Patents by Inventor Jennifer A. Doudna

Jennifer A. Doudna 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).

  • CRISPR-CAS EFFECTOR POLYPEPTIDES AND METHODS OF USE THEREOF
    Publication number: 20210301271
    Abstract: The present disclosure provides RNA-guided CRISPR-Cas effector proteins, nucleic acids encoding same, and compositions comprising same. The present disclosure provides ribonucleoprotein complexes comprising: an RNA-guided CRISPR-Cas effector protein of the present disclosure; and a guide RNA. The present disclosure provides methods of modifying a target nucleic acid, using an RNA-guided CRISPR-Cas effector protein of the present disclosure and a guide RNA. The present disclosure provides methods of modulating transcription of a target nucleic acid.
    Type: Application
    Filed: April 8, 2021
    Publication date: September 30, 2021
    Inventors: Jennifer A. Doudna, Basem Al-Shayeb, Jillian F. Banfield, Patrick Pausch
  • RNA-GUIDED NUCLEIC ACID MODIFYING ENZYMES AND METHODS OF USE THEREOF
    Publication number: 20210284981
    Abstract: The present disclosure provides CasX proteins, nucleic acids encoding the CasX proteins, and modified host cells comprising the CasX proteins and/or nucleic acids encoding same CasX proteins are useful in a variety of applications, which are provided. The present disclosure provides CasX guide RKAs that bind to and provide sequence specificity to the CasX proteins, nucleic acids encoding the CasX guide RNAs, and modified host cells comprising the CasX guide RNAs and/or nucleic acids encoding same. CasX guide RNAs are useful in a variety of applications, which are provided. The present disclosure provides archaeal Cas9 polypeptides and nucleic acids encoding same, as well as their associated archaeal Cas9 guide RNAs and nucleic acids encoding same.
    Type: Application
    Filed: July 23, 2019
    Publication date: September 16, 2021
    Inventors: Jennifer A. Doudna, Jillian F. Banfield, David Burstein, Steven C. Strutt, Lucas Benjamin Harrington
  • Type V CRISPR/Cas effector proteins for cleaving ssDNAs and detecting target DNAs
    Patent number: 11118224
    Abstract: Provided are compositions and methods for detecting a target DNA (double stranded or single stranded) in a sample. In some embodiments, a subject method includes: (a) contacting the sample with: (i) a type V CRISPR/Cas effector protein (e.g., a Cas12 protein such as Cas12a, Cas12b, Cas12c, Cas12d, Cas12e); (ii) a guide RNA (comprising a region that binds to the type V CRISPR/Cas effector protein, and a guide sequence that hybridizes with the target DNA); and (iii) a detector DNA that is single stranded (i.e., a “single stranded detector DNA”) and does not hybridize with the guide sequence of the guide RNA; and (b) measuring a detectable signal produced by cleavage (by the type V CRISPR/Cas effector protein) of the single stranded detector DNA. Also provided are compositions and methods for cleaving single stranded DNAs (e.g., non-target ssDNAs), e.g., inside of a cell.
    Type: Grant
    Filed: June 9, 2020
    Date of Patent: September 14, 2021
    Assignee: The Regents of the University of California
    Inventors: Jennifer A. Doudna, Janice S. Chen, Lucas Benjamin Harrington, Enbo Ma
  • Modified site-directed modifying polypeptides and methods of use thereof
    Patent number: 11118194
    Abstract: The present disclosure provides modified site-directed modifying polypeptides, and ribonucleoproteins comprising the modified polypeptides. The modified site-directed modifying polypeptides are modified for passive entry into target cells. The modified site-directed modifying polypeptides are useful in a variety of methods for target nucleic acid modification, which methods are also provided.
    Type: Grant
    Filed: December 15, 2016
    Date of Patent: September 14, 2021
    Assignee: The Regents of the University of California
    Inventors: Jennifer A. Doudna, Brett T. Staahl, Anirvan Ghosh
  • METHODS FOR DETECTING AND SEQUENCING A TARGET NUCLEIC ACID
    Publication number: 20210269858
    Abstract: The present disclosure provides methods for characterizing a target DNA present in a sample. The methods involve contacting the sample with a type V CRISPR/Cas effector protein and one or more guide RNAs, where the contacting generates a cleavage product comprising a 5? overhang; and ligating a double-stranded nucleic acid adapter to the cleavage product, to generate a ligation product. The ligation product includes the target DNA, which can be sequenced. The sample can be subjected to one or more amplification steps prior to the contacting step, with primers that provide for amplification of nucleic acids of, e.g., specific pathogens, categories of pathogens, two or more different pathogens, or two or more different categories of pathogens.
