WO2010132092A3 - Cytidine deaminase fusions and related methods - Google Patents

Cytidine deaminase fusions and related methods Download PDF

Info

Publication number
WO2010132092A3
WO2010132092A3 PCT/US2010/001340 US2010001340W WO2010132092A3 WO 2010132092 A3 WO2010132092 A3 WO 2010132092A3 US 2010001340 W US2010001340 W US 2010001340W WO 2010132092 A3 WO2010132092 A3 WO 2010132092A3
Authority
WO
WIPO (PCT)
Prior art keywords
cytidine deaminase
fusion molecules
related methods
provides methods
deaminase fusions
Prior art date
Application number
PCT/US2010/001340
Other languages
French (fr)
Other versions
WO2010132092A2 (en
Inventor
Carlos F. Barbas
Dae Hee Kim
Original Assignee
The Scripps Research Institute
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by The Scripps Research Institute filed Critical The Scripps Research Institute
Publication of WO2010132092A2 publication Critical patent/WO2010132092A2/en
Publication of WO2010132092A3 publication Critical patent/WO2010132092A3/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/102—Mutagenizing nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/78—Hydrolases (3) acting on carbon to nitrogen bonds other than peptide bonds (3.5)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y305/00—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5)
    • C12Y305/04—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amidines (3.5.4)
    • C12Y305/04001—Cytosine deaminase (3.5.4.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y305/00—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5)
    • C12Y305/04—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amidines (3.5.4)
    • C12Y305/04005—Cytidine deaminase (3.5.4.5)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/80—Fusion polypeptide containing a DNA binding domain, e.g. Lacl or Tet-repressor

Abstract

The present invention provides fusion molecules comprising a cytidine deaminase polypeptide and a single stranded DNA binding protein. The invention also provides methods of using the fusion molecules to induce mutations in target genes or polynucleotide sequences. The invention further provides methods of evolving target proteins or polypeptides with the cytidine deaminase fusion molecules disclosed herein.
PCT/US2010/001340 2009-05-12 2010-05-06 Cytidine deaminase fusions and related methods WO2010132092A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US21610309P 2009-05-12 2009-05-12
US61/216,103 2009-05-12

Publications (2)

Publication Number Publication Date
WO2010132092A2 WO2010132092A2 (en) 2010-11-18
WO2010132092A3 true WO2010132092A3 (en) 2011-03-10

Family

ID=43085493

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2010/001340 WO2010132092A2 (en) 2009-05-12 2010-05-06 Cytidine deaminase fusions and related methods

Country Status (1)

Country Link
WO (1) WO2010132092A2 (en)

