DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
PRIORITIZED EXAMINATION (TRACK I)
The request filed April 16, 2026, for Prioritized Examination for an original nonprovisional application (Track I) was granted 05/11/2026.
Priority
Applicant’s claim to priority from International Application No. PCT/US2024/034189 filed 06/14/2024 and from US Provisional Applications No. 63/580,925 filed 09/06/2023 and 63/508,469 filed 06/15/2023, is hereby acknowledged.
Election/Restrictions
Applicant’s election of Invention group I (Claims 1-26, drawn to a
pharmaceutical composition comprising a nucleic acid encoding for a base editor system comprising a programmable DNA binding protein domain fused to an adenosine deaminase domain, and a guide polynucleotide) and Species (A8 (claim 2 (e); B8 (An amino acid sequence 90% identical to SEQ ID NO: 426); C1 (a recombinant base editor comprising a linker of amino acid sequence of SEQ ID NO: 357); D2 (a base editor comprising an amino acid sequence that is 100% identical to SEQ ID NO: 446) and E (a guide RNA comprising a spacer comprising the nucleotide sequence of SEQ ID NO: 561, the nucleotide sequence of SEQ ID NO: 566, the modification pattern of SEQ ID NO: 575 of claim 21 and no covalently attached peptide)) in the reply filed on 07/14/2026 is acknowledged.
Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 27-30 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made and considered without traverse in the reply filed on 07/14/2026.
Application Status
This Application is a CON of Application No. 19/416,825 filed 12/11/2025, which is also a CON of International Application No. PCT/US2024/034189 filed 06/14/2024.
Claims 1-30 are currently pending. Claims 27-30 are withdrawn. Therefore, claims 1-26 are under consideration in this Office Action.
Information Disclosure Statement
The information disclosure statements (IDSs) submitted on 04/16/2026 (one IDS), 05/04/2026 (11 IDSs) and 06/26/2026 (one IDS) are hereby acknowledged. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the
information disclosure statements are being considered by the examiner.
Drawings
The Drawings filed on 04/16/2026 are hereby acknowledged and are
acceptable: the nucleic acid and amino acid sequences’ SEQ ID Nos for Figures 1, 5B, 25B, 30B and 34A are disclosed in the “Brief Description of the Drawings” section of the Specification (pages 47 -59) as required and in accordance with 37 CFR 1.821(d).
Specification
The use of the terms “lipofectamine”, “MessengerMax” (page 48, lines 6, 13, 19, 22, 25, 28, 31, 34; page 49, lines 3, 6, 9; page 194, line 3), “ Meso Scale Discovery” (page 208, lines 28-29) which are trade names or marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore, the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claim 5 is objected to because of the following informalities: “ a period is missing after “SEQ ID NO: 1” to indicate the finality and limitation of the claim. Appropriate correction is required.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-4, 8, 10-12 and 14-17 are rejected under 35 U.S.C. §103 as being unpatentable over Gaudelli (Gaudelli, et al. US Patent No. 11,155,803 B2, published October 26, 2021; cited on IDS filed 05/04/2026 (18-pages, patent#10)) in view of Cleaver (Cleaver, S. et al. US Patent No. 12,565,666 B2, published March 3, 2026, benefitting from priority of International Application PCT/US2021/020943 filed March 4, 2021, and provisional Applications Nos: 63/035,674 filed June 5, 2020, and 62/985,264 filed March 4, 2020).
Regarding claim 1, it recites “1. A nucleic acid encoding a base editor comprising a nucleic acid programmable DNA binding protein (napDNAbp) domain and an adenosine deaminase domain, wherein the napDNAbp domain comprises an alteration selected from the group consisting of M1135L, E1250K, A1283D, Q1136Y, R1337K, R765A, and Q768A of an amino acid sequence, or a fragment thereof lacking an N-terminal methionine, that is at least 90% identical to:
1 MDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAE 60
61 ATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFG 120
121 NIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSD 180
181 VDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGN 240
241 LIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAI 300
301 LLSDILRVNTEITKAPLSASMVKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYA 360
361 GYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGIIPHQIHLGELH 420
421 AILRRQGDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEE 480
481 VVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFL 540
541 SGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKI 600
601 IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRLRYTGWG 660
661 RLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSL 720
721 HEHIANLAGSPAIKKGILQTVKVVDELVKVMGGHKPENIVIEMARENQTTQKGQKNSRER 780
781 MKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDH 840
841 IVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNL 900
901 TKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKS 960
961 KLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRK 1020
1021 MIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDF 1080
1081 ATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKGNSDKLIARKKDWDPKKYGGFMQPTVA 1140
1141 YSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPK 1200
1201 YSLFELENGRKRMLASAKFLQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVE 1260
1261 QHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGA 1320
1321 PRAFKYFDTTIARKEYRSTKEVLDATLIHQSITGLYETRIDLSQLGGD 1368
(SEQ ID NO: 554).”
Residues M1135, E1250, A1283, Q1136, R1337, R765 and Q768 are bolded and underlined in the reference sequence corresponding to SEQ ID NO: 554.
Regarding claim 16, it recites limitations from claim 1 and encompasses a base editor system comprising the nucleic acid claimed in claim 1.
Regarding claims 1 and 16, Gaudelli teaches base editor systems comprising nucleic acid molecules encoding for recombinant fusion proteins that comprises a programmable DNA binding protein domain (napDNAbp) and an adenosine deaminase domain (see title, abstract, column 1, lines 65-67, column 2 lines 1-20; column 49, lines 46-67; column 50, lines 25-29; column 51, lines 32-37).