    Type: Application
    Filed: May 13, 2021
    Publication date: September 2, 2021
    Inventors: Charles Chiu, Andrea Granados, Jennifer A. Doudna, Lucas B. Harrington, Janice S. Chen, Xianding Deng
  • RNA-GUIDED EFFECTOR PROTEINS AND METHODS OF USE THEREOF
    Publication number: 20210269782
    Abstract: The present disclosure provides an RNA-guided effector polypeptide having a length that is less than Streptococcus pyogenes Cas9, and that retains the ability, when complexed with a guide RNA, to bind to a target nucleic acid. The present disclosure provides a fusion polypeptide comprising: i) an RNA-guided effector polypeptide of the present disclosure; and ii) a fusion partner. The present disclosure further provides nucleic acids encoding an RNA-guided effector polypeptide, or a fusion polypeptide, of the present disclosure. Methods of using an RNA-guided effector polypeptide, or a fusion polypeptide, of the present disclosure are also provided.
    Type: Application
    Filed: June 25, 2019
    Publication date: September 2, 2021
    Inventors: Jennifer A. Doudna, David Frank Savage, Sean A. Higgins, Benjamin L. Oakes
  • CRISPR-CAS EFFECTOR POLYPEPTIDES AND METHODS OF USE THEREOF
    Publication number: 20210254038
    Abstract: The present disclosure provides RNA-guided CRISPR-Cas effector proteins, nucleic acids encoding same, and compositions comprising same. The present disclosure provides ribonucleoprotein complexes comprising: an RNA-guided CRISPR-Cas effector protein of the present disclosure; and a guide RNA. The present disclosure provides methods of modifying a target nucleic acid, using an RNA-guided CRISPR-Cas effector protein of the present disclosure and a guide RNA. The present disclosure provides methods of modulating transcription of a target nucleic acid.
    Type: Application
    Filed: May 5, 2021
    Publication date: August 19, 2021
    Inventors: Jennifer A. Doudna, Basem Al-Shayeb, Jillian F. Banfield, Patrick Pausch
  • CRISPR-CAS EFFECTOR POLYPEPTIDES AND METHODS OF USE THEREOF
    Publication number: 20210238567
    Abstract: The present disclosure provides RNA-guided CRISPR-Cas effector proteins, nucleic acids encoding same, and compositions comprising same. The present disclosure provides ribonucleoprotein complexes comprising: an RNA-guided CRISPR-Cas effector protein of the present disclosure; and a guide RNA. The present disclosure provides methods of modifying a target nucleic acid, using an RNA-guided CRISPR-Cas effector protein of the present disclosure and a guide RNA. The present disclosure provides methods of modulating transcription of a target nucleic acid.
    Type: Application
    Filed: April 13, 2021
    Publication date: August 5, 2021
    Inventors: Jennifer A. Doudna, Basem Al-Shayeb, Jillian F. Banfield, Patrick Pausch
  • METHODS AND COMPOSITIONS FOR RNA-DIRECTED TARGET DNA MODIFICATION AND FOR RNA-DIRECTED MODULATION OF TRANSCRIPTION
    Publication number: 20210230639
    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: Application
    Filed: April 1, 2021
    Publication date: July 29, 2021
    Inventors: Jennifer A. Doudna, Martin Jinek, Krzysztof Chylinski, Emmanuelle Charpentier
  • METHODS AND COMPOSITIONS FOR RNA-DIRECTED TARGET DNA MODIFICATION AND FOR RNA-DIRECTED MODULATION OF TRANSCRIPTION
    Publication number: 20210222205
    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: Application
    Filed: April 1, 2021
    Publication date: July 22, 2021
    Inventors: Jennifer A. Doudna, Martin Jinek, Krzysztof Chylinski, Emmanuelle Charpentier
  • CLASS 2 CRISPR/CAS COMPOSITIONS AND METHODS OF USE
    Publication number: 20210214697
    Abstract: Provided are compositions and methods that include one or more of: (1) a Class 2 CRISPR/Cas effector protein, a nucleic acid encoding the effector protein, and/or a modified host cell comprising the effector protein (and/or a nucleic acid encoding the same); (2) a CRISPR/Cas guide RNA that binds to and provides sequence specificity to the Class 2 CRISPR/Cas effector protein, a nucleic acid encoding the CRISPR/Cas guide RNA, and/or a modified host cell comprising the CRISPR/Cas guide RNA (and/or a nucleic acid encoding the same); and (3) a CRISPR/Cas transactivating noncoding RNA (trancRNA), a nucleic acid encoding the CRISPR/Cas trancRNA, and/or a modified host cell comprising the CRISPR/Cas trancRNA (and/or a nucleic acid encoding the same).
