Patents Examined by Jennifer Dunston
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Patent number: 11898141Abstract: Disclosed is a method of generating a set of sequence-verified nucleic acid elements for the combinatorial construction of genetic elements. The method includes: providing a plurality of nucleic acid parts; assembling nucleic acid parts to form a one or more nucleic acid elements, wherein the nucleic acid elements include at least two sequences selected from the plurality of parts; and determining the sequence of the nucleic acid elements. Further disclosed is a pool of higher-order nucleic acid constructs or amplification products thereof, comprising one or more nucleic acid elements as well as kits including a pool of sequence-verified nucleic acid elements of claims and/or a pool of higher-order nucleic acid constructs; and a plurality of primers for retrieving one or more sequence-verified nucleic acid elements and/or higher-order nucleic acid constructs.Type: GrantFiled: May 27, 2015Date of Patent: February 13, 2024Assignees: The Broad Institute, Inc., Massachusetts Institute of TechnologyInventors: Robert Nicol, Lauren Andrews, Tarjei Mikkelsen, Christopher Voigt
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Patent number: 11896651Abstract: Provided herein are compositions, methods, kits, and viral particles for treating a disease or disorder associated with a deep intronic mutation using an engineered, non-naturally occurring Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated (Cas) (CRISPR-Cas) system. In some aspects, provided herein is a self-limiting CRISPER-Cas system.Type: GrantFiled: April 15, 2016Date of Patent: February 13, 2024Assignee: GENZYME CORPORATIONInventors: Guoxiang Ruan, Abraham Scaria
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Patent number: 11898160Abstract: The present application describes a method for inducing or maintaining pluripotency in a cell by contacting the cell with a biological or chemical species that increases MUC1* activity.Type: GrantFiled: October 9, 2009Date of Patent: February 13, 2024Assignee: MINERVA BIOTECHNOLOGIES CORPORATIONInventors: Cynthia C. Bamdad, Shawn P. Fessler
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Patent number: 11891631Abstract: Fusion proteins comprising a DNA binding domain, e.g., a TAL effector repeat array (TALE) or zinc finger array, and a catalytic domain comprising a sequence that catalyzes histone demethylation, and methods of use thereof.Type: GrantFiled: April 5, 2019Date of Patent: February 6, 2024Assignee: The General Hospital CorporationInventors: Jae Keith Joung, Eric M. Mendenhall, Bradley E. Bernstein, Deepak Reyon
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Patent number: 11884925Abstract: Provided herein are CRISPR-based synthetic repression systems as well as methods and compositions using the synthetic repression systems to treat septicemia, an adverse immune response in a subject and Waldenström macroglobulinemia.Type: GrantFiled: November 7, 2019Date of Patent: January 30, 2024Assignee: ARIZONA BOARD OF REGENTS ON BEHALF OF ARIZONA STATE UNIVERSITYInventors: Samira Kiani, Mo Reza Ebrahimkhani, Farzaneh Moghadam
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Patent number: 11884917Abstract: An expression cassette for conditional expression of a single guide RNA (sgRNA) of a CRISPR/Cas9 system, the cassette includes a promoter, an sgRNA sequence, and a sequence flanked by at least a pair of recombinase recognition sites, wherein recombinase activated re-combination at the pair of recombinase recognition sites is capable of excising said flanked sequence, whereby either i) at least one of said recombinase recognition sites is located within the sgRNA sequence and said flanked sequence contains an transcription disruption sequence or ii) said flanked sequence is at least a part of the promoter or of the sgRNA sequence; methods of conditional expression of sgRNA and a reaction product of the conditional expression, i.e. sgRNA with a recombination site remnant.Type: GrantFiled: March 17, 2017Date of Patent: January 30, 2024Assignees: IMBA—INSTITUT FÜR MOLEKULARE BIOTECHNOLOGIE GMBH, CAMPUS SCIENCE SUPPORT FACILITIES GMBHInventors: Ulrich Elling, Krzysztof Chylinski, Maria Hubmann, Monika Borowska, Ivana Bilusic-Vilagos
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Patent number: 11834699Abstract: Provided herein is a method of using transposition to improve methods of sequencing RNA molecules. Provided herein is a method of tagging nucleic acid duplexes, such as DNA:RNA duplexes or DNA:DNA duplexes. The method includes the steps of providing a transposase and a transposon composition, providing one or more nucleic acid duplexes immobilized on a support, and contacting the transposase and transposon composition with the one or more nucleic acid duplexes under conditions wherein the one or more nucleic acid duplexes and transposon composition undergo a transposition reaction to produce one or more tagged nucleic acid duplexes, wherein the transposon composition comprises a double stranded nucleic acid molecule comprising a transferred strand and a non-transferred strand.Type: GrantFiled: April 1, 2019Date of Patent: December 5, 2023Assignee: Illumina Cambridge LimitedInventors: Niall Anthony Gormley, Louise Fraser, Paula Kokko-Gonzales
