IP Library Granted Patent US 12,735,689
Granted Patent B2
US 12,735,689 · App. 19/344,313 · Granted Sep 15, 2026

Compositions and methods for nucleic acid modifications

Inventors: David Rabuka (Berkeley, CA); Allison Sharrar (Berkeley, CA); Michael Schelle (Berkeley, CA); Luisa Mayumi Arake de Tacca (Berkeley, CA)
Assignee: Acrigen Biosciences
C12N9/22C12N5/0636C12N15/111C12N15/8261C12N15/86C07K2319/09C12N2310/20C12N2510/00
View Patent ↗
Loading inventors, assignments & file history…
Monitor This Case
Get email alerts when status or documents change.
Order Certified Copies
Most orders are placed with the USPTO same day — all within 24 business hours.
Order via The Patent Place →
Pre-filled with this patent's details
Quick Facts
Patent No.
US 12,735,689
App. No.
19/344,313
Granted
Sep 15, 2026
Kind
B2
Abstract

The present disclosure provides nucleases and compositions, methods, and systems thereof for nucleic acid modification. More particularly, the present disclosure provides compositions and system comprising a nuclease comprising an amino acid sequence having at least 70% identity to any of SEQ ID NOs: 1-1096 and at least one gRNA.

Claims (8)

1 . A composition comprising a nuclease, wherein the nuclease comprises the amino acid sequence of SEQ ID NO: 535.

2 . The composition of claim 1 , further comprising a fusion protein comprising the nuclease.

3 . The composition of claim 2 , wherein the fusion protein comprises a nuclear localization sequence.

4 . A kit comprising the composition of claim 1 and at least one guide ribonucleic acid (gRNA).

5 . The kit of claim 4 , wherein the at least one gRNA comprises a first region configured to interact with the nuclease and a second region configured to hybridize with a portion of a target nucleic acid.

6 . An engineered nuclease, wherein the engineered nuclease comprises the amino acid sequence of SEQ ID NO: 535.

7 . A nucleic acid encoding the engineered nuclease of claim 6 .

8 . A vector comprising the nucleic acid of claim 7 .