Gaudelli teaches recombinant fusion proteins comprising a napDNAbp and an adenosine deaminase domain from TadA protein with different alterations at position 82 (see column 2, lines 2, 11, 26, 40).
Gaudelli also teaches that the napDNAbp encoded by the polynucleotide comprises a sequence derived from Cas9 (see column 4, line 30; column 5, lines 64-67). Gaudelli also teaches that the Cas9 derived napDNAbp can be from Streptococcus pyogenes (SpCas9; see column 6, lines 51-59).
Gaudelli teaches that the SpCas9 protein can be a variant with a nickase mutation ( see column 6, lines 65-67; column 7, lines 1-7).
Gaudelli teaches that the SpCas9 can comprises amino acid substitutions based on reference sequences obtained through directed evolution (see column 103, lines 44-45; column 439, lines 60-67).
Gaudelli teaches that the amino acid substitutions can be at positions 1135 and 1337 (see column 6, lines 61-65).
Gaudelli does not teach a mutation M1135L specifically.
However, a search for SEQ ID NO: 554 leads to results with more than 90% sequence identity; one of such result is shown below (Qy =Query, instant SEQ ID NO: 554; Db = Database, USPAT’666 ‘s SEQ ID NO: 2253):
RESULT 13
US-17-929-455-2253
(NOTE: this sequence has 8 duplicates in the database searched.
See complete list at the end of this report)
Sequence 2253, US/17929455
Patent No. 12565666
GENERAL INFORMATION
APPLICANT: FLAGSHIP PIONEERING INNOVATIONS VI, LLC (en)
TITLE OF INVENTION: IMPROVED METHODS AND COMPOSITIONS FOR MODULATING A GENOME (en)
FILE REFERENCE: V2065-701020
CURRENT APPLICATION NUMBER: US/17/929,455
CURRENT FILING DATE: 2022-09-02
NUMBER OF SEQ ID NOS: 3377
SEQ ID NO 2253
LENGTH: 1368
TYPE: PRT
FEATURE:
NAME/KEY: source
LOCATION: 1..1368
QUALIFIERS: mol_type = protein
organism = synthetic construct
note = Description of Artificial Sequence: Synthetic
polypeptide
Query Match 98.9%; Score 6927; Length 1368;
Best Local Similarity 99.0%;
Matches 1355; Conservative 3; Mismatches 10; Indels 0; Gaps 0;
Qy 1 MDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAE 60
||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAE 60
Qy 61 ATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFG 120
Qy 121 NIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSD 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 NIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSD 180
Qy 181 VDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGN 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 VDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGN 240
Qy 241 LIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAI 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 LIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAI 300
Qy 301 LLSDILRVNTEITKAPLSASMVKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYA 360
|||||||||||||||||||||:||||||||||||||||||||||||||||||||||||||
Db 301 LLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYA 360
Qy 361 GYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGIIPHQIHLGELH 420
|||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Db 361 GYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELH 420
Qy 421 AILRRQGDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEE 480
|||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 AILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEE 480
Qy 481 VVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFL 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 VVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFL 540
Qy 541 SGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKI 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 SGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKI 600
Qy 601 IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRLRYTGWG 660
||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||
Db 601 IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWG 660
Qy 661 RLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSL 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 RLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSL 720
Qy 721 HEHIANLAGSPAIKKGILQTVKVVDELVKVMGGHKPENIVIEMARENQTTQKGQKNSRER 780
|||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||
Db 721 HEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRER 780
Qy 781 MKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDH 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 MKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDH 840
Qy 841 IVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNL 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 IVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNL 900
Qy 901 TKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKS 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 TKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKS 960
Qy 961 KLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRK 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 961 KLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRK 1020
Qy 1021 MIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDF 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1021 MIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDF 1080
Qy 1081 ATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKGNSDKLIARKKDWDPKKYGGFMQPTVA 1140
||||||||||||||||||||||||||||||||| ||||||||||||||||||||: ||||
Db 1081 ATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFLWPTVA 1140
Qy 1141 YSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPK 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1141 YSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPK 1200
Qy 1201 YSLFELENGRKRMLASAKFLQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVE 1260
|||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||
Db 1201 YSLFELENGRKRMLASAKQLQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVE 1260
Qy 1261 QHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGA 1320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1261 QHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGA 1320
Qy 1321 PRAFKYFDTTIARKEYRSTKEVLDATLIHQSITGLYETRIDLSQLGGD 1368
| ||||||||| ||:|||||||||||||||||||||||||||||||||
Db 1321 PAAFKYFDTTIDRKQYRSTKEVLDATLIHQSITGLYETRIDLSQLGGD 1368
As shown in the alignment above, the residue located at M1135 is mutated to L in Cleaver (US Patent No. 12 565 666 B2) in SEQ ID NO: 2253, also described in Table 9 (columns 151-152).
Thus, Cleaver teaches a sequence that is more than 90% identical to instant SEQ ID NO: 554, and that is modified with a mutation M1135L (Table 9, columns 151-152). This mutant protein correspond to a Streptococcus pyogenes Cas9 variant proposed for constructing a recombinant fusion protein comprising a napDNAbp (see column 109, lines 5-10; Table 9, columns 151-152).
In KSR Int 'l v. Teleflex, the Supreme Court, indicated that “The principles underlying [earlier] cases are instructive when the question is whether a patent claiming the combination of elements of prior art is obvious. When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable variation, § 103 likely bars its patentability”. KSR Int'l v. Teleflex lnc., 127 S. Ct. 1727, 1740 (2007).
Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention, to have substituted the napDNAbp domain from Streptococcus pyogenes taught by Gaudelli, with a SpCas9 sequence as taught by Cleaver. It would be substituting one napDNAbp domain with one that is considered as equivalent by Cleaver in the function of the recombinant fusion protein with the ability to bind DNA with specificity for targeted editing. One with ordinary skills in the art motivated in comparing the efficiency of different napDNAbp domains within the fusion protein, could have performed this modification with a reasonable expectation of success and would have arrived at the claimed invention.
Regarding claim 2, Gaudelli teaches that the SpCas9 variant can comprise mutations that give specificity for different PAM sequences AAA, TAA, CAA, GAA, TAT, GAT, or CAC (see column 144, lines 65-67). Gaudelli teaches that amino acid substitutions can be performed at positions 1135, and 1337 among others (see columns 145-146).
Cleaver teaches that the SpCas9 can comprise the amino acid substitution T1337R and one or more additional amino acid substitutions (see column 109, lines 18-20). The mutant SpCas9 protein taught in Cleaver’s SEQ ID NO: 2253 is mutated at residue 1337R (see sequence in alignment above).
Cleaver further teaches that additional mutation can be performed on this specific residue to obtain 1337K (see column 109, lines 18-25).
Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention to have further mutated the sequence of napDNAbp domain toward a lysine residue at position 1337, to optimize the efficiency of gene editing and avoid off-target effects. One with ordinary skills in the art, could have performed this modification as part of a screening assay with a reasonable expectation of success and would have arrived at the claimed invention.
Regarding claims 3 and 4, A search for SEQ ID NO: 1 with at least one alteration at position L36, I76, V82, Y147, Q154 or N157, leads to the result below (Qy =Query, instant SEQ ID NO: 1; Db = Database, Gaudelli’s SEQ ID NO: 180):
RESULT 7
US-17-127-630-180
(NOTE: this sequence has 4 duplicates in the database searched.
See complete list at the end of this report)
Sequence 180, US/17127630
Patent No. 11155803
GENERAL INFORMATION
APPLICANT: BEAM THERAPEUTICS INC.
TITLE OF INVENTION: ADENOSINE DEAMINASE BASE EDITORS AND
TITLE OF INVENTION: METHODS OF USING SAME TO
TITLE OF INVENTION: MODIFY A NUCLEOBASE IN A TARGET SEQUENCE
FILE REFERENCE: 52885-789.601
CURRENT APPLICATION NUMBER: US/17/127,630
CURRENT FILING DATE: 2020-12-18
PRIOR APPLICATION NUMBER: PCT/US20/18192
PRIOR FILING DATE: 2020-02-13
PRIOR APPLICATION NUMBER: 62/966,526
PRIOR FILING DATE: 2020-01-27
PRIOR APPLICATION NUMBER: 62/941,523
PRIOR FILING DATE: 2019-11-27
PRIOR APPLICATION NUMBER: 62/941,569
PRIOR FILING DATE: 2019-11-27
PRIOR APPLICATION NUMBER: 62/931,722
PRIOR FILING DATE: 2019-11-06
PRIOR APPLICATION NUMBER: 62/931,747
PRIOR FILING DATE: 2019-11-06
PRIOR APPLICATION NUMBER: 62/912,992
PRIOR FILING DATE: 2019-10-09
PRIOR APPLICATION NUMBER: 62/888,867
PRIOR FILING DATE: 2019-08-19
PRIOR APPLICATION NUMBER: 62/876,354
PRIOR FILING DATE: 2019-07-19
PRIOR APPLICATION NUMBER: 62/873,138
PRIOR FILING DATE: 2019-07-11
Remaining Prior Application data removed - See File Wrapper or PALM.
NUMBER OF SEQ ID NOS: 395
SEQ ID NO 180
LENGTH: 1588
TYPE: PRT
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: Description of Artificial Sequence: Synthetic
polypeptide
Query Match 99.5%; Score 870; Length 1588;
Best Local Similarity 99.4%;
Matches 166; Conservative 1; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEI 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEI 60
Qy 61 MALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDV 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 MALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDV 120
Qy 121 LHYPGMNHRVEITEGILADECAALLCYFFRMPRQVFNAQKKAQSSTD 167
|||||||||||||||||||||||||||||||||:|||||||||||||
Db 121 LHYPGMNHRVEITEGILADECAALLCYFFRMPRRVFNAQKKAQSSTD 167
Thus, Gaudelli teaches elements of claim 3, i.e., an adenosine deaminase domain comprising an alteration at amino acid position Q154R in Gaudelli’s SEQ ID NO: 180. Gaudelli also teaches an adenosine deaminase domain derived from TadA*8, comprising one or more alterations such as the combination Y147T + Q154R or V82S + Q154S, or V82S + Y147R, or I76Y + V82S + Y123H + Y147R + Q154R (see column 42, lines 24-46).
Therefore, the combination of references Gaudelli and Cleaver does teach the elements of claims 3 and 4. The obviousness of combining the references is described above.
Regarding claim 8, Gaudelli teaches a linker sequence denoted in italics in Gaudelli’s SEQ ID NO: 12, as example of recombinant napDNAbp domain derived from Cas9 in columns 3-4, and column 4, lines 29-32).
Cleaver teaches linker sequences (see columns 56, lines 16-60); Cleaver teaches that the linker can be introduced between a nuclear localization sequence and a neighboring domain (see column 182, lines 25-27).
The obviousness of combining the references is described above.
Regarding claims 10-11, Gaudelli teaches a sequence 100% identical to instant SEQ ID NO: 438, i.e., Gaudelli’s SEQ ID NO: 120, that is a nuclear localization sequence (NLS) that can be added to the recombinant fusion protein (see column 221, line 45).
