IP Library › Granted Patent US 12,454,694
Granted Patent B2
US 12,454,694 · App. 17/273,071 · Granted Oct 28, 2025

Compositions and methods for improving base editing

Inventors: John Evans (Cambridge, MA); Jason Michael Gehrke (Cambridge, MA)
Assignee: Beam Therapeutics Inc.
C12N15/62C12N9/22C12N9/78C12N15/11C12N15/86C12N15/907C12Y305/04004C12Y305/04005C07K2319/09C07K2319/80C12N2310/20C12N2710/16143C12N2800/80
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Quick Facts
Patent No.
US 12,454,694
App. No.
17/273,071
Filed
Mar 3, 2021
Granted
Oct 28, 2025
Kind
B2
Art Unit
1632
USPC
435/463
Abstract

The invention features compositions and methods for modifying a polynucleotide (e.g., DNA) using a nucleobase editor comprising a first DNA binding protein domain that is catalytically inactive, a domain having base editing activity, and a second DNA binding protein domain having nickase activity. The invention also features a fusion protein comprising a domain having base editing activity (e.g., cytidine deaminase or adenosine deaminase), and two nucleic acid programmable DNA binding protein domains (napDNAbp), a first napDNAbp comprising nickase activity and a second napDNAbp that is catalytically inactive, where at least the two napDNAbps are joined by a linker, as well as related methods for using such base editors, and kits comprising the base editors.

Claims (39)

1. A nucleobase editor system comprising

(a) a first nucleic acid programmable DNA binding protein (napDNAbp) domain that lacks nuclease activity and has nucleic acid sequence specific binding activity,

(b) a second napDNAbp domain that has nickase activity and nucleic acid sequence specific binding activity, and

(c) an adenosine deaminase domain having base editing activity and comprising an amino acid sequence having at least 95% identity to the following amino acid sequence:

(SEQ ID NO: 89)

SEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIG

LHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRI

GRVVFGVRNAKTGAAGSLMDVLHYPGMNHRVEITEGILADECAALLCYF

FRMPRQVFNAQKKAQSSTD,

wherein the first napDNAbp domain is complexed with a first guide RNA, wherein the second napDNAbp domain is complexed with a second guide RNA,

wherein the first napDNAbp and the second napDNAbp are each derived from different species, and

wherein the first guide RNA and the second guide RNA are different.

2. A nucleobase editor system comprising one or more polynucleotides encoding (a), (b), (c), and the first and second guide RNAs of claim 1 .

3. A kit comprising the nucleobase editor of claim 1 .

4. The nucleobase editor system of claim 1 , wherein the first napDNAbp domain is a catalytically inactive CRISPR-Cas (dCas), and/or wherein the second napDNAbp domain is a CRISPR-Cas nickase (nCas).

5. The nucleobase editor system of claim 1 , wherein the first or the second napDNAbp is fused to a Uracil DNA glycosylase inhibitor (UGI) domain.

6. The nucleobase editor system of claim 1 , wherein the first or the second napDNAbp is fused with one or more Nuclear Localization Signals (NLS).

7. The nucleobase editor system of claim 6 , wherein the NLS is a bipartite NLS.

8. The nucleobase editor system of claim 1 , wherein the first napDNAbp is a dCas and wherein the second napDNAbp is a nCas, and wherein the dCas domain binds a canonical PAM sequence and the nCas domain binds a non-canonical PAM sequence.

9. The nucleobase editor system of claim 1 , wherein the first napDNAbp is a dCas and wherein the second napDNAbp is a nCas, and wherein the nCas domain and the dCas domain have different PAM specificities.

10. The nucleobase editor system of claim 8 , wherein the nCas binds a non-canonical PAM sequence selected from the group consisting of NGG, NGA, NGCG, NGC, NGN, NGT, NNGRRT, NNNRRT, NGCG, NGCN, NGTN, NGTN, NGTN, and NAA.

11. The nucleobase editor system of claim 9 , wherein the dCas is derived from an S. pyogenes Cas9 and binds a PAM sequence selected from the group consisting of NGA, NGCG, NGC, NGN, NGT, NNGRRT, NNNRRT, NGCG, NGCN, NGTN, NGTN, NGTN, and NAA.

12. The nucleobase editor system of claim 1 , wherein the first and the second napDNAbp are selected from the group consisting of Cas12a, Cas12b, Cas12c, Cas12d, Cas12e, Cas12g, Cas12h, and Cas12i.

13. The nucleobase editor system of claim 1 , wherein the first napDNAbp comprises a gRNA binding domain of Cas9.

14. The nucleobase editor system of claim 13 , wherein the first napDNAbp is a dCas9 domain incapable of cleaving a target nucleic acid sequence or the reverse complement strand of the target nucleic acid sequence.

15. The nucleobase editor system of claim 1 , wherein the first or second napDNAbp domain is derived from Cas12a, Cas12b, Cas12c, Cas12d, Cas12e, Cas12g, Cas12h, or Cas12i.

16. The nucleobase editor system of claim 1 , wherein the first napDNAbp domain is a dCas9 of S. pyogenes (dSpCas9), wherein the second napDNAbp domain is a nCas9 of S. aureus (nSaCas9), wherein the dSpCas9 and the nSaCas9 are joined by a linker, and wherein the domain having base editing activity is immediately adjacent to the first napDNAbp domain.

17. A nucleobase editor system comprising

(a) a first nucleic acid programmable DNA binding protein (napDNAbp) domain that lacks nuclease activity and has nucleic acid sequence specific binding activity,

(b) a second napDNAbp domain that has nickase activity and nucleic acid sequence specific binding activity, and

(c) an adenosine deaminase domain having base editing activity and comprising the following amino acid sequence:

(SEQ ID NO: 89)

SEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIG

LHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRI

GRVVFGVRNAKTGAAGSLMDVLHYPGMNHRVEITEGILADECAALLCYF

FRMPRQVFNAQKKAQSSTD,

wherein the first napDNAbp domain is complexed with a first guide RNA, wherein the second napDNAbp domain is complexed with a second guide RNA,

wherein the first napDNAbp and the second napDNAbp are each derived from different species, and

wherein the first guide RNA and the second guide RNA are different.

