecule having a desired sequence by polymerase chain assembly. The method allows for production of oligonucleotides of any length having very high sequence fidelity to a desired sequence.
    Type: Application
    Filed: May 1, 2024
    Publication date: August 29, 2024
    Applicant: Telesis Bio, Inc.
    Inventors: John E. Gill, Lixia Fu, Daniel G. Gibson
  • Patent number: 12065684
    Abstract: The invention provides methods of synthesizing a product DNA molecule having a desired and/or defined sequence. The methods involve annealing at least one long oligonucleotide and at least one short oligonucleotide to at least one anchor strand having a sequence at least partially complementary to the at least one long and at least one short oligonucleotide. The invention also provides methods of synthesizing DNA molecules by assembling oligonucleotide members of a library that contains less than 20,000 members that can be assembled into all possible DNA sequences.
    Type: Grant
    Filed: May 13, 2021
    Date of Patent: August 20, 2024
    Assignee: TELESIS BIO INC.
    Inventors: Krishna Kannan, John E. Gill, Daniel G. Gibson, Lixia Fu
  • Patent number: 12018316
    Abstract: The invention provides methods of assembling a DNA molecule having a desired sequence. The methods involve contacting a DNA ligase with a plurality of short oligonucleotides to be assembled and performing the ligase chain reaction to thereby generate a set of polynucleotides. Oligonucleotides in the plurality overlap with and are complementary to a sequence of at least one other oligonucleotide in the plurality, and at least 50% of the oligonucleotides in the plurality are 6-30 nucleotides in length. The set of polynucleotides produced are contacted with a DNA polymerase and dNTPs in a mixture to join the set of polynucleotides and thereby create a DNA molecule having a desired sequence by polymerase chain assembly. The method allows for production of oligonucleotides of any length having very high sequence fidelity to a desired sequence.
    Type: Grant
    Filed: February 25, 2021
    Date of Patent: June 25, 2024
    Assignee: TELESIS BIO INC.
    Inventors: John E. Gill, Lixia Fu, Daniel G. Gibson
  • Publication number: 20230264202
    Abstract: The present invention provides a system for receiving biological sequence information and activating the synthesis of a biological entity. The system has a receiving unit for receiving a signal encoding biological sequence information transmitted from a transmitting unit. The transmitting unit can be present at a remote location from the receiving unit. The system also has an assembly unit connected to the receiving unit, and the assembly unit assembles the biological entity according to the biological sequence information. Thus, according to the present invention biological sequence information can be digitally transmitted to a remote location and the information converted into a biological entity, for example a protein useful as a vaccine, immediately upon being received by the receiving unit and without further human intervention after preparing the system for receipt of the information.
    Type: Application
    Filed: March 31, 2023
    Publication date: August 24, 2023
    Inventors: J. Craig Venter, Daniel Gibson, John E. Gill
  • Publication number: 20230151402
    Abstract: The invention provides methods for synthesizing a product DNA molecule of any possible DNA sequence from a universal library of overlapping oligonucleotides. The method involves combining a plurality of the overlapping oligonucleotides in a reaction pool, where the sequences of the plurality of oligonucleotides comprise at least a sub-sequence of the product DNA molecule. The method also involves annealing the plurality of oligonucleotides, performing a ligation step, and performing an amplification step to thereby synthesize a sub-sequence of the product DNA molecule. The invention can be used to synthesize a DNA molecule of any possible sequence from the universal library, which can be accomplished through a hierarchal assembly scheme. In one embodiment the universal library comprises fewer than 10,000 pre-manufactured oligonucleotides that can be synthesized into the any possible DNA sequence. In any embodiment the product DNA molecule has an error rate of less than 1 error per 2,000 nucleotides.
    Type: Application
    Filed: November 15, 2021
    Publication date: May 18, 2023
    Inventors: John E. Gill, Lixia Fu, Sydney Kerr, Michelle Vargas, Daniel G. Gibson
  • Patent number: 11618029
    Abstract: The present invention provides a system for receiving biological sequence information and activating the synthesis of a biological entity. The system has a receiving unit for receiving a signal encoding biological sequence information transmitted from a transmitting unit. The transmitting unit can be present at a remote location from the receiving unit. The system also has an assembly unit connected to the receiving unit, and the assembly unit assembles the biological entity according to the biological sequence information. Thus, according to the present invention biological sequence information can be digitally transmitted to a remote location and the information converted into a biological entity, for example a protein useful as a vaccine, immediately upon being received by the receiving unit and without further human intervention after preparing the system for receipt of the information.
