Patents Assigned to Gen9, Inc.
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Patent number: 10207240Abstract: Methods and devices are provided for manipulating droplets on a support using surface tension properties, moving the droplets along a predetermined path and merging two droplets together enabling a number of chemical reactions. Disclosed are methods for controlling the droplets volumes. Disclosed are methods and devices for synthesizing at least one oligonucleotide having a predefined sequence. Disclosed are methods and devices for synthesizing and/or assembling at least one polynucleotide product having a predefined sequence from a plurality of different oligonucleotides having a predefined sequence.Type: GrantFiled: November 3, 2010Date of Patent: February 19, 2019Assignee: Gen9, Inc.Inventors: Joseph Jacobson, Larry Li-Yang Chu, Senthil Ramu
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Patent number: 10202608Abstract: Certain aspects of the present invention provide methods for assembling nucleic acid molecules using iterative activation of one or more vector-encoded traits to progressively assemble a longer nucleic acid insert. Aspects of the invention also provide kits, compositions, devices, and systems for assembling synthetic nucleic acids using iterative activation of one or more vector-encoded traits.Type: GrantFiled: September 30, 2011Date of Patent: February 12, 2019Assignee: Gen9, Inc.Inventor: William J. Blake
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Publication number: 20190010530Abstract: Aspects of the disclosure relate to compositions and methods for polynucleotide assembly. In some embodiments, a terminator oligonucleotide is provided.Type: ApplicationFiled: December 21, 2016Publication date: January 10, 2019Applicant: Gen9, Inc.Inventor: Ishtiaq Saaem
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Publication number: 20180355353Abstract: Artificial transcription terminators and their use are provided herein. In one aspect, a non-naturally occurring nucleic acid sequence can comprise a Y-X-Z stem-loop, wherein: Y is a nucleotide sequence of 10 to 30 nucleotides in length; X is a nucleotide sequence of 3 to 12 nucleotides in length, each nucleotide therein not base pairing with any other nucleotide within X; and Z is a nucleotide sequence of 10 to 50 nucleotides in length and having at least 70% complementarity to Y.Type: ApplicationFiled: November 29, 2016Publication date: December 13, 2018Applicant: Gen9, Inc.Inventor: Ishtiaq E. Saaem
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Patent number: 10081807Abstract: Methods and compositions relate to the sorting and cloning of high fidelity nucleic acids using high throughput sequencing. Specifically, nucleic acid molecules having the desired predetermined sequence can be sorted from a pool comprising a plurality of nucleic acids having correct and incorrect sequences.Type: GrantFiled: April 24, 2013Date of Patent: September 25, 2018Assignee: Gen9, Inc.Inventors: Joseph Jacobson, Martin J. Goldberg, Li-yun A. Kung, Daniel Schindler, Michael E. Hudson
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Patent number: 10053719Abstract: Aspects of the invention relate to methods, compositions for synthesizing high fidelity oligonucleotides.Type: GrantFiled: March 13, 2014Date of Patent: August 21, 2018Assignee: Gen9, Inc.Inventors: Ishtiaq E. Saaem, Michael E. Hudson, Stephen F. Archer, Sophea Sann-Rorth, Ellen J. Sanchez, Joseph Jacobson
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Patent number: 9968902Abstract: Certain aspects of the present invention provide devices and methods for preparing oligonucleotides and for assembling nucleic acid molecules using microfluidic devices.Type: GrantFiled: November 20, 2015Date of Patent: May 15, 2018Assignee: Gen9, Inc.Inventor: Larry Li-Yang Chu
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Patent number: 9938553Abstract: Disclosed are devices and methods to synthesize polynucleotides and libraries of polynucleotides such as libraries of oligonucleotides. In exemplary embodiments, the device includes a support having a plurality of features. Each feature contains a plurality of oligonucleotides. Within each feature, each of the plurality of oligonucleotides includes an identical predetermined subunit sequence of X nucleosides and a degenerate sequence of Y nucleosides. A predetermined combination of a subset of the features can be used to produce a polynucleotide having a predetermined sequence of Z nucleosides.Type: GrantFiled: April 8, 2016Date of Patent: April 10, 2018Assignee: Gen9, Inc.Inventor: Joseph Jacobson