Assignments (3)
SECURITY INTEREST Recorded Mar 6, 2026
From: BEAM THERAPEUTICS INC.
To: SIXTH STREET LENDING PARTNERS, AS ADMINISTRATIVE AGENT
Reel/Frame 075021/0929 →
SECURITY INTEREST Recorded Feb 24, 2026
From: BEAM THERAPEUTICS INC.; GUIDE THERAPEUTICS, LLC; BBBR, LLC
To: SIXTH STREET LENDING PARTNERS, AS ADMINISTRATIVE AGENT
Reel/Frame 074955/0064 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Feb 9, 2022
From: EVANS, JOHN; GEHRKE, JASON MICHAEL
To: BEAM THERAPEUTICS INC.
Reel/Frame 058939/0199 →
Continuity (2)
Provisional Application 62728698 · Sep 7, 2018
Related Publication 20220127622A1 · Apr 28, 2022
References Cited (400)
US 7915114B2 · Hsiao et al. · 2011 [cited by applicant]
US 9068179B1 · Liu et al. · 2015 [cited by applicant]
US 9322037B2 · Liu et al. · 2016 [cited by applicant]
US 9388430B2 · Liu et al. · 2016 [cited by applicant]
US 9512446B1 · Joung et al. · 2016 [cited by applicant]
US 9737604B2 · Liu et al. · 2017 [cited by applicant]
US 9840699B2 · Liu et al. · 2017 [cited by applicant]
US 10113163B2 · Liu et al. · 2018 [cited by applicant]
US 10167457B2 · Liu et al. · 2019 [cited by applicant]
US 10465176B2 · Liu et al. · 2019 [cited by applicant]
US 10526401B2 · Muir et al. · 2020 [cited by applicant]
US 10682410B2 · Liu et al. · 2020 [cited by applicant]
US 10745677B2 · Maianti et al. · 2020 [cited by applicant]
US 10912833B2 · Liu et al. · 2021 [cited by applicant]
US 10947530B2 · Liu et al. · 2021 [cited by applicant]
US 11053481B2 · Liu et al. · 2021 [cited by applicant]
US 11124782B2 · Liu et al. · 2021 [cited by applicant]
US 11142550B2 · Muir et al. · 2021 [cited by applicant]
US 11142760B2 · Slaymaker et al. · 2021 [cited by applicant]
US 11155803B2 · Gaudelli et al. · 2021 [cited by applicant]
US 11193123B2 · Halperin · 2021 [cited by applicant]
US 11214780B2 · Liu et al. · 2022 [cited by applicant]
US 11268082B2 · Liu et al. · 2022 [cited by applicant]
US 11306324B2 · Liu et al. · 2022 [cited by applicant]
US 11319532B2 · Liu et al. · 2022 [cited by applicant]
US 11479767B2 · Smith et al. · 2022 [cited by applicant]
US 11542496B2 · Liu et al. · 2023 [cited by applicant]
US 11732274B2 · Liu et al. · 2023 [cited by applicant]
US 11752202B2 · Slaymaker · 2023 [cited by examiner]
US 12129478B1 · Chen et al. · 2024 [cited by applicant]
US 12241096B2 · Joung et al. · 2025 [cited by applicant]
US 12275952B2 · Chen · 2025 [cited by applicant]
US 12312613B2 · Kleinstiver et al. · 2025 [cited by applicant]
US 20040003420A1 · Kuhn et al. · 2004 [cited by applicant]
US 20040115184A1 · Smith et al. · 2004 [cited by applicant]
US 20050222030A1 · Allison · 2005 [cited by applicant]
US 20110104787A1 · Church et al. · 2011 [cited by applicant]
US 20130109048A1 · Giugliano et al. · 2013 [cited by applicant]
US 20140068797A1 · Doudna et al. · 2014 [cited by applicant]
US 20140186958A1 · Zhang et al. · 2014 [cited by applicant]
US 20140273226A1 · Wu · 2014 [cited by applicant]
US 20140273230A1 · Chen et al. · 2014 [cited by applicant]
US 20140356956A1 · Church et al. · 2014 [cited by applicant]
US 20150071903A1 · Liu et al. · 2015 [cited by applicant]
US 20150165054A1 · Liu et al. · 2015 [cited by applicant]
US 20150166980A1 · Liu et al. · 2015 [cited by applicant]
US 20150166982A1 · Liu et al. · 2015 [cited by applicant]
US 20150166984A1 · Liu et al. · 2015 [cited by applicant]
US 20150166985A1 · Liu et al. · 2015 [cited by applicant]
US 20150344549A1 · Muir et al. · 2015 [cited by applicant]
US 20160046961A1 · Jinek et al. · 2016 [cited by applicant]
US 20160200779A1 · Liu et al. · 2016 [cited by applicant]
US 20160201089A1 · Gersbach et al. · 2016 [cited by applicant]
US 20160208243A1 · Zhang et al. · 2016 [cited by applicant]
US 20160304846A1 · Liu et al. · 2016 [cited by applicant]
US 20160355797A1 · Konermann et al. · 2016 [cited by applicant]
US 20170121693A1 · Liu et al. · 2017 [cited by applicant]
US 20170233703A1 · Xie et al. · 2017 [cited by applicant]
US 20170247671A1 · Yung et al. · 2017 [cited by applicant]
US 20170275648A1 · Barrangou et al. · 2017 [cited by applicant]
US 20170327804A9 · Joung et al. · 2017 [cited by applicant]
US 20180002736A1 · O'Connell et al. · 2018 [cited by applicant]
US 20180073012A1 · Liu et al. · 2018 [cited by applicant]
US 20180127780A1 · Liu et al. · 2018 [cited by applicant]
US 20180170984A1 · Harris et al. · 2018 [cited by applicant]
US 20180179503A1 · Maianti et al. · 2018 [cited by applicant]
US 20180216095A1 · Thanos et al. · 2018 [cited by applicant]
US 20180237787A1 · Maianti et al. · 2018 [cited by applicant]
US 20180298421A1 · Carpenter et al. · 2018 [cited by applicant]
US 20180312828A1 · Liu et al. · 2018 [cited by applicant]
US 20190002875A1 · Cheng et al. · 2019 [cited by applicant]
US 20190010471A1 · Zhang et al. · 2019 [cited by applicant]
US 20190010481A1 · Joung et al. · 2019 [cited by applicant]
US 20190093099A1 · Liu et al. · 2019 [cited by applicant]
