Patents by Inventor Jonathan S. Gootenberg
Jonathan S. Gootenberg 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).
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Publication number: 20240100192Abstract: This disclosure provides systems, methods, and compositions for site specific genetic engineering comprising the use of CRISPR effectors and trans-splicing. The disclosure also relates to methods of using the systems and compositions for treating diseases as well as diagnostics.Type: ApplicationFiled: August 24, 2023Publication date: March 28, 2024Inventors: Omar Osama Abudayyeh, Jonathan S. Gootenberg, Wenyuan Zhou, Alisan Kayabolen, Cian Franz Schmitt-Ulms
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Publication number: 20240084364Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA-targeting systems comprising a novel DNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA Methods for making and using and uses of such systems, methods, and compositions and products from such methods and uses are also disclosed and claimed.Type: ApplicationFiled: August 17, 2023Publication date: March 14, 2024Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows of Harvard CollegeInventors: Feng ZHANG, Bernd ZETSCHE, Jonathan S. GOOTENBERG, Omar O. ABUDAYYEH, Ian SLAYMAKER
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Publication number: 20230383288Abstract: This disclosure provides systems, methods, and compositions for RNA-guided RNA-targeting CRISPR effectors for the treatment of diseases, and for use as diagnostics. In addition, nucleotide deaminase functionalized CRISPR systems for RNA editing RNA knockdown, viral resistance, splicing modulation, RNA tracking, translation modulation, and epi-transcriptomic modifications are disclosed.Type: ApplicationFiled: May 24, 2023Publication date: November 30, 2023Inventors: Omar Osama Abudayyeh, Jonathan S. Gootenberg, Wenyuan Zhou, Hiroshi Nishimasu, Kazuki Kato, Cian Franz Schmitt-Ulms
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Patent number: 11781172Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA-targeting systems comprising a novel DNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA. Methods for making and using and uses of such systems, methods, and compositions and products from such methods and uses are also disclosed and claimed.Type: GrantFiled: April 30, 2019Date of Patent: October 10, 2023Assignees: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, PRESIDENT AND FELLOWS OF HARVARD COLLEGEInventors: Feng Zhang, Bernd Zetsche, Jonathan S. Gootenberg, Omar O. Abudayyeh, Ian Slaymaker
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Patent number: 11773412Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered RNA-targeting systems comprising a novel RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.Type: GrantFiled: June 24, 2022Date of Patent: October 3, 2023Assignees: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows of Harvard College, Rutgers, the State University of New Jersey, Skolkovo Institute of Science and Technology, The United States of America, as represented by the Secretary, Department of Health and Human ServicesInventors: Konstantin Severinov, Feng Zhang, Yuri I. Wolf, Sergey Shmakov, Ekaterina Semenova, Leonid Minakhin, Kira S. Makarova, Eugene Koonin, Silvana Konermann, Julia Joung, Jonathan S. Gootenberg, Omar O. Abudayyeh, Eric S. Lander
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Publication number: 20230123513Abstract: RNA editing tools for use in systems designed to measure RNA in vivo and manipulate specific cell types are disclosed herein. An RNA sensor system comprising a) a single-stranded RNA (ssRNA) sensor comprising a stop codon and a payload; optionally wherein the ssRNA sensor further comprises a normalizing gene; and b) an adenosine deaminase acting on RNA (ADAR) deaminase; wherein the sensor is capable of binding to a ssRNA target to form a double-stranded RNA (dsRNA) duplex that becomes a substrate for the ADAR deaminase; wherein the substrate comprises a mispairing within the stop codon; and wherein the mispairing is editable by the ADAR deaminase, which editing can effectively remove the stop codon so as to enable translation and expression of the payload. A method of quantifying ribonucleic acid (RNA) levels using the RNA sensor system is also disclosed.Type: ApplicationFiled: June 14, 2022Publication date: April 20, 2023Inventors: Kaiyi Jiang, Rohan Neil Krajeski, Omar Osama Abudayyeh, Jonathan S. Gootenberg, Yifan Zhang, Fei Chen, Xi Chen, Jeremy G. Koob