    Type: Application
    Filed: October 31, 2018
    Publication date: July 15, 2021
    Inventors: Jennifer A. Doudna, David Burstein, Janice S. Chen, Lucas B. Harrington, David Paez-Espino, Jillian F. Banfield
  • Methods and compositions for nucleic acid integration
    Patent number: 11053271
    Abstract: The disclosure provides methods and compositions for the integration (insertion) of a donor DNA molecule into a target DNA molecule. In general, the methods include contacting a target DNA molecule with a linear donor DNA molecule and a Cas 1 protein, where the target DNA molecule includes an AT-rich region (e.g., in some cases positioned 5 and within 50 nucleotides of a region that forms a DNA cruciform structure), where the contacting is not in a bacterial or archaeal cell (e.g., the contacting is in vitro outside of a cell, inside of a eukaryotic cell, etc.), and provides for integration of the donor DNA molecule into the target DNA molecule.
    Type: Grant
    Filed: December 21, 2015
    Date of Patent: July 6, 2021
    Assignee: The Regents of the University of California
    Inventors: James K. Nunez, Jennifer A. Doudna
  • Methods of generating nucleic acid fragments
    Patent number: 11046941
    Abstract: Provided herein are methods of using a Cas1 polypeptide to generate nucleic fragments from a DNA substrate. These methods may be performed in vitro or in vivo. Also provided are methods of screening for modulators of Cas1.
    Type: Grant
    Filed: October 1, 2018
    Date of Patent: June 29, 2021
    Assignee: The Regents of the University of California
    Inventors: Blake Wiedenheft, Kaihong Zhou, Jennifer A. Doudna
  • Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription
    Patent number: 11028412
    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: October 29, 2020
    Date of Patent: June 8, 2021
    Assignees: The Regents of the University of California, University of Vienna
    Inventors: Jennifer A. Doudna, Martin Jinek, Krzysztof Chylinski, Emmanuelle Charpentier
  • Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription
    Patent number: 11008589
    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: November 23, 2020
    Date of Patent: May 18, 2021
    Assignees: The Regents of the University of California, University of Vienna
    Inventors: Jennifer A. Doudna, Martin Jinek, Krzysztof Chylinski, Emmanuelle Charpentier
  • Variant Cas9 polypeptides comprising internal insertions
    Patent number: 11008555
    Abstract: The present disclosure provides variant Cas9 polypeptides, where a variant Cas9 polypeptide of the present disclosure comprises an internal insertion of a heterologous polypeptide. The present disclosure provides nucleic acids comprising nucleotide sequences encoding the variant Cas9 polypeptides. The present disclosure provides host cells comprising a variant Cas9 polypeptide of the present disclosure, or comprising a nucleic acid encoding a variant Cas9 polypeptide of the present disclosure. The present disclosure provides methods of binding and/or modifying a target nucleic acid, involving use of a variant Cas9 polypeptide of the present disclosure.
    Type: Grant
    Filed: September 15, 2016
    Date of Patent: May 18, 2021
    Assignee: The Regents of the University of California
    Inventors: Benjamin Oakes, David Savage, Dana Nadler, Abraham I. Flamholz, Jennifer A. Doudna
  • Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription
    Patent number: 11008590
    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: November 23, 2020
    Date of Patent: May 18, 2021
    Assignees: The Regents of The University of California, University of Vienna, Emmanuelle Charpentier
    Inventors: Jennifer A. Doudna, Martin Jinek, Krzysztof Chylinski, Emmanuelle Charpentier
  • Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription
    Patent number: 11001863
    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: November 23, 2020
    Date of Patent: May 11, 2021
    Assignees: The Regents of the University of California, University of Vienna, Emmanuelle Charpentier
    Inventors: Jennifer A. Doudna, Martin Jinek, Krzysztof Chylinski, Emmanuelle Charpentier
  • Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription
    Patent number: 10988780
    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: July 21, 2020
    Date of Patent: April 27, 2021
    Assignees: The Regents of the University of California, University of Vienna
    Inventors: Jennifer A. Doudna, Martin Jinek, Krzysztof Chylinski, Emmanuelle Charpentier
  • Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription
    Patent number: 10988782
    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: October 29, 2020
    Date of Patent: April 27, 2021
    Assignees: The Regents of the University of California, University of Vienna, Emmanuelle Charpentier
    Inventors: Jennifer A. Doudna, Martin Jinek, Krzysztof Chylinski, Emmanuelle Charpentier