Patents Examined by Catherine Konopka
  • Patent number: 11981892
    Abstract: The disclosure provides novel methods and compositions for gene editing. In particular, the disclosure relates to compositions and methods of making modified nucleic acid donor templates for highly efficient and precise gene editing.
    Type: Grant
    Filed: April 15, 2019
    Date of Patent: May 14, 2024
    Assignee: UNIVERSITY OF MASSACHUSETTS
    Inventors: Craig Cameron Mello, Krishna Sumanth Ghanta, Gregoriy Dokshin, Aamir Mir, Hassan Gneid, Jonathan Kenneth Watts, Erik Joseph Sontheimer
  • Patent number: 11976306
    Abstract: Thermostable Cas9 nucleases. The present invention relates to the field of genetic engineering and more particularly to nucleic acid editing and genome modification. The present invention provides an isolated Cas protein or polypeptide fragment thereof having an amino acid sequence of SEQ ID NO: 1 or a sequence of at least 77% identity therewith. The Cas protein or polypeptide is capable of binding, cleaving, marking or modifying a double stranded target polynucleotide at a temperature in the range 20° C. and 100° C. inclusive. The invention further provides isolated nucleic acid molecules encoding said Cas9 nucleases, expression vectors and host cells. The invention also provides PAM sequences recognized by the Cas protein or polypeptide, The Cas9 nucleases disclosed herein provide novel tools for genetic engineering in general, in particular at elevated temperatures.
    Type: Grant
    Filed: August 16, 2017
    Date of Patent: May 7, 2024
    Assignees: Stichting Voor De Technische Wetenschappen, WAGENINGEN UNIVERSITEIT
    Inventors: John Van Der Oost, Richard Van Kranenburg, Elleke Fenna Bosma, Ioannis Mougiakos, Prarthana Mohanraju
  • Patent number: 11970711
    Abstract: The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and/or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and/or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.
    Type: Grant
    Filed: September 21, 2021
    Date of Patent: April 30, 2024
    Assignees: The Regents of the University of California, University of Vienna
    Inventors: Jennifer A. Doudna, Martin Jinek, Krzysztof Chylinski, Emmanuelle Charpentier
  • Patent number: 11946067
    Abstract: The present invention concerns a genetic tool comprising at least two distinct nucleic acids optimized to facilitate the transformation and modification by homologous recombination of a bacterium of the genus Clostridium, typically a solventogenic bacterium.
    Type: Grant
    Filed: May 24, 2019
    Date of Patent: April 2, 2024
    Assignee: IFP ENERGIES NOUVELLES
    Inventors: Nicolas Lopes Ferreira, François Wasels, Gwladys Chartier
  • Patent number: 11920151
    Abstract: Provided are: a composition for DNA double-strand breaks (DSBs), comprising (1) a cytosine deaminase and an inactivated target-specific endonuclease, (2) a guide RNA, and (3) a uracil-specific excision reagent (USER); a method for producing DNA double-strand breaks by means of a cytosine deaminase using the composition; a method for analyzing a DNA nucleic acid sequence to which base editing has been introduced by means of a cytosine deaminase; and a method for identifying (or measuring or detecting) base editing, base editing efficiency at an on-target site, an off-target site, and/or target specificity by means of a cytosine deaminase.
    Type: Grant
    Filed: September 13, 2017
    Date of Patent: March 5, 2024
    Assignees: TOOLGEN INCORPORATED, SEOUL NATIONAL UNIVERSITY R&Db FOUNDATION, INSTITUTE FOR BASIC SCIENCE
    Inventor: Daesik Kim
  • Patent number: 11913081
    Abstract: A proximity dependent split T7 RNAP (RNA polymerase) sensor using continuous molecular evolution is described. The versatility of the platform is described by creating robust light and small molecule-responsive genetic sensors. The activity-responsive RNAP platform dramatically simplifies and expands genetic circuit creation, and opens new opportunities in protein engineering, synthetic biology, and bioengineering.
    Type: Grant
    Filed: June 6, 2017
    Date of Patent: February 27, 2024
    Assignee: The University of Chicago
    Inventors: Bryan C. Dickinson, Jinyue Pu, Julia Zinkus
  • Patent number: 11913017
    Abstract: A guide RNA comprising: a gRNA spacer sequence at the 5? end of the guide RNA, wherein the spacer sequence is complementary to a target gene, a scaffold sequence that binds to Cas9, and an RNA capture and sequencing domain comprising: a barcode sequence, and a primer binding sequence; nucleic acids and vectors encoding the guide RNA; cells expressing the guide RNA; and a library comprising a plurality of guide RNAs. Also disclosed are methods of introducing a genetic perturbation into a cell, methods of assessing an effect of at least one genetic perturbation on RNA expression in a cell, methods of identifying nucleic acid sequences associated with a disease state and a method of identifying candidate therapeutic agents.