US 20190225955A1 · Liu et al. · 2019 [cited by applicant]
US 20190367891A1 · Liu et al. · 2019 [cited by applicant]
US 20190382775A1 · Tan et al. · 2019 [cited by applicant]
US 20200063127A1 · Lu et al. · 2020 [cited by applicant]
US 20200190493A1 · Liu et al. · 2020 [cited by applicant]
US 20200308571A1 · Joung et al. · 2020 [cited by applicant]
US 20200399619A1 · Maianti et al. · 2020 [cited by applicant]
US 20210130800A1 · Zhang · 2021 [cited by applicant]
US 20210198330A1 · Liu et al. · 2021 [cited by applicant]
US 20210252118A1 · Slaymaker et al. · 2021 [cited by applicant]
US 20210277379A1 · Gaudelli et al. · 2021 [cited by applicant]
US 20210317440A1 · Liu et al. · 2021 [cited by applicant]
US 20210371858A1 · Evans · 2021 [cited by applicant]
US 20210380955A1 · Bryson et al. · 2021 [cited by applicant]
US 20220047637A1 · Lamothe-Dreuzy et al. · 2022 [cited by applicant]
US 20220098572A1 · Slaymaker et al. · 2022 [cited by applicant]
US 20220119785A1 · Liu et al. · 2022 [cited by applicant]
US 20220127594A1 · Gaudelli et al. · 2022 [cited by applicant]
US 20220133790A1 · Gehrke · 2022 [cited by applicant]
US 20220136012A1 · Gaudelli et al. · 2022 [cited by applicant]
US 20220169998A1 · Joung et al. · 2022 [cited by applicant]
US 20220170027A1 · Gaudelli et al. · 2022 [cited by applicant]
US 20220220462A1 · Liu et al. · 2022 [cited by applicant]
US 20220290115A1 · Liu et al. · 2022 [cited by applicant]
US 20220290134A1 · Jin et al. · 2022 [cited by applicant]
US 20220290164A1 · Ran et al. · 2022 [cited by applicant]
US 20220307003A1 · Liu · 2022 [cited by applicant]
US 20220387622A1 · Gehrke et al. · 2022 [cited by applicant]
US 20230075877A1 · Gaudelli et al. · 2023 [cited by applicant]
US 20230080198A1 · Gaudelli · 2023 [cited by applicant]
US 20230101597A1 · Gaudelli et al. · 2023 [cited by applicant]
US 20230108687A1 · Liu et al. · 2023 [cited by applicant]
US 20230140953A1 · Slaymaker et al. · 2023 [cited by applicant]
US 20230159956A1 · Bryson et al. · 2023 [cited by applicant]
US 20230212575A1 · Odate et al. · 2023 [cited by applicant]
US 20230348883A1 · Liu et al. · 2023 [cited by applicant]
US 20230383277A1 · Cafferty et al. · 2023 [cited by applicant]
US 20230407277A1 · Joung et al. · 2023 [cited by applicant]
US 20240132867A1 · Gaudelli et al. · 2024 [cited by applicant]
CN 103088008A · 2013 [cited by applicant]
CN 105934516A · 2016 [cited by applicant]
CN 106061510A · 2016 [cited by applicant]
CN 106916852A · 2017 [cited by applicant]
CN 107043779A · 2017 [cited by applicant]
CN 107109413A · 2017 [cited by applicant]
CN 107532161A · 2018 [cited by applicant]
CN 108064282A · 2018 [cited by applicant]
CN 108290933A · 2018 [cited by applicant]
CN 108513575A · 2018 [cited by applicant]
CN 108699116A · 2018 [cited by applicant]
CN 109295186A · 2019 [cited by applicant]
CN 109328231A · 2019 [cited by applicant]
CN 109957569A · 2019 [cited by applicant]
CN 110214180A · 2019 [cited by applicant]
EP 2877490B1 · 2018 [cited by applicant]
EP 3956349A1 · 2022 [cited by applicant]
JP 2017500035A · 2017 [cited by applicant]
JP 6629734A2 · 2020 [cited by applicant]
KR 20160050069A · 2016 [cited by applicant]
WO 1997025416A2 · 1997 [cited by applicant]
WO 2001038547A2 · 2001 [cited by applicant]
WO 2002068676A2 · 2002 [cited by applicant]
WO 2002103028A2 · 2002 [cited by applicant]
WO 2010132092A2 · 2010 [cited by applicant]
WO 2011075627A1 · 2011 [cited by applicant]
WO 2013045632A1 · 2013 [cited by applicant]
WO 2013176772A1 · 2013 [cited by applicant]
WO 2013188037A2 · 2013 [cited by applicant]
WO 2014004336A2 · 2014 [cited by applicant]
WO 2014089290A1 · 2014 [cited by applicant]
WO 2014184143A1 · 2014 [cited by applicant]
WO 2014184741A1 · 2014 [cited by applicant]
WO 2014186686A2 · 2014 [cited by applicant]
WO 2015006294A2 · 2015 [cited by applicant]
WO 2015006498A2 · 2015 [cited by applicant]
WO 2015021426A1 · 2015 [cited by applicant]
WO 2015089277A1 · 2015 [cited by applicant]
WO 2015089406A1 · 2015 [cited by applicant]
WO 2015090230A1 · 2015 [cited by applicant]
WO 2015092024A2 · 2015 [cited by applicant]
WO 2015133554A1 · 2015 [cited by applicant]
WO 2015142675A2 · 2015 [cited by applicant]
WO 2015191693A2 · 2015 [cited by applicant]
WO 2016011210A2 · 2016 [cited by applicant]
WO 2016016343A1 · 2016 [cited by applicant]
WO 2016061368A1 · 2016 [cited by applicant]
WO 2016069910A1 · 2016 [cited by applicant]
WO 2016072399A1 · 2016 [cited by applicant]
WO 2016073649A1 · 2016 [cited by applicant]
WO 2016075612A1 · 2016 [cited by applicant]
WO 2016094304A2 · 2016 [cited by applicant]
WO 2016138038A1 · 2016 [cited by applicant]
WO 2016142532A2 · 2016 [cited by applicant]
WO 2016172727A1 · 2016 [cited by applicant]
WO 2016183438A1 · 2016 [cited by applicant]
WO 2016196308A1 · 2016 [cited by applicant]
WO 2016196388A1 · 2016 [cited by applicant]
WO 2016196655A1 · 2016 [cited by applicant]