Cleaver teaches a sequence that comprises instant SEQ ID NO: 438 and is also 100% identical on contiguous 22 amino acids of instant SEQ ID NO: 438, i.e., Cleaver’s SEQ ID NO: 1582, that can be added to the recombinant fusion protein (see column 182, lines 30-31).
Therefore, the combination of references Gaudelli and Cleaver renders elements of claims 10 and 11 obvious. The obviousness of the combination of references is described above.
Regarding claim 12, a search for instant SEQ ID NO: 446 leads to Gaudelli’s SEQ ID NO: 182. As shown below, Gaudelli teaches sequences encoding for base editor comprising an amino acid sequence that is at least 90% identical to instant SEQ ID NO: 446 (Qy). See alignment below with Gaudelli’s SEQ ID NO: 182 (Db):
RESULT 3
US-17-127-630-182
(NOTE: this sequence has 4 duplicates in the database searched.
See complete list at the end of this report)
Sequence 182, US/17127630
Patent No. 11155803
GENERAL INFORMATION
APPLICANT: BEAM THERAPEUTICS INC.
TITLE OF INVENTION: ADENOSINE DEAMINASE BASE EDITORS AND
TITLE OF INVENTION: METHODS OF USING SAME TO
TITLE OF INVENTION: MODIFY A NUCLEOBASE IN A TARGET SEQUENCE
FILE REFERENCE: 52885-789.601
CURRENT APPLICATION NUMBER: US/17/127,630
CURRENT FILING DATE: 2020-12-18
PRIOR APPLICATION NUMBER: PCT/US20/18192
PRIOR FILING DATE: 2020-02-13
PRIOR APPLICATION NUMBER: 62/966,526
PRIOR FILING DATE: 2020-01-27
PRIOR APPLICATION NUMBER: 62/941,523
PRIOR FILING DATE: 2019-11-27
PRIOR APPLICATION NUMBER: 62/941,569
PRIOR FILING DATE: 2019-11-27
PRIOR APPLICATION NUMBER: 62/931,722
PRIOR FILING DATE: 2019-11-06
PRIOR APPLICATION NUMBER: 62/931,747
PRIOR FILING DATE: 2019-11-06
PRIOR APPLICATION NUMBER: 62/912,992
PRIOR FILING DATE: 2019-10-09
PRIOR APPLICATION NUMBER: 62/888,867
PRIOR FILING DATE: 2019-08-19
PRIOR APPLICATION NUMBER: 62/876,354
PRIOR FILING DATE: 2019-07-19
PRIOR APPLICATION NUMBER: 62/873,138
PRIOR FILING DATE: 2019-07-11
Remaining Prior Application data removed - See File Wrapper or PALM.
NUMBER OF SEQ ID NOS: 395
SEQ ID NO 182
LENGTH: 1588
TYPE: PRT
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: Description of Artificial Sequence: Synthetic
polypeptide
Query Match 98.5%; Score 8026; Length 1588;
Best Local Similarity 98.7%;
Matches 1566; Conservative 6; Mismatches 15; Indels 0; Gaps 0;
Qy 1 SEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVHNNRVIGEGWNRAIGLHDPTAHAEIM 60
|||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Db 2 SEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIM 61
Qy 61 ALRQGGLVMQNYRLYDATLYTTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDVL 120
|||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Db 62 ALRQGGLVMQNYRLYDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDVL 121
Qy 121 HYPGMNHRVEITEGILADECAALLCTFFRMPRSVFKAQKKAQSSTDSGGSSGGSSGSETP 180
||||||||||||||||||||||||| |||||| || ||||||||||||||||||||||||
Db 122 HYPGMNHRVEITEGILADECAALLCRFFRMPRRVFNAQKKAQSSTDSGGSSGGSSGSETP 181
Qy 181 GTSESATPESSGGSSGGSDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSI 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 182 GTSESATPESSGGSSGGSDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSI 241
Qy 241 KKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEE 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 242 KKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEE 301
Qy 301 SFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIK 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 302 SFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIK 361
Qy 361 FRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLE 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 362 FRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLE 421
Qy 421 NLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIG 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 422 NLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIG 481
Qy 481 DQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMVKRYDEHHQDLTLLKALVRQQL 540
||||||||||||||||||||||||||||||||||||||:|||||||||||||||||||||
Db 482 DQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQL 541
Qy 541 PEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQR 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 542 PEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQR 601
Qy 601 TFDNGIIPHQIHLGELHAILRRQGDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFA 660
||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Db 602 TFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFA 661
Qy 661 WMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNE 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 662 WMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNE 721
Qy 721 LTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGV 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 722 LTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGV 781
Qy 781 EDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLF 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 782 EDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLF 841
Qy 841 DDKVMKQLKRLRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLT 900
|||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||
Db 842 DDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLT 901
Qy 901 FKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGGHKPENIVIEM 960
||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||
Db 902 FKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEM 961
Qy 961 ARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMY 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 962 ARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMY 1021
Qy 1021 VDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYW 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1022 VDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYW 1081
Qy 1081 RQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKY 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1082 RQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKY 1141
Qy 1141 DENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1142 DENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK 1201
Qy 1201 LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLI 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1202 LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLI 1261
Qy 1261 ETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKGNSDKLIARK 1320
|||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Db 1262 ETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARK 1321
Qy 1321 KDWDPKKYGGFLQPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLE 1380
|||||||||||: |||||||||||||||||||||||||||||||||||||||||||||||
Db 1322 KDWDPKKYGGFVSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLE 1381
Qy 1381 AKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAKFLQKGNELALPSKYVNFLYLASHYE 1440
||||||||||||||||||||||||||||||||||: ||||||||||||||||||||||||
Db 1382 AKGYKEVKKDLIIKLPKYSLFELENGRKRMLASARELQKGNELALPSKYVNFLYLASHYE 1441
Qy 1441 KLKGSPKDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILDDANLDKVLSAYNKHRDKPIR 1500
||||||:|||||||||||||||||||||||||||||||| ||||||||||||||||||||
Db 1442 KLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIR 1501
Qy 1501 EQAENIIHLFTLTNLGAPRAFKYFDTTIARKEYKSTKEVLDATLIHQSITGLYETRIDLS 1560
|||||||||||||||||| ||||||||| ||:|:||||||||||||||||||||||||||
Db 1502 EQAENIIHLFTLTNLGAPAAFKYFDTTIDRKQYRSTKEVLDATLIHQSITGLYETRIDLS 1561
Qy 1561 QLGGDEGADKRTADGSEFESPKKKRKV 1587
|||||||||||||||||||||||||||
Db 1562 QLGGDEGADKRTADGSEFESPKKKRKV 1588
Therefore, Gaudelli teaches a base editor that is at least 90% identical to SEQ ID NO: 446. The obviousness of the combination of the references Gaudelli and Cleaver is described above.