    Type: Grant
    Filed: June 28, 2017
    Date of Patent: February 27, 2024
    Assignee: The Regents of the University of California
    Inventors: Kun Zhang, Prashant Mali, Yan Wu, Dongxin Zhao
  • Patent number: 11905549
    Abstract: Provided is a method of modifying a target site in the genome of a eukaryotic cell, the method comprising: (1) a step of introducing into the cell, introduction nucleic acids comprising (a) a template nucleic acid comprising a nucleic acid sequence encoding an RNA-guided nuclease, (b) a template nucleic acid comprising a nucleic acid sequence encoding a guide RNA, or a guide RNA, and (c) a template nucleic acid comprising a nucleic acid sequence encoding a selectable marker; and (2) a step of selecting a cell expressing the selectable marker, wherein the number of moles (C) of (c) the template nucleic acid comprising a nucleic acid sequence encoding a selectable marker, subjected to the step (1), is smaller than any of the number of moles (A) of (a) the template nucleic acid comprising a nucleic acid sequence encoding an RNA-guided nuclease and the number of moles (B) of (b) the template nucleic acid comprising a nucleic acid sequence encoding a guide RNA, or the guide RNA.
    Type: Grant
    Filed: August 9, 2017
    Date of Patent: February 20, 2024
    Assignee: GENAHEAD BIO, INC.
    Inventor: Tsukasa Sugo
  • Patent number: 11896678
    Abstract: The present disclosure provides compositions and methods for the treatment of PPARG activated cancer. For example, the present disclosure provides PPARG signaling modulators for the treatment of bladder cancer. In particular, therapeutic and/or prophylactic compositions and uses of PPARG inverse-agonists are described.
    Type: Grant
    Filed: March 28, 2018
    Date of Patent: February 13, 2024
    Assignees: Dana-Farber Cancer Institute, Inc., The Broad Institute, Inc.
    Inventors: Jonathan Goldstein, Matthew Meyerson, Craig Strathdee
  • Patent number: 11879134
    Abstract: A native Type I-B and heterologous Type II Clustered Regularly-Interspaced Short Palindromic Repeat/cas systems were developed and characterize to improve the ability to engineer C. thermocellum and other thermophilic microbes. The native Type I-B system was engineered for genome editing. For the Type I-B system, an engineered strain, termed LL1586, yielded 40% genome editing efficiency at the pyrF locus. When recombineering machinery was expressed the efficiency was increased to 71%. For the Type II GeoCas9 system, 12.5% genome editing efficiency was observed. When recombineering machinery was expressed, this increased to 94%. By combining the thermophilic CRISPR system (either Type I-B or Type II) with the recombinases, a new tool was developed that allows for efficient CRISPR editing. The tools provided herein enable CRISPR technologies to better engineer C. thermocellum, including engineering C. thermocellum for both increased lignocellulose degradation and biofuel production.
    Type: Grant
    Filed: September 4, 2020
    Date of Patent: January 23, 2024
    Assignee: The Regents of the University of Colorado, a body corporate
    Inventors: Carrie Eckert, Julie E. Walker
  • Patent number: 11873485
    Abstract: Programmable guide RNAs (gRNAs) play a central role in the CRISPR revolution sweeping biology and medicine by directing the function of a Cas protein effector to a target gene of choice. To achieve programmable control over regulatory scope, the activity of a conditional guide RNA (cgRNA) depends on the presence or absence of an RNA trigger, allowing for cell-selective regulation of CRISPR/Cas function. Unlike a standard gRNA, a cgRNA is programmable at multiple levels, with the target-binding sequence controlling the target of Cas activity (edit, silence, induce, or bind a gene of choice) and the trigger binding sequence controlling the scope of Cas activity. cgRNA mechanisms that are allosteric allow for independent design of the target and trigger sequences, providing the flexibility to select the regulatory target and scope independently.
    Type: Grant
    Filed: January 25, 2022
    Date of Patent: January 16, 2024
    Assignee: California Institute of Technology
    Inventors: Lisa Hochrein, Mikhail H. Hanewich-Hollatz, Zhewei Chen, Heyun Li, Shashank Gandhi, Marianne Bronner, Niles A. Pierce
  • Patent number: 11866726
    Abstract: Disclosed herein are genome editing systems and related methods which allow for the detection and quantitative measurement of all possible on-target gene editing outcomes, including targeted integration. The compositions and methods described herein rely on the use of donor templates comprising a 5? homology arm, a cargo, a one or more priming sites, a 3? homology arm, and optionally stuffer sequence.
    Type: Grant
    Filed: July 13, 2018
    Date of Patent: January 9, 2024
    Assignee: Editas Medicine, Inc.