Continuity (5)
Continuation 19261682 · Jul 7, 2025
Continuation 19056056 · Feb 18, 2025
Continuation 18696667 · Sep 28, 2022
Provisional Application 63249296 · Sep 28, 2021
Related Publication 20260022359A1 · Jan 22, 2026
References Cited (150)
US 5034506A · Summerton et al. · 1991 [cited by applicant]
US 5736396A · Bruder et al. · 1998 [cited by applicant]
US 8546553B2 · Terns et al. · 2013 [cited by applicant]
US 8697359B1 · Zhang · 2014 [cited by applicant]
US 8771945B1 · Zhang · 2014 [cited by applicant]
US 8795965B2 · Zhang · 2014 [cited by applicant]
US 8865406B2 · Zhang et al. · 2014 [cited by applicant]
US 8871445B2 · Cong et al. · 2014 [cited by applicant]
US 8889356B2 · Zhang · 2014 [cited by applicant]
US 8889418B2 · Zhang et al. · 2014 [cited by applicant]
US 8895308B1 · Zhang et al. · 2014 [cited by applicant]
US 8906616B2 · Zhang et al. · 2014 [cited by applicant]
US 8932814B2 · Cong et al. · 2015 [cited by applicant]
US 8945839B2 · Zhang · 2015 [cited by applicant]
US 8993233B2 · Zhang et al. · 2015 [cited by applicant]
US 8999641B2 · Zhang et al. · 2015 [cited by applicant]
US 9115348B2 · Haurwitz et al. · 2015 [cited by applicant]
US 9149049B2 · Manoury et al. · 2015 [cited by applicant]
US 9404098B2 · Terns et al. · 2016 [cited by applicant]
US 9493844B2 · Sastry-Dent et al. · 2016 [cited by applicant]
US 9567603B2 · Joung et al. · 2017 [cited by applicant]
US 9637739B2 · Siksnys et al. · 2017 [cited by applicant]
US 9663782B2 · Yu et al. · 2017 [cited by applicant]
US 9885026B2 · Brouns et al. · 2018 [cited by applicant]
US 9951342B2 · Barrangou et al. · 2018 [cited by applicant]
US 10087431B2 · Wiedenheft et al. · 2018 [cited by applicant]
US 10227610B2 · Chen et al. · 2019 [cited by applicant]
US 10266850B2 · Doudna et al. · 2019 [cited by applicant]
US 10601748B2 · Lan et al. · 2020 [cited by applicant]
US 10604771B2 · Cannon et al. · 2020 [cited by applicant]
US 10760064B2 · Joung et al. · 2020 [cited by applicant]
US 20100076057A1 · Sontheimer et al. · 2010 [cited by applicant]
US 20110293703A1 · Mahon et al. · 2011 [cited by applicant]
US 20130244279A1 · De Fougerolles et al. · 2013 [cited by applicant]
US 20130245107A1 · De Fougerolles et al. · 2013 [cited by applicant]
US 20130252281A1 · De Fougerolles et al. · 2013 [cited by applicant]
US 20130302401A1 · Ma et al. · 2013 [cited by applicant]
US 20140113376A1 · Sorek et al. · 2014 [cited by applicant]
US 20140179770A1 · Zhang et al. · 2014 [cited by applicant]
US 20140186843A1 · Zhang et al. · 2014 [cited by applicant]
US 20140186919A1 · Zhang et al. · 2014 [cited by applicant]
US 20140189896A1 · Zhang et al. · 2014 [cited by applicant]
US 20140199767A1 · Barrangou et al. · 2014 [cited by applicant]
US 20140201857A1 · Fahrenkrug et al. · 2014 [cited by applicant]
US 20140212869A1 · Sampas et al. · 2014 [cited by applicant]
US 20140242664A1 · Zhang et al. · 2014 [cited by applicant]
US 20140242699A1 · Zhang · 2014 [cited by applicant]
US 20140273230A1 · Chen et al. · 2014 [cited by applicant]
US 20140287938A1 · Zhang et al. · 2014 [cited by applicant]
US 20140294773A1 · Brouns et al. · 2014 [cited by applicant]
US 20140309487A1 · Lee et al. · 2014 [cited by applicant]
US 20140310828A1 · Lee et al. · 2014 [cited by applicant]
US 20140310830A1 · Zhang et al. · 2014 [cited by applicant]
US 20140315985A1 · May et al. · 2014 [cited by applicant]
US 20140349400A1 · Jakimo et al. · 2014 [cited by applicant]
US 20140357530A1 · Zhang et al. · 2014 [cited by applicant]
US 20150031134A1 · Zhang et al. · 2015 [cited by applicant]
US 20150050699A1 · Siksnys et al. · 2015 [cited by applicant]
US 20210017249A1 · Sather et al. · 2021 [cited by applicant]
US 20210024958A1 · Miller et al. · 2021 [cited by applicant]
US 20240271113A1 · Harrington et al. · 2024 [cited by applicant]
US 20250179455A1 · Rabuka et al. · 2025 [cited by applicant]
US 20250179456A1 · Rabuka et al. · 2025 [cited by applicant]