Regarding claims 14 and 15, Gaudelli teaches that the constructs can be delivered as plasmid and as mRNA (see column 109, lines 42-56; column 335, lines 36-67; column 336, lines 1-67). Gaudelli teaches that delivering an ABE8 editor as a nucleic acid-based delivery system, e.g., an mRNA has on-target editing efficiency that can be higher (see column 335, lines 49-51).
Cleaver teaches a system for modifying DNA comprising a polypeptide or a nucleic acid, and said nucleic acid can be either DNA or mRNA (see column 1, lines 49, 63; column 2, lines 50 and 63).
The obviousness of the combination of references, Gaudelli and Cleaver, is described above.
Regarding claim 17, Gaudelli teaches a system for gene editing comprising a recombinant fusion protein and a guide RNA, that is a sgRNA (see Figures 2A, 56; column 104, lines 29-30).
Cleaver also teaches sgRNA in the gene editing system (see column 125, lines 46-48; column 171, lines 31-45).
The obviousness of the combination of references, Gaudelli and Cleaver, is described above.
Claims 5-6, 9, 18-20 and 22-26 are rejected under 35 U.S.C. §103 as being unpatentable over Gaudelli (Gaudelli, et al. US Patent No. 11,155,803 B2, published October 26, 2021; cited on IDS filed 05/04/2026 (18-pages, patent#10)) in view of Cleaver (Cleaver, S. et al. US Patent No. 12,565,666 B2, published March 3, 2026, benefitting from priority of International Application PCT/US2021/020943 filed March 4, 2021, and provisional Applications Nos: 63/035,674 filed June 5, 2020, and 62/985,264 filed March 4, 2020), as applied to claims 1,3-4, 8, 16 and 17 above and in further view of Bryson (Bryson, D. et al. WO 2019/217943 A1; published November 14, 2019; cited on IDS filed 05/04/2026 (17 pages-WIPO doc #37)).
The rejections of claims 1, 3-4, 16 and 17 are described above. The
obviousness of the combination of Gaudelli and Cleaver is described above. The elements of claims 1, 3-4, 16 and 17 are rendered obvious by the combination of references.
However, regarding claims 5 and 6, the combination of references does not render elements of claims 5 and 6 obvious, i.e., “wherein the adenosine deaminase domain comprises the amino acid alterations L36H, l76Y, V82T, Y147T, Q154S, and N157K referenced to SEQ ID NO: 1” (claim 5) and “wherein the adenosine deaminase domain comprises an amino acid sequence that is at least 90% identical to the following amino acid sequence: SEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVHNNRVIGEGWNRAIGLHDPTAHAEIMALRQGGLVMQNYRLYDATLYTTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDVLHYPGMNHRVEITEGILADECAALLCTFFRMPRSVFKAQKKAQSSTD (SEQ ID NO: 426).” (claim 6).
Regarding claims 5 and 6, a search for SEQ ID NO: 426 with at least one alteration at position L36, I76, V82, Y147, Q154 or N157, leads to the result below (Qy =Query, instant SEQ ID NO: 426; Db = Database, Gaudelli’s SEQ ID NO: 182):
RESULT 2
US-17-127-630-182
(NOTE: this sequence has 4 duplicates in the database searched.
See complete list at the end of this report)
Sequence 182, US/17127630
Patent No. 11155803
GENERAL INFORMATION
APPLICANT: BEAM THERAPEUTICS INC.
TITLE OF INVENTION: ADENOSINE DEAMINASE BASE EDITORS AND
TITLE OF INVENTION: METHODS OF USING SAME TO
TITLE OF INVENTION: MODIFY A NUCLEOBASE IN A TARGET SEQUENCE
FILE REFERENCE: 52885-789.601
CURRENT APPLICATION NUMBER: US/17/127,630
CURRENT FILING DATE: 2020-12-18
PRIOR APPLICATION NUMBER: PCT/US20/18192
PRIOR FILING DATE: 2020-02-13
PRIOR APPLICATION NUMBER: 62/966,526
PRIOR FILING DATE: 2020-01-27
PRIOR APPLICATION NUMBER: 62/941,523
PRIOR FILING DATE: 2019-11-27
PRIOR APPLICATION NUMBER: 62/941,569
PRIOR FILING DATE: 2019-11-27
PRIOR APPLICATION NUMBER: 62/931,722
PRIOR FILING DATE: 2019-11-06
PRIOR APPLICATION NUMBER: 62/931,747
PRIOR FILING DATE: 2019-11-06
PRIOR APPLICATION NUMBER: 62/912,992
PRIOR FILING DATE: 2019-10-09
PRIOR APPLICATION NUMBER: 62/888,867
PRIOR FILING DATE: 2019-08-19
PRIOR APPLICATION NUMBER: 62/876,354
PRIOR FILING DATE: 2019-07-19
PRIOR APPLICATION NUMBER: 62/873,138
PRIOR FILING DATE: 2019-07-11
Remaining Prior Application data removed - See File Wrapper or PALM.