    Type: Grant
    Filed: May 14, 2021
    Date of Patent: April 4, 2023
    Assignee: Telesis Bio Inc.
    Inventors: J. Craig Venter, Daniel Gibson, John E. Gill
  • Publication number: 20210355519
    Abstract: The invention provides methods of synthesizing a product DNA molecule having a desired and/or defined sequence. The methods involve annealing at least one long oligonucleotide and at least one short oligonucleotide to at least one anchor strand having a sequence at least partially complementary to the at least one long and at least one short oligonucleotide. After annealing, at least one long oligonucleotide bound to an anchor strand abuts at least one short oligonucleotide bound to the same anchor strand. The anchor strand has one or more non-standard nucleotides, and optionally one or more degenerate nucleotides. The method involves ligating the abutting at least one long oligonucleotide and at least one short oligonucleotide to form a dsDNA molecule. The invention also provides methods of synthesizing DNA molecules by assembling oligonucleotide members of a library that contains less than 20,000 members that can be assembled into all possible DNA sequences.
    Type: Application
    Filed: May 13, 2021
    Publication date: November 18, 2021
    Inventors: Krishna Kannan, John E. Gill, Daniel G. Gibson, Lixia Fu
  • Publication number: 20210340598
    Abstract: The invention provides compositions and methods for assembling a DNA molecule having a desired sequence. The methods involve contacting a DNA polymerase, dNTPs, and a plurality of pairs of oligonucleotides. The oligonucleotides of a pair have a portion of the desired sequence, and an internal sequence that overlaps and is complementary to an internal sequence of the other oligonucleotide of the pair, and, when arranged in order, they have at least a portion of the desired sequence. The oligonucleotides also have a 3? or a 5? primer binding sequence having a binding site for a primer. The oligonucleotides that correspond to the end oligonucleotides of the desired sequence also have a universal 3? flanking sequence and a universal 5? flanking sequence, respectively.
    Type: Application
    Filed: July 12, 2021
    Publication date: November 4, 2021
    Inventors: John E. Gill, Daniel G. Gibson, Lixia Fu
  • Publication number: 20210283615
    Abstract: The present invention provides a system for receiving biological sequence information and activating the synthesis of a biological entity. The system has a receiving unit for receiving a signal encoding biological sequence information transmitted from a transmitting unit. The transmitting unit can be present at a remote location from the receiving unit. The system also has an assembly unit connected to the receiving unit, and the assembly unit assembles the biological entity according to the biological sequence information. Thus, according to the present invention biological sequence information can be digitally transmitted to a remote location and the information converted into a biological entity, for example a protein useful as a vaccine, immediately upon being received by the receiving unit and without further human intervention after preparing the system for receipt of the information.
    Type: Application
    Filed: May 14, 2021
    Publication date: September 16, 2021
    Inventors: J. Craig Venter, Daniel Gibson, John E. Gill
  • Publication number: 20210277446
    Abstract: The invention provides methods of assembling a DNA molecule having a desired sequence. The methods involve contacting a DNA ligase with a plurality of short oligonucleotides to be assembled and performing the ligase chain reaction to thereby generate a set of polynucleotides. Oligonucleotides in the plurality overlap with and are complementary to a sequence of at least one other oligonucleotide in the plurality, and at least 50% of the oligonucleotides in the plurality are 6-30 nucleotides in length. The set of polynucleotides produced are contacted with a DNA polymerase and dNTPs in a mixture to join the set of polynucleotides and thereby create a DNA molecule having a desired sequence by polymerase chain assembly. The method allows for production of oligonucleotides of any length having very high sequence fidelity to a desired sequence.
    Type: Application
    Filed: February 25, 2021
    Publication date: September 9, 2021
    Inventors: John E. Gill, Lixia Fu, Daniel G. Gibson
  • Patent number: 11060137
    Abstract: The invention provides compositions and methods for assembling a DNA molecule having a desired sequence. The methods involve contacting a DNA polymerase, dNTPs, and a plurality of pairs of oligonucleotides. The oligonucleotides of a pair have a portion of the desired sequence, and an internal sequence that overlaps and is complementary to an internal sequence of the other oligonucleotide of the pair, and, when arranged in order, they have at least a portion of the desired sequence. The oligonucleotides also have a 3? or a 5? primer binding sequence having a binding site for a primer. The oligonucleotides that correspond to the end oligonucleotides of the desired sequence also have a universal 3? flanking sequence and a universal 5? flanking sequence, respectively.