WO WO2014118272A1 · 2014 [cited by applicant]
WO WO2018073393A2 · 2018 [cited by applicant]
WO WO2020142754A2 · 2020 [cited by applicant]
WO WO2021046526A1 · 2021 [cited by applicant]
WO WO2021092130A1 · 2021 [cited by applicant]
WO WO2021178933A2 · 2021 [cited by applicant]
WO WO2021178934A1 · 2021 [cited by applicant]
WO WO2023028444A1 · 2023 [cited by applicant]
WO WO2023056291A1 · 2023 [cited by applicant]
WO WO2024020346A2 · 2024 [cited by applicant]
Safari F et al. Cell Biosci. May 9, 2019;9:36 (Year: 2019). [cited by examiner]
GenBank MBR6223972 (Year: 2021). [cited by examiner]
Altschul, Stephen F. et al. Basic Local Alignment Search Tool. Journal of Molecular Biology 215(3):403-410 (1990). [cited by applicant]
Altschul, Stephen F. et al. Gapped BLAST and PSI-BLAST: a new Generation of Protein Database Search Programs. Nucleic Acids Research 25(17):3389-3402 (1997). [cited by applicant]
Ausubel, Frederick M. et al. Current Protocols in Molecular Biology. John Wiley & Sons (1989). [cited by applicant]
Basha, Genc. et al. Influence of cationic lipid composition on gene silencing properties of lipid nanoparticle formulations of siRNA in antigen-presenting cells. Molecular Therapy 19(12):2186-2200 (2011). [cited by applicant]
Biegert, Andreas, and Johannes Söding. Sequence context-specific profiles for homology searching. Proceedings of the National Academy of Sciences 106(10):3770-3775 (2009). [cited by applicant]
Bloem, L. J. et al. GenBank Accession No. S62283. Version No. S62283.1. 5-HT1C serotonin receptor {promoter region} [mice, Genomic, 1859 nt]: pp. 1-2. Record Created Aug. 25, 1993. Retrieved Dec. 13, 2024. Retrieved fro… [cited by applicant]
Braasch, Dwaine A, and David R. Corey. Novel antisense and peptide nucleic acid strategies for controlling gene expression. Biochemistry 41(14):4503-4510 (2002). [cited by applicant]
Brinkman, Eva K. et al. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic acids research 42(22):e168, 1-8 (2014). [cited by applicant]
Cebrian-Serrano, Alberto, and Benjamin Davies. CRISPR-Cas orthologues and variants: optimizing the repertoire, specificity and delivery of genome engineering tools. Mammalian genome 28(7-8):247-261 (2017). [cited by applicant]
Chen, Kunling et al. CRISPR/Cas genome editing and precision plant breeding in agriculture. Annual review of plant biology 70(1):667-697 (2019). [cited by applicant]
Chial, Heidi. Rare genetic disorders: learning about genetic disease through gene mapping, SNPs, and microarray data. Nature education 1(1):192 (2008). [cited by applicant]
Clement, Kendell. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nature Biotechnology 37(3):224-226 (2019). [cited by applicant]
Doudna, Jennifer A, and Emmanuelle Charpentier. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346(6213):1258096, 1-11 (2014). [cited by applicant]
EP22877526.8 Extended European Search Report dated Jul. 14, 2025. [cited by applicant]
EP25178326.2 Extended European Search Report dated Jul. 24, 2025. [cited by applicant]
Gao, Pu. et al. Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition. Cell research 26(8):901-913 (2016). [cited by applicant]
Glick, Bernard R, and John E, Thompson. Methods in Plant Molecular Biology and Biotechnology. CRC Press :1-177 (1993). [cited by applicant]
Gusfield, Dan. Algorithms on strings, trees and sequences: computer science and computational biology. Cambridge University Press (1997). [cited by applicant]
Harrington Sequence Alignment (a sequence alignment of SEQ ID No. 534 of Harrington aligned with instantly recited SEQ ID No. 545, aligned Mar. 20, 2025, SEQ ID No. 534 published Aug. 15, 2024 with effective filing date… [cited by applicant]
Heigwer, Florian. Et al. E-CRISP: fast CRISPR target site identification. Nature methods 11(2):122-123 (2014). [cited by applicant]
Jinek, Martin. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816-821 (2012). [cited by applicant]