NUMBER OF SEQ ID NOS: 395
SEQ ID NO 182
LENGTH: 1588
TYPE: PRT
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: Description of Artificial Sequence: Synthetic
polypeptide
Query Match 96.3%; Score 841; Length 1588;
Best Local Similarity 97.0%;
Matches 161; Conservative 0; Mismatches 5; Indels 0; Gaps 0;
Qy 1 SEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVHNNRVIGEGWNRAIGLHDPTAHAEIM 60
|||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Db 2 SEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIM 61
Qy 61 ALRQGGLVMQNYRLYDATLYTTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDVL 120
|||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Db 62 ALRQGGLVMQNYRLYDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDVL 121
Qy 121 HYPGMNHRVEITEGILADECAALLCTFFRMPRSVFKAQKKAQSSTD 166
||||||||||||||||||||||||| |||||| || ||||||||||
Db 122 HYPGMNHRVEITEGILADECAALLCRFFRMPRRVFNAQKKAQSSTD 167
The alignment above shows clearly that Gaudelli’s SEQ ID NO: 182 comprises multiple alterations compared to SEQ ID NO: 426. However, the sequence taught by Gaudelli is 96% identical to instant SEQ ID NO: 426, and comprises alteration l76Y, Y147R, and Q154R.
An alignment of Gaudelli’s SEQ ID NO:182 with SEQ ID NO: 1 is shown below (Qy= instant SEQ ID NO: 1; Db= Gaudelli’s SEQ ID NO: 182):
RESULT 1
AASEQ2_07302026_144133
Query Match 97.9%; Score 856; DB 1; Length 1585;
Best Local Similarity 98.2%;
Matches 164; Conservative 1; Mismatches 2; Indels 0; Gaps 0;
Qy 1 MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEI 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEI 60
Qy 61 MALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDV 120
||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
Db 61 MALRQGGLVMQNYRLYDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDV 120
Qy 121 LHYPGMNHRVEITEGILADECAALLCYFFRMPRQVFNAQKKAQSSTD 167
|||||||||||||||||||||||||| ||||||:|||||||||||||
Db 121 LHYPGMNHRVEITEGILADECAALLCRFFRMPRRVFNAQKKAQSSTD 167
Compared to SEQ ID NO: 1, the sequence SEQ ID NO: 182 taught by Gaudelli comprises only 3 alterations (l76Y, Y147R, and Q154R) ( also in SEQ ID NO: 186 with H123Y123H reversion, see column 319).
Gaudelli teaches other combinations such as Y147T and Q154S (see column 317; SEQ ID NO:185), V82S and Q154R (column 319; SEQ ID NO: 187).
Gaudelli also teaches that at position 82, the modification can be V82X, wherein X can be any amino acid other than “V” (see column 457, lines 38-41).
Therefore, the combination of references Gaudelli and Cleaver does not teach a sequence comprising the amino acid alterations L36H, I76Y, V82T, Y147T, Q154S, and N157K, all in the same sequence.
However, Bryson teaches multiple combinations of mutations in the adenosine deaminase, such as H36X, Q154X, and K157X compared to the TadA reference sequence (see [0393]-[0394]).
Bryson’s teaching are specifically relevant to one with ordinary skills in the art since, Bryson also teaches a base editor system for correcting a pathogenic single nucleotide polymorphism (SNP) in a gene, wherein the base editor system comprises a base editor comprising a polynucleotide-programmable DNA-binding domain (napDNAbp), a deaminase domain and a guide polynucleotide (see [0018]).
Bryson teaches a SpCas9 derived napDNAbp domain that is more than 98% identical to instant SEQ ID NO: 554 (see [0013]). See alignment below (Qy = Query; instant SEQ ID NO: 554); Db = Database, Bryson’s sequence shown in [0013]):
Query Match 98.6%; Score 6905; DB 1; Length 1368;
Best Local Similarity 98.9%;
Matches 1353; Conservative 1; Mismatches 14; Indels 0; Gaps 0;
Qy 1 MDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAE 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAE 60
Qy 61 ATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFG 120
Qy 121 NIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSD 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 NIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSD 180
Qy 181 VDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGN 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 VDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGN 240
Qy 241 LIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAI 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 LIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAI 300
Qy 301 LLSDILRVNTEITKAPLSASMVKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYA 360
|||||||||||||||||||||:||||||||||||||||||||||||||||||||||||||
Db 301 LLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYA 360
Qy 361 GYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGIIPHQIHLGELH 420
|||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Db 361 GYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELH 420
Qy 421 AILRRQGDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEE 480
|||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 AILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEE 480
Qy 481 VVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFL 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 VVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFL 540
Qy 541 SGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKI 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 SGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKI 600
Qy 601 IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRLRYTGWG 660
||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||
Db 601 IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWG 660
Qy 661 RLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSL 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 RLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSL 720
Qy 721 HEHIANLAGSPAIKKGILQTVKVVDELVKVMGGHKPENIVIEMARENQTTQKGQKNSRER 780
|||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||
Db 721 HEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRER 780
Qy 781 MKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDH 840
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 MKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDA 840
Qy 841 IVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNL 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 IVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNL 900
Qy 901 TKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKS 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 TKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKS 960
Qy 961 KLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRK 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 961 KLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRK 1020
Qy 1021 MIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDF 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1021 MIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDF 1080
Qy 1081 ATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKGNSDKLIARKKDWDPKKYGGFMQPTVA 1140
||||||||||||||||||||||||||||||||| |||||||||||||||||||| ||||
Db 1081 ATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVA 1140
Qy 1141 YSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPK 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1141 YSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPK 1200
Qy 1201 YSLFELENGRKRMLASAKFLQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVE 1260
||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||
Db 1201 YSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVE 1260
Qy 1261 QHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGA 1320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1261 QHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGA 1320
Qy 1321 PRAFKYFDTTIARKEYRSTKEVLDATLIHQSITGLYETRIDLSQLGGD 1368
| ||||||||| || | |||||||||||||||||||||||||||||||
Db 1321 PAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD 1368
Bryson also teaches that the adenosine deaminase domain may comprise single, double, or multiple mutations up to 11-12 mutations (see page 152, [0404]).