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Patent number: 9925510Abstract: Methods and apparatus relate to the synthesis of high fidelity polynucleotides and to the reduction of sequence errors generated during synthesis of nucleic acids on a solid support. Specifically, design of support-bound template oligonucleotides is disclosed. Assembly methods include cycles of annealing, stringent wash and extension of polynucleotides comprising a sequence region complementary to immobilized template oligonucleotides. The error free synthetic nucleic acids generated therefrom can be used for a variety of applications, including synthesis of biofuels and value-added pharmaceutical products.Type: GrantFiled: November 20, 2015Date of Patent: March 27, 2018Assignee: Gen9, Inc.Inventors: Joseph Jacobson, Larry Li-Yang Chu
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Patent number: 9856471Abstract: Disclosed are methods for synthesizing and/or assembling at least one polynucleotide product having a predefined sequence from a plurality of different oligonucleotides. In exemplary embodiments, the methods involve synthesis and/or amplification of different oligonucleotides immobilized on a solid support, release of synthesized/amplified oligonucleotides in solution to form droplets, recognition and removal of error-containing oligonucleotides, moving or combining two droplets to allow hybridization and/or ligation between two different oligonucleotides, and further chain extension reaction following hybridization and/or ligation to hierarchically generate desired length of polynucleotide products.Type: GrantFiled: June 27, 2014Date of Patent: January 2, 2018Assignee: Gen9, Inc.Inventors: Joseph Jacobson, George Church, Larry Li-Yang Chu
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Patent number: 9422600Abstract: Methods and apparatus relate to reduction of sequence errors generated during synthesis of nucleic acids on a microarray chip. The error reduction can include synthesis of complementary stands (to template strands), using a short universal primer complementary to the template strands and polymerase. Heteroduplex can be formed be melting and re-annealing complementary stands and template strands. The heteroduplexes containing a mismatch can be recognized and cleaved by a mismatch endonuclease. The mismatch-containing cleaved heteroduplexes can be removed from the microarray chip using a global buffer exchange. The error free synthetic nucleic acids generated therefrom can be used for a variety of applications, including synthesis of biofuels and value-added pharmaceutical products.Type: GrantFiled: June 20, 2011Date of Patent: August 23, 2016Assignee: Gen9, Inc.Inventors: Senthil Ramu, Joseph Jacobson
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Patent number: 9388407Abstract: Disclosed are devices and methods to synthesize polynucleotides and libraries of polynucleotides such as libraries of oligonucleotides. In exemplary embodiments, the device includes a support having a plurality of features. Each feature contains a plurality of oligonucleotides. Within each feature, each of the plurality of oligonucleotides includes an identical predetermined subunit sequence of X nucleosides and a degenerate sequence of Y nucleosides. A predetermined combination of a subset of the features can be used to produce a polynucleotide having a predetermined sequence of Z nucleosides.Type: GrantFiled: March 31, 2014Date of Patent: July 12, 2016Assignee: Gen9, Inc.Inventor: Joseph Jacobson
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Patent number: 9295965Abstract: Methods and apparatus relate to the synthesis of polynucleotides having a predefined sequence on a support. Assembly methods include primer extension to generate overlapping construction oligonucleotides and assembly of the polynucleotides of interest onto an anchor support-bound oligonucleotides. Methods and apparatus for selection of polynucleotides having the predefined sequence and/or length are disclosed.Type: GrantFiled: November 10, 2011Date of Patent: March 29, 2016Assignee: Gen9, Inc.Inventors: Joseph Jacobson, Li-yun A. Kung, Andrew Kirk Wilson, Senthil Ramu, Daniel Schindler, Mike Hudson