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Publication number: 20230045095Abstract: This disclosure provides compositions, methods, and systems comprising a papillomaviral delivery vehicle for the delivery of gene editing material to cells. The papillomaviral delivery vehicle comprises a papillomavirus-derived capsid and DNA encoding a gene editing material encapsulated by the capsid. The papillomaviral delivery vehicle can be transduced into a cell under conditions conducive for the cell to synthesize the gene editing material. The cell can comprise a polynucleotide target and the gene editing material can target the polynucleotide target. The polynucleotide target can be a DNA polynucleotide target or RNA polynucleotide target.Type: ApplicationFiled: June 17, 2022Publication date: February 9, 2023Inventors: Omar Osama Abudayyeh, Jonathan S. Gootenberg
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Publication number: 20220372525Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered RNA-targeting systems comprising a novel RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.Type: ApplicationFiled: June 24, 2022Publication date: November 24, 2022Inventors: Konstantin Severinov, Feng Zhang, Yuri I. Wolf, Sergey Shmakov, Ekaterina Semenova, Leonid Minakhin, Kira S. Makarova, Eugene Koonin, Silvana Konermann, Julia Joung, Jonathan S. Gootenberg, Omar O. Abudayyeh, Eric S. Lander
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Patent number: 11421250Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered RNA-targeting systems comprising a novel RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.Type: GrantFiled: December 16, 2017Date of Patent: August 23, 2022Assignees: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows of Harvard College, Rutgers, The State University of New Jersey, Skolkovo Institute of Science and Technology, The United States of America, as represented by the Secretary, Department of Health and Human ServicesInventors: Konstantin Severinov, Feng Zhang, Yuri I. Wolf, Sergey Shmakov, Ekaterina Semenova, Leonid Minakhin, Kira S. Makarova, Eugene Koonin, Silvana Konermann, Julia Joung, Jonathan S. Gootenberg, Omar O. Abudayyeh, Eric S. Lander
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Patent number: 11180751Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA or RNA-targeting systems comprising a novel DNA or RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.Type: GrantFiled: December 14, 2017Date of Patent: November 23, 2021Assignees: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows of Harvard College, Rutgers, the State University of New Jersey, The United States of America, as represented by the Secretary, Department of Health and Human Services, Skolkovo Institute of Science and TechnologyInventors: Eugene Koonin, Feng Zhang, Yuri I. Wolf, Sergey Shmakov, Konstantin Severinov, Ekaterina Semenova, Leonid Minakhin, Kira S. Makarova, Silvana Konermann, Julia Joung, Jonathan S. Gootenberg, Omar O. Abudayyeh
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Publication number: 20210348157Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA or RNA-targeting systems comprising a novel DNA or RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.Type: ApplicationFiled: April 30, 2021Publication date: November 11, 2021Inventors: Eugene Koonin, Feng Zhang, Yuri I. Wolf, Sergey Shmakov, Konstantin Severinov, Ekaterina Semenova, Leonid Minakhin, Kira S. Makarova, Silvana Konermann, Julia Joung, Jonathan S. Gootenberg, Omar O. Abudayyeh
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Publication number: 20210348156Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA or RNA-targeting systems comprising a novel DNA or RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.Type: ApplicationFiled: April 30, 2021Publication date: November 11, 2021Inventors: Eugene Koonin, Feng Zhang, Yuri I. Wolf, Sergey Shmakov, Konstantin Severinov, Ekaterina Semenova, Leonid Minakhin, Kira S. Makarova, Silvana Konermann, Julia Joung, Jonathan S. Gootenberg, Omar O. Abudayyeh
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Patent number: 11091798Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA-targeting systems comprising a novel DNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA. Methods for making and using and uses of such systems, methods, and compositions and products from such methods and uses are also disclosed and claimed.Type: GrantFiled: July 27, 2018Date of Patent: August 17, 2021Assignees: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, PRESIDENT AND FELLOWS OF HARVARD COLLEGEInventors: Feng Zhang, Bernd Zetsche, Jonathan S. Gootenberg, Omar O. Abudayyeh, Ian Slaymaker