Families Citing this family (36)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2012104843A1 (en) 2011-02-06 2012-08-09 Yeda Research And Development Co.Ltd. At The Weizmann Institute Of Science Affinity maturated t cell receptors and use thereof
JP6224689B2 (en) * 2012-03-15 2017-11-01 ニユー・イングランド・バイオレイブス・インコーポレイテツド Methods and compositions for distinguishing cytosine from modifications thereof and for methylome analysis
US9303079B2 (en) 2012-04-02 2016-04-05 Moderna Therapeutics, Inc. Modified polynucleotides for the production of cytoplasmic and cytoskeletal proteins
CN102766617A (en) * 2012-07-12 2012-11-07 昆明理工大学 Bacteriophage TSP4 dCTP (deoxycytidine triphosphate) deaminase and polynucleotide coding same
US9163284B2 (en) 2013-08-09 2015-10-20 President And Fellows Of Harvard College Methods for identifying a target site of a Cas9 nuclease
US9322037B2 (en) 2013-09-06 2016-04-26 President And Fellows Of Harvard College Cas9-FokI fusion proteins and uses thereof
US9526784B2 (en) 2013-09-06 2016-12-27 President And Fellows Of Harvard College Delivery system for functional nucleases
US9228207B2 (en) 2013-09-06 2016-01-05 President And Fellows Of Harvard College Switchable gRNAs comprising aptamers
LT3066201T (en) 2013-11-07 2018-08-10 Editas Medicine, Inc. Crispr-related methods and compositions with governing grnas
US20150165054A1 (en) * 2013-12-12 2015-06-18 President And Fellows Of Harvard College Methods for correcting caspase-9 point mutations
WO2015133554A1 (en) * 2014-03-05 2015-09-11 国立大学法人神戸大学 Genomic sequence modification method for specifically converting nucleic acid bases of targeted dna sequence, and molecular complex for use in same
US10077453B2 (en) 2014-07-30 2018-09-18 President And Fellows Of Harvard College CAS9 proteins including ligand-dependent inteins
DK3348638T3 (en) 2015-09-09 2023-02-13 Univ Kobe Nat Univ Corp METHOD OF CONVERTING GENOME SEQUENCE FROM GRAM-POSITIVE BACTERIA BY SPECIFICALLY CONVERTING NUCLEIC ACID BASE INTO THE INTENDED DNA SEQUENCE, AND MOLECULAR COMPLEX USED THEREFOR
EP3365357B1 (en) 2015-10-23 2024-02-14 President and Fellows of Harvard College Evolved cas9 proteins for gene editing
EP3382019B1 (en) 2015-11-27 2022-05-04 National University Corporation Kobe University Method for converting monocot plant genome sequence in which nucleic acid base in targeted dna sequence is specifically converted, and molecular complex used therein
WO2018017144A1 (en) 2016-07-19 2018-01-25 Brandeis University Compositions and methods for identifying rna binding polypeptide targets
AU2017306676B2 (en) 2016-08-03 2024-02-22 President And Fellows Of Harvard College Adenosine nucleobase editors and uses thereof
AU2017308889B2 (en) 2016-08-09 2023-11-09 President And Fellows Of Harvard College Programmable Cas9-recombinase fusion proteins and uses thereof
US11542509B2 (en) 2016-08-24 2023-01-03 President And Fellows Of Harvard College Incorporation of unnatural amino acids into proteins using base editing
SG11201903089RA (en) 2016-10-14 2019-05-30 Harvard College Aav delivery of nucleobase editors
WO2018119359A1 (en) 2016-12-23 2018-06-28 President And Fellows Of Harvard College Editing of ccr5 receptor gene to protect against hiv infection
US10995333B2 (en) 2017-02-06 2021-05-04 10X Genomics, Inc. Systems and methods for nucleic acid preparation
WO2018145041A1 (en) * 2017-02-06 2018-08-09 10X Genomics, Inc. Systems and methods for nucleic acid preparation
WO2018165504A1 (en) 2017-03-09 2018-09-13 President And Fellows Of Harvard College Suppression of pain by gene editing
US11542496B2 (en) 2017-03-10 2023-01-03 President And Fellows Of Harvard College Cytosine to guanine base editor
IL306092A (en) 2017-03-23 2023-11-01 Harvard College Nucleobase editors comprising nucleic acid programmable dna binding proteins
WO2018209320A1 (en) 2017-05-12 2018-11-15 President And Fellows Of Harvard College Aptazyme-embedded guide rnas for use with crispr-cas9 in genome editing and transcriptional activation
WO2018218166A1 (en) * 2017-05-25 2018-11-29 The General Hospital Corporation Using split deaminases to limit unwanted off-target base editor deamination
JP2020534795A (en) 2017-07-28 2020-12-03 プレジデント アンド フェローズ オブ ハーバード カレッジ Methods and Compositions for Evolving Base Editing Factors Using Phage-Supported Continuous Evolution (PACE)
WO2019139645A2 (en) 2017-08-30 2019-07-18 President And Fellows Of Harvard College High efficiency base editors comprising gam
US11795443B2 (en) 2017-10-16 2023-10-24 The Broad Institute, Inc. Uses of adenosine base editors
MX2021007835A (en) 2018-12-27 2021-08-11 Lifeedit Therapeutics Inc Polypeptides useful for gene editing and methods of use.
US11946040B2 (en) 2019-02-04 2024-04-02 The General Hospital Corporation Adenine DNA base editor variants with reduced off-target RNA editing
JP2022526908A (en) 2019-03-19 2022-05-27 ザ ブロード インスティテュート，インコーポレーテッド Editing Methods and Compositions for Editing Nucleotide Sequences
EP4079765A4 (en) * 2019-12-18 2024-02-14 Univ East China Normal Fusion protein that improves gene editing efficiency and application thereof
AU2021267940A1 (en) 2020-05-08 2022-12-08 President And Fellows Of Harvard College Methods and compositions for simultaneous editing of both strands of a target double-stranded nucleotide sequence