WO 2016205711A1 · 2016 [cited by applicant]
WO 2016205759A1 · 2016 [cited by applicant]
WO 2017011721A1 · 2017 [cited by applicant]
WO 2017048969A1 · 2017 [cited by applicant]
WO 2017049166A1 · 2017 [cited by applicant]
WO 2017070632A2 · 2017 [cited by applicant]
WO 2017070633A2 · 2017 [cited by applicant]
WO 2017077386A1 · 2017 [cited by applicant]
WO 2017079703A1 · 2017 [cited by applicant]
WO 2017079705A1 · 2017 [cited by applicant]
WO 2017093804A2 · 2017 [cited by applicant]
WO 2017132580A2 · 2017 [cited by applicant]
WO 2017165862A1 · 2017 [cited by applicant]
WO 2017173054A1 · 2017 [cited by applicant]
WO 2017180993A1 · 2017 [cited by applicant]
WO 2017184768A1 · 2017 [cited by applicant]
WO 2017189308A1 · 2017 [cited by applicant]
WO 2018020323A2 · 2018 [cited by applicant]
WO 2018027036A1 · 2018 [cited by applicant]
WO 2018027078A1 · 2018 [cited by applicant]
WO 2018035388A1 · 2018 [cited by applicant]
WO 2018041973A1 · 2018 [cited by applicant]
WO 2018071868A1 · 2018 [cited by applicant]
WO 2018085690A1 · 2018 [cited by applicant]
WO 2018089664A1 · 2018 [cited by applicant]
WO 2018119354A1 · 2018 [cited by applicant]
WO 2018119359A1 · 2018 [cited by applicant]
WO 2018129129A1 · 2018 [cited by applicant]
WO 2018160768A1 · 2018 [cited by applicant]
WO 2018165629A1 · 2018 [cited by applicant]
WO 2018176009A1 · 2018 [cited by applicant]
WO 2018213708A1 · 2018 [cited by applicant]
WO 2018213726A1 · 2018 [cited by applicant]
WO 2018218188A2 · 2018 [cited by applicant]
WO 2019005884A1 · 2019 [cited by applicant]
WO 2019005886A1 · 2019 [cited by applicant]
WO 2019023680A1 · 2019 [cited by applicant]
WO 2019040650A1 · 2019 [cited by applicant]
WO 2019071274A1 · 2019 [cited by applicant]
WO 2019079347A1 · 2019 [cited by applicant]
WO 2019120310A1 · 2019 [cited by applicant]
WO 2019139645A2 · 2019 [cited by applicant]
WO 2019183000A1 · 2019 [cited by applicant]
WO 2019217941A1 · 2019 [cited by applicant]
WO 2019217942A1 · 2019 [cited by applicant]
WO 2019217943A1 · 2019 [cited by applicant]
WO 2019217944A1 · 2019 [cited by applicant]
WO 2019226953A1 · 2019 [cited by applicant]
WO 2020028823A1 · 2020 [cited by applicant]
WO 2020041751A1 · 2020 [cited by applicant]
WO 2020051561A1 · 2020 [cited by applicant]
WO 2020051562A2 · 2020 [cited by applicant]
WO 2020112870A1 · 2020 [cited by applicant]
WO 2020160514A1 · 2020 [cited by applicant]
WO 2020160517A1 · 2020 [cited by applicant]
WO 2020163396A1 · 2020 [cited by applicant]
WO 2020168051A1 · 2020 [cited by applicant]
WO 2020168075A1 · 2020 [cited by applicant]
WO 2020168088A1 · 2020 [cited by applicant]
WO 2020168122A1 · 2020 [cited by applicant]
WO 2020168132A1 · 2020 [cited by applicant]
WO 2020168133A1 · 2020 [cited by applicant]
WO 2020168135A1 · 2020 [cited by applicant]
WO 2020214842A1 · 2020 [cited by applicant]
WO 2020236936A1 · 2020 [cited by applicant]
WO 2020236982A1 · 2020 [cited by applicant]
WO 2021020884A2 · 2021 [cited by applicant]
WO 2021022043A2 · 2021 [cited by applicant]
WO 2021042062A2 · 2021 [cited by applicant]
WO 2021050571A1 · 2021 [cited by applicant]
WO 2021055459A1 · 2021 [cited by applicant]
WO 2021081264A1 · 2021 [cited by applicant]
WO 2021087182A1 · 2021 [cited by applicant]
WO 2021108717A2 · 2021 [cited by applicant]
WO 2021158921A2 · 2021 [cited by applicant]
WO 2021175288A1 · 2021 [cited by applicant]
WO 2021207651A2 · 2021 [cited by applicant]
WO 2022008935A1 · 2022 [cited by applicant]
WO 2022015969A1 · 2022 [cited by applicant]
WO 2022056254A2 · 2022 [cited by applicant]
WO 2022056324A1 · 2022 [cited by applicant]
WO 2022081890A1 · 2022 [cited by applicant]
WO 2022112404A1 · 2022 [cited by applicant]
WO 2022148955A1 · 2022 [cited by applicant]
WO 2022150367A1 · 2022 [cited by applicant]
WO 2022150372A1 · 2022 [cited by applicant]
WO 2022150706A2 · 2022 [cited by applicant]
WO 2022204574A1 · 2022 [cited by applicant]
WO 2023279118A2 · 2023 [cited by applicant]
WO 2023288304A2 · 2023 [cited by applicant]
WO 2023034959A2 · 2023 [cited by applicant]
WO 2023047338A1 · 2023 [cited by applicant]
WO 2023049299A2 · 2023 [cited by applicant]
WO 2023125814A1 · 2023 [cited by applicant]
WO 2023155901A1 · 2023 [cited by applicant]
WO 2023193536A1 · 2023 [cited by applicant]
WO 2023227669A3 · 2023 [cited by applicant]
WO 2023247753A1 · 2023 [cited by applicant]
WO 2023248110A1 · 2023 [cited by applicant]
WO 2024040083A1 · 2024 [cited by applicant]
WO 2024063273A1 · 2024 [cited by applicant]
WO 2024073385A2 · 2024 [cited by applicant]
WO 2024179426A2 · 2024 [cited by applicant]
WO 2024226156A1 · 2024 [cited by applicant]
WO 2024227047A2 · 2024 [cited by applicant]
WO 2024259364A2 · 2024 [cited by applicant]
Yan et al. Highly Efficient A T to G C Base Editing byCas9n-Guided tRNA Adenosine Deaminase in Rice. Mol Plant. Apr. 2, 2018;11( 4):631-634 . . . (Year: 2018). [cited by examiner]
