Comparative characterization of Cas12f orthologs reveals mechanistic features underlying enhanced genome editing efficiency

Guan, K.; Fregoso Ocampo, R.; Matheus Carnevali, P. B.; Castelle, C. J.; Gonzalez-Osorio, L.; Castanzo, D. T.; Brothers, M.; Dangerfield, T. L.; Hooper, M. M.; Appleby, N.; Krudop, I.; Lamothe, R. C.; Aliaga Goltsman, D. S.; Alexander, L. M.; Butterfield, C. N.; Johnson, K. A.; Brown, C. T.; Taylor, D. W.

doi:10.1101/2025.08.14.670346

bioRxiv · 10.1101/2025.08.14.670346

Comparative characterization of Cas12f orthologs reveals mechanistic features underlying enhanced genome editing efficiency

Guan, K.·Fregoso Ocampo, R.·Matheus Carnevali, P. B.·Castelle, C. J.·Gonzalez-Osorio, L.·Castanzo, D. T.·Brothers, M.·Dangerfield, T. L.·Hooper, M. M.·Appleby, N.·Krudop, I.·Lamothe, R. C.·Aliaga Goltsman, D. S.·Alexander, L. M.·Butterfield, C. N.·Johnson, K. A.·Brown, C. T.·Taylor, D. W.

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Abstract

Miniature CRISPR-Cas12f nucleases are attractive candidates for therapeutic genome editing owing to their compact size and compatibility with adeno-associated virus (AAV) delivery. However, editing efficiencies in mammalian cells are lower than those of larger systems such as Cas12a and SpCas9. The extensive phylogenetic diversity of Cas12f suggests unexplored mechanistic variation with the potential for optimization. Here, we characterize a naturally occurring Cas12f ortholog discovered through metagenomics, Cas12f-MG119-28, which supports robust genome editing in human cells. Through structural, biochemical, and kinetic analyses, we compare Cas12f-MG119-28 with two recently described orthologs, Oscillibacter sp. Cas12f (OsCas12f) and Ruminiclostridium herbifermentans Cas12f (RhCas12f). These orthologs present divergent architectures and regulatory features governing PAM recognition, gRNA binding, dimerization, and DNA cleavage. Notably, Cas12f-MG119-28 achieves efficient R-loop formation via a stable dimer interface and a naturally optimized guide RNA. These discoveries elucidate key mechanistic determinants of Cas12f activity and may offer a framework for engineering compact genome editors with therapeutic potential.

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Guan, K., Fregoso Ocampo, R., Matheus Carnevali, P. B., Castelle, C. J., Gonzalez-Osorio, L., Castanzo, D. T., Brothers, M., Dangerfield, T. L., Hooper, M. M., Appleby, N., Krudop, I., Lamothe, R. C., Aliaga Goltsman, D. S., Alexander, L. M., Butterfield, C. N., Johnson, K. A., Brown, C. T., Taylor, D. W.. 2025-08-14. Comparative characterization of Cas12f orthologs reveals mechanistic features underlying enhanced genome editing efficiency. https://doi.org/10.1101/2025.08.14.670346

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