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Patent number: 11060115Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered RNA-targeting systems comprising a novel RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.Type: GrantFiled: April 7, 2017Date of Patent: July 13, 2021Assignees: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows of Harvard College, Rutgers, the State University of New Jersey, Skolkovo Institute of Science and Technology, The United States of America, as represented by the Secretary, Department of Health and Human ServicesInventors: Konstantin Severinov, Feng Zhang, Yuri I. Wolf, Sergey Shmakov, Ekaterina Semenova, Leonid Minakhin, Kira S. Makarova, Eugene Koonin, Silvana Konermann, Julia Joung, Jonathan S. Gootenberg, Omar O. Abudayyeh, Eric S. Lander
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Publication number: 20210040546Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA-targeting systems comprising a novel DNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA. Methods for making and using and uses of such systems, methods, and compositions and products from such methods and uses are also disclosed and claimed.Type: ApplicationFiled: September 28, 2020Publication date: February 11, 2021Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows of Harvard CollegeInventors: Feng ZHANG, Bernd ZETSCHE, Jonathan S. GOOTENBERG, Omar O. ABUDAYYEH, Ian SLAYMAKER
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Publication number: 20200308560Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered RNA-targeting systems comprising a novel RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.Type: ApplicationFiled: June 26, 2018Publication date: October 1, 2020Inventors: Feng Zhang, Omar O. Abudayyeh, David Benjamin Turitz Cox, Jonathan S. Gootenberg
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Publication number: 20200231975Abstract: The present disclosure provides for systems, methods, and compositions for targeting nucleic acids. In particular, the disclosure provides non-naturally occurring or engineered RNA-targeting systems comprising a novel RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.Type: ApplicationFiled: July 17, 2018Publication date: July 23, 2020Inventors: Jonathan S. Gootenberg, Omar O. Abudayyeh, Feng Zhang
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Publication number: 20200165594Abstract: The present invention offers a new approach for highly multiplexed, programmable antiviral therapies that directly target viral RNA, and can be flexibly adapted to target novel viruses or emerging outbreak pathogens. Class 2, type VI CRISPR system-based therapies can be used in combination with existing antiviral compounds for viruses where such compounds exist, either by increasing their efficacy or by preventing the evolution of specific drug resistance mutations. Perhaps most excitingly, if a virus evolves resistance to a specific guide RNA sequence, it is easy to switch to a different guide RNA sequence, or to design a new guide sequence to target the new mutation. Such approaches should prevent the widespread development of resistance to Class 2, type VI CRISPR system-based therapies.Type: ApplicationFiled: July 6, 2018Publication date: May 28, 2020Applicants: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, PRESIDENT AND FELLOWS OF HARVARD COLLEGEInventors: Feng Zhang, Jonathan S. Gootenberg, Omar O. Abudayyeh, Pardis Sabeti, Cameron Myhrvold, Catherine Amanda Freije
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Patent number: 10648020Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA-targeting systems comprising a novel DNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA. Methods for making and using and uses of such systems, methods, and compositions and products from such methods and uses are also disclosed and claimed.Type: GrantFiled: December 17, 2017Date of Patent: May 12, 2020Assignees: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, PRESIDENT AND FELLOWS OF HARVARD COLLEGEInventors: Feng Zhang, Bernd Zetsche, Jonathan S. Gootenberg, Omar O Abudayyeh, Ian Slaymaker
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Publication number: 20190382800Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered RNA-targeting systems comprising a novel RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.Type: ApplicationFiled: June 24, 2019Publication date: December 19, 2019Inventors: Konstantin Severinov, Feng Zhang, Yuri I. Wolf, Sergey Shmakov, Ekaterina Semenova, Leonid Minakhin, Kira S. Makarova, Eugene Koonin, Silvana Konermann, Julia Joung, Jonathan S. Gootenberg, Omar O. Abudayyeh, Eric S. Lander