    Type: Grant
    Filed: December 12, 2017
    Date of Patent: July 13, 2021
    Assignee: Codex DNA, Inc.
    Inventors: John E. Gill, Daniel G. Gibson, Lixia Fu
  • Patent number: 11027282
    Abstract: The present invention provides a system for receiving biological sequence information and activating the synthesis of a biological entity. The system has a receiving unit for receiving a signal encoding biological sequence information transmitted from a transmitting unit. The transmitting unit can be present at a remote location from the receiving unit. The system also has an assembly unit connected to the receiving unit, and the assembly unit assembles the biological entity according to the biological sequence information. Thus, according to the present invention biological sequence information can be digitally transmitted to a remote location and the information converted into a biological entity, for example a protein useful as a vaccine, immediately upon being received by the receiving unit and without further human intervention after preparing the system for receipt of the information.
    Type: Grant
    Filed: July 19, 2017
    Date of Patent: June 8, 2021
    Assignee: Codex DNA, Inc.
    Inventors: J. Craig Venter, Daniel Gibson, John E. Gill
  • Publication number: 20180163254
    Abstract: The invention provides compositions and methods for assembling a DNA molecule having a desired sequence. The methods involve contacting a DNA polymerase, dNTPs, and a plurality of pairs of oligonucleotides. The oligonucleotides of a pair have a portion of the desired sequence, and an internal sequence that overlaps and is complementary to an internal sequence of the other oligonucleotide of the pair, and, when arranged in order, they have at least a portion of the desired sequence. The oligonucleotides also have a 3? or a 5? primer binding sequence having a binding site for a primer. The oligonucleotides that correspond to the end oligonucleotides of the desired sequence also have a universal 3? flanking sequence and a universal 5? flanking sequence, respectively.
    Type: Application
    Filed: December 12, 2017
    Publication date: June 14, 2018
    Inventors: JOHN E. GILL, Daniel G. Gibson, Lixia Fu
  • Publication number: 20170320061
    Abstract: The present invention provides a system for receiving biological sequence information and activating the synthesis of a biological entity. The system has a receiving unit for receiving a signal encoding biological sequence information transmitted from a transmitting unit. The transmitting unit can be present at a remote location from the receiving unit. The system also has an assembly unit connected to the receiving unit, and the assembly unit assembles the biological entity according to the biological sequence information. Thus, according to the present invention biological sequence information can be digitally transmitted to a remote location and the information converted into a biological entity, for example a protein useful as a vaccine, immediately upon being received by the receiving unit and without further human intervention after preparing the system for receipt of the information.
    Type: Application
    Filed: July 19, 2017
    Publication date: November 9, 2017
    Inventors: J. Craig Venter, Daniel Gibson, John E. Gill
  • Patent number: 9718060
    Abstract: The present invention provides a system for receiving biological sequence information and activating the synthesis of a biological entity. The system has a receiving unit for receiving a signal encoding biological sequence information transmitted from a transmitting unit. The transmitting unit can be present at a remote location from the receiving unit. The system also has an assembly unit connected to the receiving unit, and the assembly unit assembles the biological entity according to the biological sequence information. Thus, according to the present invention biological sequence information can be digitally transmitted to a remote location and the information converted into a biological entity, for example a protein useful as a vaccine, immediately upon being received by the receiving unit and without further human intervention after preparing the system for receipt of the information.
    Type: Grant
    Filed: August 16, 2013
    Date of Patent: August 1, 2017
    Assignee: Synthetic Genomics, Inc.
    Inventors: J. Craig Venter, Daniel Gibson, John E. Gill
  • Publication number: 20140274808
    Abstract: The present invention provides a system for receiving biological sequence information and activating the synthesis of a biological entity. The system has a receiving unit for receiving a signal encoding biological sequence information transmitted from a transmitting unit. The transmitting unit can be present at a remote location from the receiving unit. The system also has an assembly unit connected to the receiving unit, and the assembly unit assembles the biological entity according to the biological sequence information. Thus, according to the present invention biological sequence information can be digitally transmitted to a remote location and the information converted into a biological entity, for example a protein useful as a vaccine, immediately upon being received by the receiving unit and without further human intervention after preparing the system for receipt of the information.
    Type: Application
    Filed: August 16, 2013
    Publication date: September 18, 2014
    Applicant: Synthetic Genomics, Inc.
    Inventors: J. Craig Venter, Daniel Gibson, John E. Gill