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Patent number: 11827879Abstract: RNA molecules comprising a guide sequence portion having 17-20 nucleotides in the sequence of 17-20 contiguous nucleotides set forth in any one of SEQ ID NOs: 1-3010 and compositions, methods, and uses thereof.Type: GrantFiled: November 28, 2018Date of Patent: November 28, 2023Assignee: EmendoBio, Inc.Inventors: Lior Izhar, David Baram, Joseph Georgeson, Michal Golan-Mashiach, Asael Herman, Rafi Emmanuel
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Patent number: 11827919Abstract: The present disclosure provides methods for detecting a single-stranded target RNA. The present disclosure provides methods of cleaving a precursor C2c2 guide RNA array into two or more C2c2 guide RNAs. The present disclosure provides a kit for detecting a target RNA in a sample.Type: GrantFiled: March 13, 2018Date of Patent: November 28, 2023Assignee: The Regents of the University of CaliforniaInventors: Jennifer A Doudna, Mitchell Ray O'Connell, Alexandra East-Seletsky, Spencer Charles Knight, James Harrison Doudna Cate
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Patent number: 11795452Abstract: Compositions and methods are provided herein for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and/or targeted mutagenesis. The compositions include fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a modified guide RNA, named a PEgRNA. The PEgRNA has been altered (relative to a standard guide RNA) to comprise an extended portion that provides a DNA synthesis template sequence which encodes a single strand DNA flap which is synthesized by the polymerase of the fusion protein and which becomes incorporated into the target DNA molecule.Type: GrantFiled: May 23, 2022Date of Patent: October 24, 2023Assignees: The Broad Institute, Inc., President and Fellows of Harvard CollegeInventors: David R. Liu, Andrew Vito Anzalone
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Patent number: 11767534Abstract: The invention provides methods for determining the activity of a plurality of nucleic acid regulatory elements. These methods may facilitate, e.g., the systematic reverse engineering, and optimization of mammalian cis-regulatory elements at high resolution and at a large scale. The method may include integration of multiplexed DNA synthesis and sequencing technologies to generate and quantify the transcriptional regulatory activity of e.g., thousands of arbitrary DNA sequences in parallel in cell-based as says (e.g., mammalian cell based assays).Type: GrantFiled: May 4, 2012Date of Patent: September 26, 2023Assignee: THE BROAD INSTITUTE, INC.Inventors: Tarjei Mikkelsen, Andreas Gnirke, Alexandre Melnikov, Eric S. Lander, Li Wang, Xiaolan Zhang
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Patent number: 11761001Abstract: Mbp_Argonaute proteins from prokaryotes and application thereof are provided. The Mbp_Argonaute protein consists of an amino acid sequence as shown in SEQ ID NO: 1 or a sequence with at least 50% or at least 80% of homology with the amino acid sequence as shown in SEQ ID NO: 1. An Argonaute protein gene derived from a cold-resistant prokaryote Mucilaginibacter paaluis is synthesized and named as MbpAgo, which has binding activity to single-stranded guide DNA and has nuclease activity to target RNA and/or target DNA complementarily paired with the single-stranded guide DNA, the MbpAgo can be used for the target RNA editing in vivo and in vitro to achieve site-specific modification of genetic material. The MbpAgo can modify highly-structured RNAs and not affect an endogenous RNAi pathway of animal and plant cells, provides a new and powerful tool for RNA editing with high cleavage activity and good specificity.Type: GrantFiled: June 30, 2022Date of Patent: September 19, 2023Assignee: HUBEI UNIVERSITYInventors: Lixin Ma, Wenqiang Li, Fei Wang, Ruyi He, Yang Liu
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Patent number: 11739309Abstract: 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: GrantFiled: August 16, 2021Date of Patent: August 29, 2023Assignee: The Regents of the University of CaliforniaInventors: Jennifer A. Doudna, Basem Al-Shayeb, Jillian F. Banfield, Patrick Pausch
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Patent number: 11702707Abstract: A method of determining water quality of a water sample, comprising exposing the water sample to a test cell system; generating at least one profile of ensuing changes in activities of transcription factors in the test cell system in response to such exposing; and determining from the generated at least one profile the water quality of the water sample. Computer systems and kits for carrying out the water quality determination of water specimens are also described, in which water quality can be readily and accurately determined by transcription factor activity analysis.Type: GrantFiled: September 8, 2012Date of Patent: July 18, 2023Assignee: ATTAGENE, INC.Inventors: Sergei S. Makarov, Alexander Vladimirovich Medvedev