Kaufman, Randal J. et al. Translational efficiency of polycistronic mRNAs and their utilization to express heterologous genes in mammalian cells. The EMBO Journal 6(1):187-193 (1987). [cited by applicant]
Kay, Mark A. et al. Viral vectors for gene therapy: the art of turning infectious agents into vehicles of therapeutics. Nature medicine 7(1):33-40 (2001). [cited by applicant]
Klein, Theodore M. et al. High-velocity microprojectiles for delivering nucleic acids into living cells. Nature 327(6117):70-73 (1987). [cited by applicant]
Kleinstiver, Benjamin P. et al. Engineered CRISPR-Cas12a Variants With Increased Activities and Improved Targeting Ranges for Gene, Epigenetic and Base Editing. Nature Biotechnology 37(3):276-282 (2019). [cited by applicant]
Li, Xiaosa. et al. Base editing with a Cpf1-cytidine deaminase fusion. Nature biotechnology 36(4):324-327 (2018). [cited by applicant]
Liu, Pengpeng. et al. Enhanced Cas12a editing in mammalian cells and zebrafish. Nucleic Acids Research 47(8):4169-4180 (2019). [cited by applicant]
Nair, Jayaprakash K. et al. Multivalent N-acetylgalactosamine-conjugated siRNA localizes in hepatocytes and elicits robust RNAi-mediated gene silencing. Journal of the American Chemical Society 136(49):16958-16961 (2014… [cited by applicant]
Noguchi, Hirofumi. et al. PDX-1 protein containing its own antennapedia-like protein transduction domain can transduce pancreatic duct and islet cells. Diabetes 52(7):1732-1737 (2003). [cited by applicant]
Oliva, D. et al. GenBank Accession No. X51956. Version No. X51956.1. Human ENO2 gene for neuron specific (gamma) enolase : pp. 1-5. Record created Apr. 21, 1993. Retrieved Dec. 13, 2024. Retrieved from: https://www.ncbi… [cited by applicant]
PCT/US2022/077169 International Search Report and Written Opinion dated Jan. 20, 2023. [cited by applicant]
PCT/US2023/070339 International Search Report and Written Opinion dated Jan. 23, 2024. [cited by applicant]
PCT/US2023/070339 Invitation to Pay Additional Fees dated Nov. 24, 2023. [cited by applicant]
Peng, X. GenBank Accession No. MBE6326412. Version No. MBE6326412.1. Mag: type V CRISPR-associated protein Cpf1 [Bacteroidales bacterium]: pp. 1-3. Record created Oct. 28, 2020. Retrieved Mar. 18, 2025. Retrieved from: … [cited by applicant]
Prykhozhij et al., CRISPR multitargeter: a web tool to find common and unique CRISPR single guide RNA targets in a set of similar sequences. PLoS One. Mar. 5, 2015;10(3):e0119372. doi: 10.1371/journal.pone.0119372. eCol… [cited by applicant]
Ran, Ann F. et al. Genome engineering using the CRISPR-Cas9 system. Nature Protocols 8(11):2281-2308 (2013). Published online Oct. 24, 2013. [cited by applicant]
Rogaev, E. et al. GenBank Accession No. L04147. Version No. L04147.1. Human neurofilament light chain (NEFL) gene, promoter region: pp. 1-2. Record Created Apr. 27, 1993. Retrieved Dec. 13, 2024. Retrieved from: https:/… [cited by applicant]
Safari, Fatemeh. et al. CRISPR Cpf1 proteins: structure, function and implications for genome editing. Cell and Bioscience 9:36, 1-21 (2019). [cited by applicant]
Schulz, G. E, and R.H. Schirmer. Principles of Protein Structure. Springer-Verlag :1-7 (1979). [cited by applicant]
Seed, Brian. An LFA-3 cDNA encodes a phospholipid-linked membrane protein homologous to its receptor CD2. Nature 329(6142):840-842 (1987). [cited by applicant]
Soding, Johannes. Protein homology detection by HMM-HMM comparison. Bioinformatics 21(7):951-960 (2005). Published online Nov. 5, 2004. [cited by applicant]
Trehin, Rachel. et al. Cellular Uptake but Low Permeation of Human Calcitonin-Derived Cell Penetrating Peptides and Tat (47-57) Through Well-Differentiated Epithelial Models. Pharmaceutical Research 21(7):1248-1256 (200… [cited by applicant]
UniProtKB Accession No. U2UMQ6. CRISPR-associated endonuclease Cas12a. Record created Nov. 13, 2013. Retrieved Oct. 3, 2024 at URL: https://www.uniprot.org/uniprotkb/U2UMQ6/entry pp. 1-10. [cited by applicant]