Ahern. Biochemical, Reagents Kits Offer Scientists Good Return On Investment. The Scientist Magazine (1995) (accessed at https://www.the-scientist.com/technology/biochemical-reagents-kits-offer-scientists-good-return-on… [cited by examiner]
Lange et al. Expanding the Definition of the Classical Bipartite Nuclear Localization Signal. Traffic. Mar. 2010;11(3):311-23. (Year: 2010). [cited by examiner]
Murugan et al. The Revolution Continues: Newly Discovered Systems Expand the CRISPR-Cas Toolkit. Mol Cell. Oct. 5, 2017;68(1): 15-25. (Year: 2017). [cited by examiner]
Chiang et al. CRISPR-Cas9D10A nickase-based genotypic and phenotypic screening to enhance genome editing. Sci Rep. Apr. 15, 2016:6:24356. (Year: 2016). [cited by examiner]
Pace et al. Sickle Cell Disease: Genetics, Cellular and Molecular Mechanisms, and Therapies. Anemia. 2012; 2012: 143594. (Year: 2012). [cited by examiner]
Nishimasu et al. Crystal Structure of Staphylococcus aureus Cas9. Cell. Aug. 27, 2015;162(5):1113-26. (Year: 2015). [cited by examiner]
Wang et al, “Enhanced base editing by co-expression of free uracil DNA glycosylase inhibitor,” Cell research, Oct. 2017, vol. 27, No. 10, pp. 1289-1292. [cited by applicant]
Wang et al., “Eliminating base-editor-induced genome-wide and transcriptome-wide off-target mutations,” Nature Cell Biology, 2021, pp. 1-32. [cited by applicant]
Wijesinghe et al., “Efficient deamination of 5-methylcytosines in DNA by human APOBEC3A, but not by AID or APOBEC3G,” Nucleic Acids Research, Jul. 13, 2012, vol. 40, No. 18, pp. 9206-9217. [cited by applicant]
Wolf et al., “tadA, an essential tRNA-specific adenosine deaminase from [cited by applicant]
Yan et al., “Functionally diverse type V CRISPR-Cas systems,” Science, Jan. 4, 2019, vol. 363, pp. 88-91. [cited by applicant]
Yang et al., “Engineering and optimising deaminase fusions for genome editing,” Nature Communications, 2016, vol. 7, No. 13330, pp. 1-11. [cited by applicant]
Yang et al., “PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease,” Cell, Dec. 15, 2016, vol. 167, pp. 1814-1828. [cited by applicant]
Yu et al., “Cytosine base editors with minimized unguided DNA and RNA off-target events and high on-target activity,” Nature Communications, 2020, vol. 11, No. 2052, pp. 1-10. [cited by applicant]
Zafra et al., “Optimized base editors enable efficient editing in cells, organoids and mice,” Nature Biotechnology, 2018, pp. 1-6. [cited by applicant]
Zheng et al., “DNA Editing in DNA/RNA Hybrids by Adenosine Deaminases That Act on RNA,” Nucleic Acids Research, 2017, vol. 45, No. 6, pp. 3369-3377. [cited by applicant]
Zhou et al., “Atypical behaviour and connectivity in SHANK3-mutant macaques,” Nature, Jun. 20, 2019, vol. 570, pp. 326-331. [cited by applicant]
Zuris et al., “Efficient Delivery of Genome-Editing Proteins In Vitro and In Vivo,” Nature Biotechnology, Jan. 2015, vol. 33, No. 1, pp. 73-80. [cited by applicant]
International Search Report and Written Opinion in corresponding International Patent Application No. PCT/US19/50112, mailed Feb. 25, 2020 (20 pages). [cited by applicant]
U.S. Appl. No. 14/325,815, filed Jul. 6, 2021, Liu et al. [cited by applicant]
Addgene Plasmid No. 44246, Create Date Feb. 28, 2013. [cited by applicant]
Addgene Plasmid No. 73021, Create Date Apr. 20, 2016. [cited by applicant]
Addgene Plasmid No. 79620, Create Date Aug. 4, 2016. [cited by applicant]
Alexandrov et al., “Signatures of mutational processes in human cancer,” Nature, Aug. 22, 2013, vol. 500, pp. 415-421. [cited by applicant]
Andries et al., “N1-methylpseudouridine-incorporated mRNA outperforms pseudouridine-incorporated mRNA by providing enhanced protein expression and reduced immunogenicity in mammalian cell lines and mice,” Journal of Con… [cited by applicant]
Bae et al., “Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases,” Bioinformatics, Jan. 24, 2014, vol. 30, No. 10, pp. 1473-1475. [cited by applicant]
Billon et al., “CRISPR-Mediated Base Editing Enables Efficient Disruption of Eukaryotic Genes through Induction of STOP Codons,” Molecular Cell, Sep. 21, 2017, vol. 67, pp. 1068-1079. [cited by applicant]
Branden and Tooze, “The Building Blocks,” Introduction to Protein Structure, 1999, vol. 2, pp. 3-12. [cited by applicant]
Briner et al., “Guide RNA Functional Modules Direct Cas9 Activity and Orthogonality,” Molecular Cell, Oct. 23, 2014, vol. 56, pp. 333-339. [cited by applicant]
Bulow et al., “Multienzyme systems obtained by gene fusion,” Trends in Biotechnology, Jan. 1991, vol. 9, pp. 226-231. [cited by applicant]
Cameron, Ewan R., “Recent Advances in Transgenic Technology,” Molecular Biotechnology, 1997, vol. 7, pp. 253-265. [cited by applicant]
Chatterjee et al., “A Cas9 with PAM recognition for adenine dinucleotides,” Nature Communications, 2020, vol. 11, No. 2474, pp. 1-6. [cited by applicant]
