Benjamin Kleinstiver Lab Materials

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Title	Authors	Publication
ABE8e and ABE8.20m PAM variant constructs	(unpublished)
Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer.	Mahendra C, Christie KA, Osuna BA, Pinilla-Redondo R, Kleinstiver BP, Bondy-Denomy J	Nat Microbiol. 2020 Apr;5(4):620-629. doi: 10.1038/s41564-020-0692-2. Epub 2020 Mar 26.
Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases.	Ferreira da Silva J, Tou CJ, King EM, Eller ML, Rufino-Ramos D, Ma L, Cromwell CR, Metovic J, Benning FMC, Chao LH, Eichler FS, Kleinstiver BP	Nat Biotechnol. 2024 Jul 22. doi: 10.1038/s41587-024-02324-x.
CMV and T7 promoter plasmid to express EGFP (BPK1098)	(unpublished)
CRISPR-Cas9 vectors expressing mScarlet	(unpublished)
Custom CRISPR-Cas9 PAM variants via scalable engineering and machine learning.	Silverstein RA, Kim N, Kroell AS, Walton RT, Delano J, Butcher RM, Pacesa M, Smith BK, Christie KA, Ha LL, Meis RJ, Clark AB, Spinner AD, Lazzarotto CR, Li Y, Matsubara A, Urbina EO, Dahl GA, Correia BE, Marks DS, Tsai SQ, Pinello L, De Ravin SS, Liu Q, Kleinstiver BP	Nature. 2025 Apr 22. doi: 10.1038/s41586-025-09021-y.
Discovery of widespread Type I and Type V CRISPR-Cas inhibitors.	Marino ND, Zhang JY, Borges AL, Sousa AA, Leon LM, Rauch BJ, Walton RT, Berry JD, Joung JK, Kleinstiver BP, Bondy-Denomy J	Science. 2018 Sep 6. pii: science.aau5174. doi: 10.1126/science.aau5174.
Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing.	Kleinstiver BP, Sousa AA, Walton RT, Tak YE, Hsu JY, Clement K, Welch MM, Horng JE, Malagon-Lopez J, Scarfo I, Maus MV, Pinello L, Aryee MJ, Joung JK	Nat Biotechnol. 2019 Feb 11. pii: 10.1038/s41587-018-0011-0. doi: 10.1038/s41587-018-0011-0.
Evolution of CRISPR-associated endonucleases as inferred from resurrected proteins.	Alonso-Lerma B, Jabalera Y, Samperio S, Morin M, Fernandez A, Hille LT, Silverstein RA, Quesada-Ganuza A, Reifs A, Fernandez-Penalver S, Benitez Y, Soletto L, Gavira JA, Diaz A, Vranken W, Sanchez-Mejias A, Guell M, Mojica FJM, Kleinstiver BP, Moreno-Pelayo MA, Montoliu L, Perez-Jimenez R	Nat Microbiol. 2023 Jan;8(1):77-90. doi: 10.1038/s41564-022-01265-y. Epub 2023 Jan 2.
In situ architecture of Opa1-dependent mitochondrial cristae remodeling.	Fry MY, Navarro PP, Hakim P, Ananda VY, Qin X, Landoni JC, Rath S, Inde Z, Lugo CM, Luce BE, Ge Y, McDonald JL, Ali I, Ha LL, Kleinstiver BP, Chan DC, Sarosiek KA, Chao LH	EMBO J. 2024 Feb;43(3):391-413. doi: 10.1038/s44318-024-00027-2. Epub 2024 Jan 15.