Bryson teaches that the adenosine base editor (ABE) can comprise evolved TadA variant, which can accumulate different mutations at each generation, i.e., round of directed evolution (see [0431]-[0435], see Table 2).
In Table 2, Bryson teaches different genotype of ABEs, with mutations at different positions. For example, evolution can replace an “L” at position 36 to an “H” in and an “K” at position 157 at the place of “N”, e.g., evolution from ABE5.3 to ABE5.4. This shows that these mutations can be reverted to an “H” in position 36, and to a “K” in position 157 after few generations, as shown in Table 2 and in the excerpt below:
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Therefore, Bryson teaches an ABE5.4 that has been evolved to comprise a mutation 36H, 147Y, and 157K, among other mutations.
Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention to have combined the mutations taught by Gaudelli, i.e., I76Y, Y147T, Q154S and V82X, with those taught by Bryson, i.e., 36H, 147Y, and 157K taught by Bryson in ABE5.4 variant as derived from ABE5.3. One with ordinary skills in the art, motivated in optimizing a specific recombinant fusion protein adapting to a specific gene of interest, could have performed this modification with a reasonable expectation of success as taught by Bryson, and would have arrived at the claimed invention.
Regarding claim 9, Bryson teaches a linker with a sequence that is 100% identical to instant SEQ ID NO: 357 (see page 43, [0107]; page 214, claim 54; page 221, claim 100; page 228, claim 144).
Therefore, the combination of references Gaudelli, Cleaver and Bryson teaches the elements in claim 9. The obviousness of the combination is described above.
Regarding claim 18, Bryson teaches a spacer sequence 100% identical to instant SEQ ID NO: 561 in Table 3A (page 183, [0482]). The sequence is described as “gRNA targeting sequence” corresponding to pathogenic mutation E342K in SERPINA1 gene.
Regarding claim 19, Bryson teaches a sequence that is 100% identical to instant SEQ ID NO: 566, described as gRNAs useful in the method of the invention (see [0557], 4th sequence); see excerpt below:
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Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention to have combined the base editor taught by Gaudelli modified by Cleaver, with a spacer and a gRNA taught by Bryson in the gene editing system. One with ordinary skills in the art, motivated in modifying a pathogenic mutation, such as the E342K in the SERPINA1 gene responsible for the Alpha- 1 Anti-trypsin Deficiency, using a targeted and specific system, could have performed this modification with a reasonable expectation of success as taught by Bryson, and would have arrived at the claimed invention.
Regarding claim 20, Bryson teaches that a gRNA can be modified, 2’-Ome modifications, 2’-Fluoro modification and/or phosphorothioate modification (see [0266]).
It would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention to have combined the teachings of Gaudelli, Cleaver and Bryson, and modified the system using chemical modifications to stabilize the gRNA, as taught by Bryson. One with ordinary skills in the art, motivated in a higher potency due to increased stability of the gRNA, could have performed this modification with a reasonable expectation of success and would have arrived at the claimed invention.
Regarding claims 22-26, Gaudelli teaches that the components of the base
editing system can be a base editor-encoding mRNA and a guide RNA (see column 409, lines 5-8; column 431, lines 45-67; column 432, lines 1-46). Gaudelli teaches that mRNA delivery is more effective (see column 431, lines 45-47).
Gaudelli teaches a pharmaceutical composition comprising the fusion protein base editor in complex with one or more guide polynucleotides, and a pharmaceutically acceptable excipient (column 12, lines 27-44). Gaudelli teaches that the nucleic acids encoding base editing systems according to the invention can be administered to subjects or delivered into cells in vitro or in vivo in lipid nanoparticles (see column 400, lines 55-62). Gaudelli also teaches that the lipids in the nanoparticles can be cationic (see column 402, lines 8-21; Table 11).
Cleaver also teaches a pharmaceutical composition comprising the system,
nucleic acid, polypeptide or vector, and a pharmaceutically acceptable excipient (see column 51, lines 25-33). Cleaver also teaches that the carrier for delivery of the composition can be a vesicle, a liposome, a lipid nanoparticle (column 51, lines 30-33).
Bryson also teaches that the system can be delivered using lipid nanoparticle (LNP) (see [0563]). Bryson teaches lipids suitable for nanoparticle formulations and teaches that the lipids can be cationic and helper lipids (see [0497]; Table 4).
Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention, to have formulated the gene editing system according to the teachings of Gaudelli, Cleaver and Bryson. One with ordinary skills in the art motivated in safely delivering a system with pharmaceutically acceptable components could have modified the composition to encapsule it within a lipid nanoparticle designed with a mix formulation comprising cationic and helper lipids as taught by Bryson. One with ordinary skills in the art could have performed this modification with a reasonable expectation of success and would arrived at the claimed invention.
Claim 21 is rejected under 35 U.S.C. § 103 as being unpatentable over Bryson (Bryson, D. et al. WO 2019/217943 A1; published November 14, 2019; cited on IDS filed 05/04/2026 (17pages-WIPO doc #37)) in view of Packer (Packer, M.S. et al. “Evaluation of cytosine base editing and adenine base editing as a potential treatment for alpha-1 antitrypsin deficiency”. Molecular Therapy, Vol. 30, No. 4 (April 2022), pp: 1396-1406; Supplemental information Table 2), and Klabenkova (Klabenkova, K. et al. “Chemistry of Peptide-Oligonucleotide Conjugates: A review”. Molecules, Vol. 26, 5420 (2021), p: 1-36).
Regarding claim 21, Bryson teaches a method of editing single nucleotide polymorphism using a programmable base editor systems comprising a recombinant fusion base editor polynucleotide programmable nucleotide binding protein (napDNAbp) domain and a nucleobase editing domain, in conjunction with a guide polynucleotide (see title and abstract).
Bryson teaches the use of the base editing system for correcting pathogenic mutation responsible for Alpha-1 Antitrypsin Deficiency (A1AD) (see [0003]-[0011]).
Bryson teaches using a specific guide RNA and spacer for correcting the mutation E342K in SERPINA1 gene can be performed with a base editing system ([0006]; Table 3A and Example 4, [0554]-[0557]).
Bryson teaches a sequence that is 100% identical to instant SEQ ID NO: 566, also the backbone sequence of instant SEQ ID Nos: 569 and 570), described as gRNAs useful in the method of the invention (see [0557], 4th sequence); see excerpt below:
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Bryson teaches that the guide RNA can be modified using 2’-Ome modifications, 2’-Fluoro modifications and/or phosphorothioate modifications (see [0266]). Bryson also teaches that “in some cases the guide polynucleotide comprises non-natural (or unnatural) nucleotides (e.g., peptide nucleic acid or nucleotide analogs)” ([0239]). Bryson teaches that some modifications can be biochemical modifications that can increase membrane permeability, or half-life (see [0080]).
Bryson also teaches Cell penetrating peptide sequences that can be attached at the end of base editor-Cas9 recombinant protein, and can be used as a localization
signal KRTADGSEFESPKKKRKV (see sequence in [0554]; and list of options in [0111], [0285], [0290]), see partial sequence from [0554] below :
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Bryson does not teach the exact modification patterns claimed in instant SEQ ID Nos: 569 and 570.
However, Packer teaches the sequence and the modification pattern of instant SEQ ID NO: 570, see Table 2 in Supplemental information and below:
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Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention to have used the sequence taught by Bryson and modified it according to Packer’s teaching. One with ordinary skills in the art motivated in using a potent and stable guide RNA within the base editing system taught by Bryson, would have considered modification patterns optimized for stability in cells. One with ordinary skills in the art could have performed this modification with a reasonable expectation of success and would have arrived at the claimed invention.
The combination of references Bryson and Packer renders obvious using a localization sequence that can also enhance membrane permeability of the polypeptides comprised within the base editing system, such as the sequence “KRTADGSEFESPKKKRKV”.
However, Bryson and Packer do not teach modifying and covalently linking an amino acid sequence to the guide RNA. Bryson and Packer do not teach the exact sequence of instant SEQ ID NO: 543.
However, Klabenkova teaches that the use of cell-penetrating peptide can be extended to nucleic acids for enhanced delivery (see abstract, and page 6, section 2.4).
Klabenkova teaches that the application of viral vector to the delivery of therapeutic nucleic acids is hampered by the immunogenicity and safety concerns, therefore the use of alternative and safer non-viral vectors and strategies, e.g., peptide conjugates (see section 2.4, 4th paragraph).
Klabenkova teaches the use of Cell-penetrating peptides (CPPs) (see Table 1, page 9). Klabenkova teaches the use of “recombinant” synthetic peptides comprising a fragment of the SV40 antigen (PKKKRKV) (see Table 1 and section 7, and Figure 4).
Klabenkova also teaches conjugation approaches, stating that conjugation via thioether or disulfide bonds is widely used for the synthesis of peptide-oligonucleotide conjugates (POCs) ( see section 9.1, Figure 9; and Figure 11):
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Klabenkova teaches that the cysteine residue in a peptide often serves as a source of the thiol group (see page 17, section 9.1, 2nd paragraph).
Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention, to have modified the localization signal taught by Bryson, i.e., “KRTADGSEFESPKKKRKV” with a cysteine at the 5’ end of the CPP sequence for conjugating with the 3’ end of the guide RNA, as taught by Klabenkova. One with ordinary skills in the art motivated in avoiding viral vectors and transforming the method of delivery of the whole system, polypeptides and polynucleotides, to a safer and non-viral method, could have performed this modification with a reasonable expectation of success and would have arrived at the claimed invention.
Allowable Subject Matter
SEQ ID Nos: 426 and 575 appear to be free of prior art.
Claims 7 and 13 are objected to as being dependent upon a rejected base claim but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
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/A.D./Examiner, Art Unit 1636
/NANCY J LEITH/Primary Examiner, Art Unit 1636
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