Chester et al., “The apolipoprotein B mRNA editing complex performs a multifunctional cycle and suppresses honsense-mediated decay,” The EMBO Journal, 2003, vol. 22, No. 15, pp. 3971-3982. [cited by applicant]
Chichili et al., “Linkers in the structural biology of protein-protein interactions,” Protein Science, 2013, vol. 22, pp. 153-167. [cited by applicant]
Chylinski et al., “The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems,” RNA Biology, May 2013, vol. 10, No. 5, pp. 726-737. [cited by applicant]
Collantes et al., “Development and Characterization of a Modular CRISPR and RNA Aptamer Mediated Base Editing System,” The CRISPR Journal, 2021, vol. 4, No. 1, pp. 58-68. [cited by applicant]
Cong et al., “Multiplex Genome Engineering Using CRISPR/Cas Systems,” Science, Feb. 15, 2013, vol. 339, No. 6121, pp. 819-823. [cited by applicant]
Deltcheva et al., “CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III,” Nature, Mar. 31, 2011, vol. 471, pp. 602-607. [cited by applicant]
Endo et al., “Toward establishing an efficient and versatile gene targeting system in higher plants,” Biocatalysis and Agricultural Biotechnology, 2014, vol. 3, pp. 2-6. [cited by applicant]
Ferretti et al., “Complete genome sequence of an M1 strain of [cited by applicant]
Fonfara et al., “Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems,” Nucleic Acids Research, 2014, vol. 42, No. 4, pp. 2577-2590. [cited by applicant]
Freshney et al., “Culture of Animal Cells, A Manual of Basic Technique,” Food and Chemical Toxicology, 1983, vol. 23, No. 3, pp. 403-404. [cited by applicant]
Fu et al., “Human cell based directed evolution of adenine base editors with improved efficiency,” Nature Communications, 2021, vol. 12, No. 5897, pp. 1-11. [cited by applicant]
Gardlik et al., “Vectors and delivery systems in gene therapy,” Medical Science Monitor, 2005, vol. 11, No. 4, pp. RA110-RA121. [cited by applicant]
Gasiunas et al., “Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria,” Proceedings of the National Academy of Sciences of the United States of America, Sep. 4, 2012, pp… [cited by applicant]
Gasiunas et al., “RNA-dependent DNA endonuclease Cas9 of the CRISPR system: Holy Grail of genome editing?” Trends in Microbiology, Nov. 2013, vol. 21, No. 11, pp. 562-567. [cited by applicant]
Gaudelli et al., “Directed evolution of adenine base editors with increased activity and therapeutic application,” Nature Biotechnology, 2020, pp. 1-15. [cited by applicant]
Gaudelli et al., “Programmable base editing of A⋅T to G⋅C in genomic DNA without DNA cleavage,” Nature, Nov. 23, 2017, vol. 551, pp. 464-471. [cited by applicant]
GenBank Accession No. NM_000295.4, “ [cited by applicant]
Grunewald et al., “CRISPR DNA base editors with reduced RNA off-target and self-editing activities,” Nature Biotechnology, Sep. 2019, vol. 37, No. 9, pp. 1041-1048. [cited by applicant]
Guilinger et al., “Fusion of catalytically inactive Cas9 to Fokl nuclease improves the specificity of genome modification,” Nature Biotechnology, 2014, pp. 1-6. [cited by applicant]
Guo et al., “Protein tolerance to random amino acid change,” Proceedings of the National Academy of Sciences of the United States of America, Jun. 22, 2004, vol. 101, No. 25, pp. 9205-9210. [cited by applicant]
Hill et al., “Functional Analysis of Conserved Histidines in ADP-Glucose Pyrophosphorylase from [cited by applicant]
Houdebine, Louis-Marie, “The methods to generate transgenic animals and to control transgene expression,” Journal of Biotechnology, 2002, vol. 98, pp. 145-160. [cited by applicant]
Hu et al., “Evolved Cas9 variants with broad PAM compatibility and high DNA specificity,” Nature, Apr. 5, 2018, vol. 556, pp. 57-63. [cited by applicant]
Huang et al., “DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A,” Genome Biology, 2017, vol. 18, No. 176, pp. 1-11. [cited by applicant]
Jeong et al., “Adenine base editor engineering reduces editing of bystander cytosines,” Nature Biotechnology, 2021, pp. 1-12. [cited by applicant]
Jeong et al., “Precise adenine base editors that exhibit minimized cytosine catalysis,” Research Square, 2020, pp. 1-15. [cited by applicant]
Jha et al., “Single amino acid substitutions in recombinant plant-derived human α1-proteinase inhibitor confer enhanced stability and functional efficacy,” Biochimica et Biophysica Acta, 2014, vol. 1840, pp. 416-427. [cited by applicant]
Jiang et al., “Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope,” Nature Communications, 2020, vol. 11, No. 1979, pp. 1-9. [cited by applicant]
Jinek et al., “A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity,” Science, Aug. 17, 2012, vol. 337, No. 6096, pp. 816-821. [cited by applicant]
Jinek et al., “RNA-programmed genome editing in human cells,” eLife, 2013, vol. 2, No. e00471, pp. 1-9. [cited by applicant]
Jore et al., “Structural basis for CRISPR RNA-guided DNA recognition by Cascade,” Nature Structural & Molecular Biology, May 2011, vol. 18, No. 5, pp. 529-537. [cited by applicant]