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	ID	Plasmid	Gene/Insert	Vector Type	Publication
100.110.551022.139999	139999	pCAG-CBE4max-SpRY-P2A-EGFP (RTW5133)	human codon optimized CBE4max SpCas9 variant named SpRY with P2A-EGFP	Mammalian Expression, CRISPR	Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science. 2020 Apr 17;368(6488):290-296. doi: 10.1126/science.aba8853. Epub 2020 Mar 26.
100.66.617783.140003	140003	pCMV-T7-ABEmax(7.10)-SpRY-P2A-EGFP (RTW5025)	human codon optimized ABEmax(7.10) SpCas9 variant named SpRY with P2A-EGFP	Mammalian Expression, CRISPR	Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science. 2020 Apr 17;368(6488):290-296. doi: 10.1126/science.aba8853. Epub 2020 Mar 26.
100.59.557797.133962	133962	pCMV-T7-EGFP (BPK1098)	EGFP	Mammalian Expression	CMV and T7 promoter plasmid to express EGFP (BPK1098) (unpublished)
100.57.360513.139998	139998	pCAG-CBE4max-SpG-P2A-EGFP (RTW4552)	human codon optimized CBE4max SpCas9 variant named SpG with P2A-EGFP	Mammalian Expression, CRISPR	Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science. 2020 Apr 17;368(6488):290-296. doi: 10.1126/science.aba8853. Epub 2020 Mar 26.
100.25.498257.140002	140002	pCMV-T7-ABEmax(7.10)-SpG-P2A-EGFP (RTW4562)	human codon optimized ABEmax(7.10) SpCas9 variant named SpG with P2A-EGFP	Mammalian Expression, CRISPR	Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science. 2020 Apr 17;368(6488):290-296. doi: 10.1126/science.aba8853. Epub 2020 Mar 26.
100.21.032116.139996	139996	pCMV-T7-SpG-HF1-P2A-EGFP (RTW5000)	human codon optimized SpCas9 variant named SpG-HF1 with BPNLS-3xFLAG-P2A-EGFP	Mammalian Expression, CRISPR	Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science. 2020 Apr 17;368(6488):290-296. doi: 10.1126/science.aba8853. Epub 2020 Mar 26.
100.7.846473.139989	139989	pCMV-T7-SpRY-P2A-EGFP (RTW4830)	human codon optimized SpCas9 variant named SpRY with BPNLS-3xFLAG-P2A-EGFP	Mammalian Expression, CRISPR	Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science. 2020 Apr 17;368(6488):290-296. doi: 10.1126/science.aba8853. Epub 2020 Mar 26.
100.4.984386.107941	107941	pCAG-enAsCas12a(E174R/S542R/K548R)-NLS(nuc)-3xHA (AAS848)	human codon optimized enAsCas12a (E174R/S542R/K548R)	Mammalian Expression	Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol. 2019 Feb 11. pii: 10.1038/s41587-018-0011-0. doi: 10.1038/s41587-018-0011-0.
100.4.509945.139997	139997	pCMV-T7-SpRY-HF1-P2A-EGFP (RTW5008)	human codon optimized SpCas9 variant named SpRY-HF1 with BPNLS-3xFLAG-P2A-EGFP	Mammalian Expression, CRISPR	Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science. 2020 Apr 17;368(6488):290-296. doi: 10.1126/science.aba8853. Epub 2020 Mar 26.
50.1044.212800.185912	185912	pCMV-T7-ABE8e-nSpRY-P2A-EGFP (KAC1069)	human codon optimized ABE8e-nSpRY-P2A-EGFP	Mammalian Expression	Optimization of base editors for the functional correction of SMN2 as a treatment for spinal muscular atrophy. Nat Biomed Eng. 2023 Dec 6. doi: 10.1038/s41551-023-01132-z.

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	ID	Pooled Library	Vector Type	Publication
	160132	p11-3’_8xN_PAM-site1 (RTW554)	CRISPR	Scalable characterization of the PAM requirements of CRISPR-Cas enzymes using HT-PAMDA. Nat Protoc. 2021 Feb 5. pii: 10.1038/s41596-020-00465-2. doi: 10.1038/s41596-020-00465-2.
	160133	p11-3’_8xN_PAM-site2 (RTW555)	CRISPR	Scalable characterization of the PAM requirements of CRISPR-Cas enzymes using HT-PAMDA. Nat Protoc. 2021 Feb 5. pii: 10.1038/s41596-020-00465-2. doi: 10.1038/s41596-020-00465-2.
	160135	p11-5’_10xN_PAM-site4 (RTW574)	CRISPR	Scalable characterization of the PAM requirements of CRISPR-Cas enzymes using HT-PAMDA. Nat Protoc. 2021 Feb 5. pii: 10.1038/s41596-020-00465-2. doi: 10.1038/s41596-020-00465-2.