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Patent number: 11680254Abstract: The present invention encompasses engineered meganucleases which recognize and cleave a recognition sequence within the human PCSK9 gene. The present invention also encompasses methods for using such engineered meganucleases in a pharmaceutical composition and in methods for treating or reducing the symptoms of cholesterol-related disorders, such as hypercholesterolemia. Further, the invention encompasses pharmaceutical compositions comprising engineered meganuclease proteins, nucleic acids encoding engineered meganucleases, and the use of such compositions for treating cholesterol-related disorders, such as hypercholesterolemia.Type: GrantFiled: April 20, 2018Date of Patent: June 20, 2023Assignee: PRECISION BIOSCIENCES, INC.Inventors: Victor Bartsevich, Derek Jantz, James Jefferson Smith, Janel Lape
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Patent number: 11680267Abstract: The present disclosure provides a nucleic acid sequence for regulating the transcription of a nucleic acid fragment of interest, wherein the nucleic acid sequence comprises at least 2 copies of TetO-operator sequences capable of binding to a transactivator rtTA regulatable by tetracycline or a derivative thereof, and 1 copy of minimal promoter sequence containing a TATA box sequence, and at least 1 copy of a CuO-operator sequence capable of binding to a transcription repressor CymR regulatable by cumate. The present disclosure also provides a vector and a host cell containing the nucleic acid sequence, and a method for inducing the expression of a nucleic acid fragment of interest in a host cell.Type: GrantFiled: September 16, 2020Date of Patent: June 20, 2023Assignee: Shenzhen Eureka Biotechnology Co., Ltd.Inventors: Bofu Xue, Yinhui Yang, Ke Liu, Mo Ma
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Patent number: 11674154Abstract: In some aspects, the disclosure relates to compositions and methods for treating fibrodysplasia ossificans progressiva (FOP) in a subject. In some aspects, the disclosure provides isolated nucleic acids, and vectors such as rAAV vectors, configured to express transgenes that inhibit (e.g., decrease) expression of mutated AVCR1 gene in muscle cells or connective tissues.Type: GrantFiled: December 2, 2021Date of Patent: June 13, 2023Assignee: University of MassachusettsInventors: Jae-Hyuck Shim, Guangping Gao, Jun Xie, Yeon-Suk Yang, Jung min Kim, Sachin Chaugule
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Patent number: 11643672Abstract: The invention pertains to an inducible CRISPR system for controlling expression of a CRISPR complex with an inducible fusion promoter. One embodiment of the invention provides HIV LTR-minimal Drosophila hsp70 fusion promoter that can be used for inducible co-expression of gRNA and Cas9 in HIV-infected cells to target cellular cofactors such as Cyclin T1. A single introduction of such embodiment leads to sustained suppression of HIV replication in stringent, chronically infected HeLa-CD4 cell lines as well as in T-cell lines. In another embodiment, the invention further relates to enhancement of HIV suppression by incorporating cis-acting ribozymes immediately upstream of the gRNA in the inducible CRISPR system construct. The inducible fusion promoter is adaptable for other tissue- or cell-type specific expression of the inducible CRISPR system.Type: GrantFiled: October 1, 2021Date of Patent: May 9, 2023Assignee: THE FLORIDA INTERNATIONAL UNIVERSITY BOARD OF TRUSTERSInventors: Hoshang Jehangir Unwalla, Srinivasan Chinnapaiyan
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Patent number: 11643652Abstract: Compositions and methods are provided herein for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and/or targeted mutagenesis. The compositions include fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a modified guide RNA, named an PEgRNA. The PEgRNA has been altered (relative to a standard guide RNA) to comprise an extended portion that provides a DNA synthesis template sequence which encodes a single strand DNA flap which is synthesized by the polymerase of the fusion protein and which becomes incorporated into the target DNA molecule.Type: GrantFiled: March 31, 2021Date of Patent: May 9, 2023Assignees: The Broad Institute, Inc., President and Fellows of Harvard CollegeInventors: David R. Liu, Andrew Vito Anzalone, James William Nelson
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Patent number: 11613742Abstract: Provided herein are CasX:gNA systems comprising CasX polypeptides, guide nucleic acids (gNA), and optionally donor template nucleic acids useful in the modification of a SOD1 gene. The systems are also useful for introduction into cells, for example eukaryotic cells having mutations in the SOD1 protein or the SOD1 regulatory element. Also provided are methods of using such CasX:gNA systems to modify cells having such mutations and utility in methods of treatment of a subject with a SOD1-related disease.Type: GrantFiled: September 23, 2021Date of Patent: March 28, 2023Assignee: SCRIBE THERAPEUTICS INC.Inventors: Benjamin Oakes, Sean Higgins, Hannah Spinner, Sarah Denny, Brett T. Staahl, Kian Taylor, Katherine Baney, Isabel Colin, Maroof Adil, Cole Urnes