U.S. Appl. No. 63/368,722, inventor Ladha; Alim, filed Jul. 18, 2022. [cited by applicant]
U.S. Appl. No. 63/368,724, inventor Ladha; Alim, filed Jul. 18, 2022. [cited by applicant]
U.S. Appl. No. 63/368,726, inventor Ladha; Alim, filed Jul. 18, 2022. [cited by applicant]
U.S. Appl. No. 63/368,728, inventor Ladha; Alim, filed Jul. 18, 2022. [cited by applicant]
U.S. Appl. No. 63/368,730, inventor Ladha; Alim, filed Jul. 18, 2022. [cited by applicant]
U.S. Appl. No. 63/368,731, inventor Ladha; Alim, filed Jul. 18, 2022. [cited by applicant]
U.S. Appl. No. 63/368,734, inventor Ladha; Alim, filed Jul. 18, 2022. [cited by applicant]
U.S. Appl. No. 63/368,735, inventor Ladha; Alim, filed Jul. 18, 2022. [cited by applicant]
U.S. Appl. No. 63/368,736, inventor Ladha; Alim, filed Jul. 18, 2022. [cited by applicant]
U.S. Appl. No. 63/368,737, inventor Ladha; Alim, filed Jul. 18, 2022. [cited by applicant]
U.S. Appl. No. 63/368,738, inventor Ladha; Alim, filed Jul. 18, 2022. [cited by applicant]
U.S. Appl. No. 63/368,741, inventor Ladha; Alim, filed Jul. 18, 2022. [cited by applicant]
U.S. Appl. No. 63/368,742, inventor Ladha; Alim, filed Jul. 18, 2022. [cited by applicant]
U.S. Appl. No. 63/368,744, inventor Ladha; Alim, filed Jul. 18, 2022. [cited by applicant]
U.S. Appl. No. 63/495,198, inventor Giedrius; Gasiunas, filed Apr. 10, 2023. [cited by applicant]
U.S. Appl. No. 19/056,045 Office Action dated Jul. 28, 2025. [cited by applicant]
U.S. Appl. No. 19/056,045 Office Action dated Mar. 25, 2025. [cited by applicant]
U.S. Appl. No. 19/056,045 Office Action dated May 21, 2025. [cited by applicant]
U.S. Appl. No. 19/056,056 Corrected Notice of Allowability dated Jul. 18, 2025. [cited by applicant]
U.S. Appl. No. 19/056,056 Notice of Allowance dated Jun. 3, 2025. [cited by applicant]
U.S. Appl. No. 19/056,056 Office Action dated Apr. 4, 2025. [cited by applicant]
Wahlestedt, Claes et al. Potent and Nontoxic Antisense Oligonucleotides Containing Locked Nucleic Acids. PNAS USA 97(10):5633-5638 (2000). [cited by applicant]
Walther, W., et al., (2000), Viral Vectors for Gene Transfer, Drugs 60: 249-71. [cited by applicant]
Walton, Russell T. et al. Unconstrained Genome Targeting with near-PAMless Engineered CRISPR-Cas9 Variants. Science 368(6488):290-296 (2020). [cited by applicant]
Wang, Jing. et al. Cyclohexene nucleic acids (CeNA): serum stable oligonucleotides that activate RNase H and increase duplex stability with complementary RNA. Journal of the American Chemical Society 122(36):8595-8602 (… [cited by applicant]
Wender, Paul A. et al. The design, synthesis, and evaluation of molecules that enable or enhance cellular uptake: Peptoid molecular transporters. Proceedings of the National Academy of Sciences of the United States of A… [cited by applicant]
Xiao, et al. A novel significance score for gene selection and ranking. Bioinformatics 30(6):801-807 (2014). [cited by applicant]
Xie, F. et al. GenBank Accession No. MBR6223972. Version No. MBR6223972. 1MAG: type V CRISPR-associated protein Cas12a/Cpf1 [Lachnospiraceae bacterium]. pp. 1-3. Record created Apr. 22, 2021. Retrieved May 28, 2025. Ret… [cited by applicant]
Yamano, Takashi. et al. Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1. Molecular cell 67(4):633-645-e1-e3 (2017). [cited by applicant]
Zender, Lars. et al. VP22-mediated intercellular transport of p53 in hepatoma cells in vitro and in vivo. Cancer gene therapy 9(6):489-496 (2002). [cited by applicant]
Zhu, Lihua Julie. Overview of guide RNA design tools for CRISPR-Cas9 genome editing technology. Frontiers in Biology 10(4):289-296 (2015). [cited by applicant]
Zhu, Pengli. et al. The relationship of retinal vessel diameters and fractal dimensions with blood pressure and cardiovascular risk factors. PloS one 9(9):e106551, 1-10 (2014). [cited by applicant]