Non-Patent Citations (5)

* Cited by examiner, † Cited by third party
Title
BESMER, E. ET AL.: "The regulation of somatic hypermutation.", CURR. OPIN. IMMUNOL., vol. 16, no. ISSUE, April 2004 (2004-04-01), pages 241 - 245 *
CHAUDHURI, J. ET AL.: "Replication protein A interacts with AID to promote deamination of somatic hypermutation targets", NATURE, vol. 430, August 2004 (2004-08-01), pages 992 - 998 *
DICKERSON, S. K. ET AL.: "AID mediates hypermutation by deaminating single stranded DNA.", J. EXP. MED., vol. 197, no. 10, 19 May 2003 (2003-05-19), pages 1291 - 1296 *
PHAM, P. ET AL.: "Processive AID-catalysed cytosine deamination on single- stranded DNA simulates somatic hypermutation.", NATURE, vol. 424, July 2003 (2003-07-01), pages 103 - 107, XP002302398, DOI: doi:10.1038/nature01760 *
WEILL, J. C. ET AL.: "PRA tightens AID to ENA editing", NATURE IMMUNOLOGY, vol. 5, no. 9, September 2004 (2004-09-01), pages 876 - 878 *

Also Published As

Publication number Publication date
WO2010132092A2 (en) 2010-11-18

Similar Documents

Publication Publication Date Title
WO2010132092A3 (en) Cytidine deaminase fusions and related methods
EP2274442A4 (en) Consensus sequences of chikungunya viral proteins, nucleic acid molecules encoding the same, and compositions and methods for using the same
WO2009142773A3 (en) Multivalent fibronectin based scaffold domain proteins
WO2007095350A3 (en) Compositions and methods for use of pigment epithelial derived factor (pedf) peptide fragments
WO2010120514A3 (en) Antigen-binding proteins comprising recombinant protein scaffolds
WO2006007373A3 (en) Polynucleotides encoding mature ahasl proteins for creating imidazolinone-tolerant plants
WO2008132568A3 (en) Fusion proteins binding to growth factors
EP2350670A4 (en) Membrane-integrated viral dna-packaging motor protein connector biosensor for dna sequencing and other uses
WO2010115052A3 (en) Induced pluripotent stem cells
WO2011137319A3 (en) Stabilized fibronectin domain compositions, methods and uses
WO2013182910A3 (en) Transcription activator-like effector (tale) fusion protein
EP2037737A4 (en) Proteins, nucleic acids encoding the same and associated methods of use
WO2011123813A3 (en) Binding fusion proteins, binding fusion protein-drug conjugates, xten-drug conjugates and methods of making and using same
WO2008028977A3 (en) Serum albumin binding proteins with long half-lives
WO2008084115A3 (en) Lactococcus promoters and uses thereof
EP2010556A4 (en) Homogeneous erythropoietin and other peptides and proteins, methods and intermediates for their preparation
IN2012DN02981A (en)
WO2008127457A3 (en) Nucleic acids encoding recombinant protein a
WO2009097017A3 (en) Antibodies and fc fusion protein modifications with enhanced persistence or pharmacokinetic stability in vivo and methods of use thereof
MX2023002848A (en) Dna modifying enzymes and active fragments and variants thereof and methods of use.
WO2009019441A3 (en) Granulocyte colony stimulating factor
IL213749A0 (en) Dgati nucleic acids and proteins and methods of use thereof
WO2007061762A3 (en) Non-viral gene delivery complex
WO2014152247A8 (en) Improved tnf binding proteins
WO2016210124A3 (en) Characterization and directed evolution of a methyl binding domain protein for high-sensitivity dna methylation analysis

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 10775185

Country of ref document: EP

Kind code of ref document: A2

NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 10775185

Country of ref document: EP

Kind code of ref document: A2