Kappel et al., “Regulating gene expression in transgenic animals,” Current Opinion in Biotechnology, 1992, vol. 3, pp. 548-553. [cited by applicant]
Kim et al., “Adenine base editors catalyze cytosine conversions in human cells,” Nature Biotechnology, Oct. 2019, vol. 37, pp. 1145-1148. [cited by applicant]
Kim et al., “Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins,” Genome Research, 2014, vol. 24, pp. 1012-1019. [cited by applicant]
Kim et al., “Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions,” Nature Biotechnology, 2017, pp. 1-7. [cited by applicant]
Kim et al., “Rescue of high-specificity Cas9 variants using sgRNAs with matched 5′ nucleotides,” Genome Biology, 2017, vol. 18, No. 218, pp. 1-6. [cited by applicant]
Kim et al., “Transcriptional Repression by Zinc Finger Peptides,” The Journal of Biological Chemistry, Nov. 21, 1997, vol. 272, No. 47, pp. 29795-29800. [cited by applicant]
Kim et al., “Structural and Kinetic Characterization of [cited by applicant]
Bolukbasi et al., “DNA-binding-domain fusions enhance the targeting range and precision of Cas9,” Nature Methods, Dec. 2015, vol. 12, Article No. 12, pp. 1150-1156. [cited by applicant]
Burstein et al., “New CRISPR-Cas systems from uncultivated microbes,” Nature, Feb. 9, 2017, vol. 542, Article No. 7640, pp. 237-241. [cited by applicant]
Cheng et al., “Cloning, expression and activity identification of human innate immune protein apolipoprotein B mRNA editing enzyme catalytic subunit 3A(APOBEC3A),” Chinese Journal of Cellular and Molecular Immunology, 2… [cited by applicant]
Eid et al., “CRISPR base editors: genome editing without double-stranded breaks,” Biochemical Journal, 2018, vol. 475, pp. 1955-1964. [cited by applicant]
Ekstrand et al., “Frequent alterations of the PI3K/AKT/mTOR pathways in hereditary nonpolyposis colorectal cancer,” Familial Cancer, 2010, vol. 9, pp. 125-129. [cited by applicant]
Grunewald et al., “Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors,” Nature, May 16, 2019, vol. 569, pp. 433-437 and pp. 438-453 containing Methods, Figures, Tables and Report Summary… [cited by applicant]
Hua et al., “Expanding the base editing scope in rice by using Cas9 variants,” Plant Biotechnology Journal, 2019, vol. 17, pp. 499-504. [cited by applicant]
Huang et al., “Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors,” Nature Biotechnology, Jun. 2019, vol. 37, Article No. 6, pp. 626-631. [cited by applicant]
Jin et al., “Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice,” Science, Apr. 19, 2019, vol. 364, pp. 292-295. [cited by applicant]
Kaya et al., “A bacterial Argonaute with noncanonical guide RNA specificity,” Proceedings of the National Academy of Sciences of the United States of America, Apr. 12, 2016, vol. 113, No. 15, pp. 4057-4062. [cited by applicant]
Komor et al., “CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes,” Cell, Jan. 12, 2017, vol. 168, pp. 20-36. [cited by applicant]
Kury et al., “De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder,” The American Journal of Human Genetics, Feb. 2, 2017, vol. 100, pp. 352-363. [cited by applicant]
Lavergne et al., “Defects in type IIA von Willebrand disease: a cysteine 509 to arginine substitution in the mature von Willebrand factor disrupts a disulphide loop involved in the interaction with platelet glycoprotein… [cited by applicant]
Lee et al., “CRISPR-Pass: Gene Rescue of Nonsense Mutations Using Adenine Base Editors,” Molecular Therapy, Aug. 2019, vol. 27, No. 8, pp. 1364-1371. [cited by applicant]
Lee et al., “Cytosine but not adenine base editor generates mutations in mice,” bioRxiv, 2019, pp. 1-24. [cited by applicant]
Micozzi et al., “Human cytidine deaminase: A biochemical characterization of its naturally occurring variants,” International Journal of Biological Macromolecules, Feb. 2014, vol. 63, pp. 64-74. [cited by applicant]
Plosky, Brian S., “CRISPR-Mediated Base Editing without DNA Double-Strand Breaks,” Molecular Cell, May 19, 2016, vol. 62, pp. 477-478. [cited by applicant]
Ramakrishna et al., “Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA,” Genome Research, 2014, vol. 24, pp. 1020-1027. [cited by applicant]
Ran et al., “In vivo genome editing using [cited by applicant]
Rees et al., “Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery,” Nature Communications, 2017, vol. 8, No. 15790, pp. 1-10. [cited by applicant]
Tsai et al., “GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases,” Nature Biotechnology, Feb. 2015, vol. 33, Article No. 2, pp. 187-197. [cited by applicant]
UniProt Accession No. A0A5F1IHX6, downloaded Apr. 11, 2023. [cited by applicant]
UniProt Accession No. A8AD26, downloaded Apr. 11, 2023. [cited by applicant]
Yan et al., “High-efficiency and multiplex adenine base editing in plants using new TadA variants,” Molecular Plant, May 3, 2021, vol. 14, pp. 722-731. [cited by applicant]