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Publication number: 20150368687Abstract: Aspects of the invention relate to methods, compositions for synthesizing high fidelity oligonucleotides.Type: ApplicationFiled: March 13, 2014Publication date: December 24, 2015Applicant: Gen9, Inc.Inventors: Ishtiaq E. Saaem, Michael E. Hudson, Stephen F. Archer, Sophea Sann-Rorth, Ellen J. Fanti, Joseph Jacobson
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Patent number: 9216414Abstract: Certain aspects of the present invention provide devices and methods for preparing oligonucleotides and for assembling nucleic acid molecules using microfluidic devices.Type: GrantFiled: November 19, 2010Date of Patent: December 22, 2015Assignee: Gen9, Inc.Inventor: Larry Li-Yang Chu
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Patent number: 9217144Abstract: Methods and apparatus relate to the synthesis of high fidelity polynucleotides and to the reduction of sequence errors generated during synthesis of nucleic acids on a solid support. Specifically, design of support-bound template oligonucleotides is disclosed. Assembly methods include cycles of annealing, stringent wash and extension of polynucleotides comprising a sequence region complementary to immobilized template oligonucleotides. The error free synthetic nucleic acids generated therefrom can be used for a variety of applications, including synthesis of biofuels and value-added pharmaceutical products.Type: GrantFiled: January 6, 2011Date of Patent: December 22, 2015Assignee: Gen9, Inc.Inventors: Joseph Jacobson, Larry Li-Yang Chu
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Patent number: 9187777Abstract: Disclosed are compositions, methods and devices for the in situ synthesis of nucleic acids. In an exemplary embodiment, a support-bound oligonucleotide is elongated by addition of one or more nucleotides by hybridization of a partially double-stranded oligonucleotide, ligation and removal of unwanted nucleotides.Type: GrantFiled: May 26, 2011Date of Patent: November 17, 2015Assignee: Gen9, Inc.Inventors: Joseph Jacobson, Senthil Ramu, Daniel Schindler
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Patent number: 9150853Abstract: Disclosed are methods, compositions and devices for screening a protein library for proteins having a desired activity, such as capable of catalyzing the formation of a bond between two reactants. In an exemplary embodiments, a plurality of proteins are expressed in vitro from a plurality of nucleic acids, the plurality of proteins are exposed with two single stranded oligonucleotides having complementary sequences, each oligonucleotide having a reactant and a fluorophore, the fluorescence of the protein-reactant-oligonucleotide-fluorophore complexes is detected and the complexes showing detectable fluorescence energy transfer are isolated, thereby isolating proteins having the desired enzymatic activity.Type: GrantFiled: March 13, 2013Date of Patent: October 6, 2015Assignee: Gen9, Inc.Inventors: Michael E. Hudson, Joseph Jacobson
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Publication number: 20150203839Abstract: Aspects of the invention relate to methods, compositions and algorithms for designing and producing a target nucleic acid. The method can include: (1) providing a plurality of blunt-end double-stranded nucleic acid fragments having a restriction enzyme recognition sequence at both ends thereof; (2) producing via enzymatic digestion a plurality of cohesive-end double-stranded nucleic acid fragments each having two different and non-complementary overhangs; (3) ligating the plurality of cohesive-end double-stranded nucleic acid fragments with a ligase; and (4) forming a linear arrangement of the plurality of cohesive-end double-stranded nucleic acid fragments, wherein the unique arrangement comprises the target nucleic acid.Type: ApplicationFiled: August 23, 2012Publication date: July 23, 2015Applicant: Gen9, Inc.Inventors: Joseph Jacobson, Daniel Schindler, Scott S. Lawton
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Patent number: 9051666Abstract: There is disclosed a process for in vitro synthesis and assembly of long, gene-length polynucleotides based upon assembly of multiple shorter oligonucleotides synthesized in situ on a microarray platform. Specifically, there is disclosed a process for in situ synthesis of oligonucleotide fragments on a solid phase microarray platform and subsequent, “on device” assembly of larger polynucleotides composed of a plurality of shorter oligonucleotide fragments.Type: GrantFiled: September 14, 2012Date of Patent: June 9, 2015Assignee: Gen9, Inc.Inventor: Andrew V. Oleinikov