    Inventors: Cecilia Cotta-Ramusino, Carrie M. Margulies
  • Patent number: 11859232
    Abstract: A method of selecting an agent for treating a disease of a subject is disclosed which includes identifying genes which bring about resistance to a cytotoxic agent in haploid human embryonic stem (ES) cells. Once the gene is identified, the method includes analyzing the sequence and/or expression of the gene in a cell sample of the subject, wherein an alteration in the sequence and/or level of expression of the gene as compared to the sequence and/or expression of the gene in a control sample is indicative that the agent should be ruled out as a monotherapy for treating the disease in the subject.
    Type: Grant
    Filed: June 19, 2016
    Date of Patent: January 2, 2024
    Assignee: YISSUM RESEARCH DEVELOPMENT COMPANY OF THE HEBREW UNIVERSITY OF JERUSALEM LTD.
    Inventor: Nissim Benvenisty
  • Patent number: 11845929
    Abstract: The present disclosure generally relates to genome editing systems and methods and compounds and compositions for use in Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) genome editing systems. Disclosed herein are modified nucleic acids that modulate the activity of genome editing.
    Type: Grant
    Filed: July 7, 2017
    Date of Patent: December 19, 2023
    Assignee: OHIO STATE INNOVATION FOUNDATION
    Inventors: Yizhou Dong, Bin Li
  • Patent number: 11840694
    Abstract: The present invention relates to a polypeptide comprising at least one at least one deletion selected from the group consisting of ?HNH (?775-909), ARuvCIII-b (?1002-1074), AREC1-a (?510-655), AREC1-b (?525-587), AREC1-c (?662-710), AREC2 (?180-308), AREC2-a (?212-244), AREC2-b (?244-276), AREC2-c (?276-308), AREC2-d (?199-283), AREC2-e (?198-257), AREC2-f (?235-286), AREC2-g (?217-266), AREC3 (?498-712) and combinations thereof, wherein the position numbering is in accordance with SEQ ID NO: 1 encoding for S. pyogenes Cas9, and wherein the polypeptide has CRISPR-Cas DNA-binding activity. The polypeptide may further comprises a missense mutations selected from G12R, T13K, T13R, N14K, N497K, T657K, T657R, N767K, T770K, T770R, Q920K, Q920R, S1109R, D1135K, D1135R, S1338R and combinations thereof. Also claimed are nucleic acid molecules encoding for said polypeptides, compositions and method of site-directed engineering of a target DNA thereof.
    Type: Grant
    Filed: October 17, 2017
    Date of Patent: December 12, 2023
    Assignees: NANYANG TECHNOLOGICAL UNIVERSITY, AGENCY FOR SCIENCE, TECHNOLOGY AND RESEARCH
    Inventors: Meng How Tan, Kean Hean Ooi
  • Patent number: 11833225
    Abstract: Provided herein are gene-editing methods and compositions for improving the efficiency of deleting segments of DNA from cells, cells that are genetically modified using the disclosed methods and compositions, and methods of treatment using the genetically modified cells.
    Type: Grant
    Filed: May 24, 2019
    Date of Patent: December 5, 2023
    Assignee: CRISPR THERAPEUTICS AG
    Inventors: Elizabeth Paik, Mauricio Cortes
  • Patent number: 11827676
    Abstract: The present invention refers to methods for selectively recognizing a base pair in a DNA sequence by a polypeptide, to modified polypeptides which specifically recognize one or more base pairs in a DNA sequence and, to DNA which is modified so that it can be specifically recognized by a polypeptide and to uses of the polypeptide and DNA in specific DNA targeting as well as to methods of modulating expression of target genes in a cell.
    Type: Grant
    Filed: February 4, 2020
    Date of Patent: November 28, 2023
    Inventors: Ulla Bonas, Jens Boch, Sebastian Schornack, Thomas Lahaye
  • Patent number: 11814645
    Abstract: The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and/or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and/or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.
    Type: Grant
    Filed: April 1, 2021
    Date of Patent: November 14, 2023
    Assignees: The Regents of the University of California, University of Vienna
    Inventors: Jennifer A. Doudna, Martin Jinek, Krzysztof Chylinski, Emmanuelle Charpentier
  • Patent number: 11807869
    Abstract: A CRISPR-Cas3 system was successfully established in a eukaryotic cell.
    Type: Grant
    Filed: June 8, 2018
    Date of Patent: November 7, 2023
    Assignee: OSAKA UNIVERSITY
    Inventors: Tomoji Mashimo, Junji Takeda, Hiroyuki Morisaka, Kazuto Yoshimi
  • Patent number: 11795453
    Abstract: The present invention relates to compositions and methods for increasing the rate of site specific insertion of a donor DNA sequence to the genome. More specifically, the method introduces a donor DNA template containing at least one transcription factor binding site to a cell in order to favor specific insertion of a donor template sequence at a target site by homology directed repair (HDR).
    Type: Grant
    Filed: October 30, 2017
    Date of Patent: October 24, 2023
    Assignee: EMENDOBIO, INC.
    Inventors: David Baram, Lior Izhar, Rafi Emmanuel