Yang et al., “Increasing targeting scope of adenosine base editors in mouse and rat embryos through fusion of TadA deaminase with Cas9 variants,” Protein & Cell, 2018, vol. 9, No. 9, pp. 814-819. [cited by applicant]
Yeh et al., “In vivo base editing of post-mitotic sensory cells,” Nature Communications, 2018, vol. 9, No. 2184, pp. 1-10. [cited by applicant]
Zhang et al., “Progress in base editing technology based on CRISPR/Cas9 system and its application in medical research,” Chinese Journal of Pharmacology and Toxicology, Jul. 2018, vol. 32, No. 7, pp. 507-514 [English Ab… [cited by applicant]
Zhou et al., “Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis,” Nature, Jul. 11, 2019, vol. 571, pp. 275-278 and 14 pages containing Methods, Extended Figures, and Report Summary (… [cited by applicant]
Zuo et al., “Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos,” Science, Apr. 19, 2019, vol. 364, Article No. 6437, pp. 289-292. [cited by applicant]
Qianqian, Xiong, “Advances in Diagnosis and Treatment of Glycogen Storage Diseases,” Journal of Stroke and Neurological Diseases, 2017, vol. 34, No. 10, pp. 957-960 [English Abstract]. [cited by applicant]
Qing et al., “Research progress on double-stranded RNA-specific adenosine deaminase—DSRAD/ADAR1,” Foreign Medical Sciences, 2004, vol. 3, pp. 129-132 [English Abstract Only]. [cited by applicant]
Rajamohan et al., “Current status of drug screening and disease modelling in human pluripotent stem cells,” Bioessays, 2012, vol. 35, pp. 281-298. [cited by applicant]
Ribeiro et al., “Protein Engineering Strategies to Expand CRISPR-Cas9 Applications,” Hindawi: International Journal of Genomics, 2018, vol. 2018, Article No. 1652567, pp. 1-12. [cited by applicant]
Ryu et al., “Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy,” Nature Biotechnology, Jun. 2018, vol. 36, No. 6, pp. 536-539. [cited by applicant]
Sang et al., “A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily,” Nucleic Acids Research, Sep. 30, 2015, vol. 43, No. 17, pp. 8452-8463. [cited by applicant]
Sangkitporn et al., “Hb G Makassar (Beta 6: Glu→ Ala) in a Thai Family,” Journal of the Medical Association of Thailand, May 2002, vol. 85, No. 5, pp. 577-582. [cited by applicant]
Shah et al., “Efficient and versatile CRISPR engineering of human neurons in culture to model neurological disorders,” Wellcome Open Research, Nov. 15, 2016, vol. 1, No. 13, pp. 1-18 and pp. 19-21 containing Open Peer R… [cited by applicant]
Shah et al., “MeCP2 mutations: progress towards understanding and treating Rett syndrome,” Genome Medicine, 2017, vol. 9, No. 17, pp. 1-4. [cited by applicant]
Shee et al., “Engineered proteins detect spontaneous DNA breakage in human and bacterial cells,” eLife, 2013, vol. 2, No. e01222, pp. 1-25. [cited by applicant]
Shen et al., “Amelioration of Alpha-1 Antitrypsin Deficiency Diseases with Genome Editing in Transgenic Mice,” Human Gene Therapy, 2018, vol. 29, No. 8, pp. 861-873. [cited by applicant]
Sinnamon et al., “Site-directed RNA repair of endogenous Mecp2 RNA in neurons,” Proceedings of the National Academy of Sciences of the United States of America, Oct. 16, 2017, pp. E9395-E9402. [cited by applicant]
Smith et al., “Efficient and Allele-Specific Genome Editing of Disease Loci in Human iPSCs,” Molecular Therapy, Mar. 2015, vol. 23, No. 3, pp. 570-577. [cited by applicant]
UniProt Accession No. P51908, Downloaded Jan. 9, 2024. [cited by applicant]
Valdmanis et al., “Future of rAAV Gene Therapy: Platform for RNAi, Gene Editing, and Beyond,” Human Gene Therapy, 2017, vol. 28, No. 4, pp. 361-372. [cited by applicant]
Wei et al., “The “new favorite” of gene editing technology-single base editors,” Hereditas, 2017, vol. 39, No. 12, pp. 1115-1121 [English Abstract]. [cited by applicant]
Werder et al., “Adenine base editing reduces misfolded protein accumulation and toxicity in alpha-1 antitrypsin deficient patient iPSC-hepatocytes,” Molecular Therapy, Nov. 2021, vol. 29, No. 11, pp. 3219-3229. [cited by applicant]
Wienert et al., “KLF1 drives the expression of fetal hemoglobin in British HPFH,” Blood, Aug. 10, 2017, vol. 130, No. 6, pp. 803-807. [cited by applicant]
Yang et al., “APOBEC: From mutator to editor,” Journal of Genetics and Genomics, 2017, vol. 44, pp. 423-437. [cited by applicant]
Yuliang et al., “Diagnosis and treatment of a1-antitrypsin deficiency,” Practical Clinical Medicine, 2017, vol. 2, pp. 104-107 [English Abstract Only]. [cited by applicant]
Zong et al., “Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion,” Nature Biotechnology, 2017, pp. 1-4. [cited by applicant]
Kitamura et al., “Uracil DNA Glycosylase Counteracts APOBEC3G-Induced Hypermutation of Hepatitis B Viral Genomes: Excision Repair of Covalently Closed Circular DNA,” PLOS Pathogens, May 2013, vol. 9, No. 5, e1003361, pp… [cited by applicant]