Daniel K Gibson

US Patent:

20110053272, Mar 3, 2011

Filed:

Mar 5, 2010

Appl. No.:

12/718911

Inventors:

Gwynedd A. Benders - Portland OR, US
John I. Glass - Germantown MD, US
Carole Lartigue - Des Arenes Bayonne, FR
Sanjay Vashee - Boyds MD, US
Mikkel A. Algire - Jessup MD, US
Hamilton O. Smith - San Diego CA, US
Charles E. Merryman - Sykesville MD, US
Vladimir N. Noskov - Montgomery Village MD, US
Ray-Yuan Chuang - Rockville MD, US
Daniel G. Gibson - Crofton MD, US
J. Craig Venter - La Jolla CA, US

International Classification:

C12N 15/74
C12N 15/82
C12N 15/85
C12N 1/21
C12N 1/15
C12N 1/19
C12N 5/10

US Classification:

435455, 435471, 435468, 4352523, 43525411, 4352542, 435419, 435348, 435325

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.

US Patent:

20110053273, Mar 3, 2011

Filed:

May 19, 2010

Appl. No.:

12/783489

Inventors:

Gwynedd A. Benders - Portland OR, US
John I. Glass - Germantown MD, US
Clyde A. Hutchison - La Jolla CA, US
Carole Lartigue - Des Arenes Bayonne, FR
Sanjay Vashee - Boyds MD, US
Mikkel A. Algire - Jessup MD, US
Hamilton O. Smith - San Diego CA, US
Charles E. Merryman - Sykesville MD, US
Vladimir N. Noskov - Montgomery Village MD, US
Ray-Yuan Chuang - Rockville MD, US
Daniel G. Gibson - Crofton MD, US
J. Craig Venter - La Jolla CA, US

Assignee:

Synthetic Genomics, Inc. - La Jolla CA

International Classification:

C12N 15/87
C12N 1/21

US Classification:

435455, 435471, 435468, 4352523

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.

US Patent:

20210355519, Nov 18, 2021

Filed:

May 13, 2021

Appl. No.:

17/320021

Inventors:

- San Diego CA, US
John E. Gill - San Marcos CA, US
Daniel G. Gibson - Carlsbad CA, US
Lixia Fu - San Diego CA, US

International Classification:

C12P 19/34

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.

US Patent:

20210340598, Nov 4, 2021

Filed:

Jul 12, 2021

Appl. No.:

17/373115

Inventors:

- San Diego CA, US
Daniel G. Gibson - Carlsbad CA, US
Lixia Fu - San Diego CA, US

International Classification:

C12Q 1/686
C12N 15/10
C07H 19/173
C07H 19/073
C12N 9/22
C12N 15/09
C12P 19/34

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.

US Patent:

20210283615, Sep 16, 2021

Filed:

May 14, 2021

Appl. No.:

17/321301

Inventors:

- San Diego CA, US
Daniel Gibson - Carlsbad CA, US
John E. Gill - San Marcos CA, US

International Classification:

B01L 7/00
C12N 15/10
C07K 14/005
C12N 7/00

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. The invention is useful, for example, for rapidly responding to viral and other biological threats that are specific to a particular locale.

US Patent:

20210284954, Sep 16, 2021

Filed:

Mar 25, 2021

Appl. No.:

17/212926

Inventors:

- San Diego CA, US
Daniel G. Gibson - Carlsbad CA, US
Daniel Strimling - La Jolla CA, US

International Classification:

C12N 1/20
C12N 15/74
C12N 9/10

Abstract:

The invention provides engineered sp. organisms that comprise a genetic modification to either or both of the lpxL and/or lpxM genes. The organisms score substantially lower in an in vitro endotoxin assay versus the unmodified or wild type organism. The organisms preserve substantially the growth rate of the corresponding unmodified organisms. The organisms can also have an exogenous nucleic acid cloned in the organism, or an exogenous nucleic acid encoding a protein, polypeptide, or peptide expressed by the organism, and optionally secreted from the organism.

US Patent:

20210277446, Sep 9, 2021

Filed:

Feb 25, 2021

Appl. No.:

17/185609

Inventors:

- San Diego CA, US
Lixia Fu - San Diego CA, US
Daniel G. Gibson - Carlsbad CA, US

International Classification:

C12Q 1/6806

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.

US Patent:

20200190539, Jun 18, 2020

Filed:

Feb 24, 2020

Appl. No.:

16/799424

Inventors:

- San Diego CA, US
Hamilton O. Smith - San Diego CA, US
Daniel Glenn Gibson - Carlsbad CA, US

International Classification:

C12N 15/90
C12Q 1/62
C12Q 1/686
C12N 9/00
C12N 9/22
C12N 9/12
C12Q 1/6862
C12P 19/34
C12N 15/66
C12N 15/64
C12N 15/10

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 ′ 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.

Author:

Daniel Gibson

ISBN #:

0312207778