%AMa, Enbo%AChen, Kai%AShi, Honglue%AStahl, Elizabeth%AAdler, Ben%ATrinidad, Marena%ALiu, Junjie%AZhou, Kaihong%AYe, Jinjuan%ADoudna, Jennifer%BJournal Name: Nucleic Acids Research; Journal Volume: 50; Journal Issue: 22; Related Information: CHORUS Timestamp: 2023-05-23 13:29:06 %D2022%IOxford University Press %JJournal Name: Nucleic Acids Research; Journal Volume: 50; Journal Issue: 22; Related Information: CHORUS Timestamp: 2023-05-23 13:29:06 %K %MOSTI ID: 10386503 %PMedium: X %TImproved genome editing by an engineered CRISPR-Cas12a %XAbstract

CRISPR-Cas12a is an RNA-guided, programmable genome editing enzyme found within bacterial adaptive immune pathways. Unlike CRISPR-Cas9, Cas12a uses only a single catalytic site to both cleave target double-stranded DNA (dsDNA) (cis-activity) and indiscriminately degrade single-stranded DNA (ssDNA) (trans-activity). To investigate how the relative potency of cis- versus trans-DNase activity affects Cas12a-mediated genome editing, we first used structure-guided engineering to generate variants of Lachnospiraceae bacterium Cas12a that selectively disrupt trans-activity. The resulting engineered mutant with the biggest differential between cis- and trans-DNase activity in vitro showed minimal genome editing activity in human cells, motivating a second set of experiments using directed evolution to generate additional mutants with robust genome editing activity. Notably, these engineered and evolved mutants had enhanced ability to induce homology-directed repair (HDR) editing by 2–18-fold compared to wild-type Cas12a when using HDR donors containing mismatches with crRNA at the PAM-distal region. Finally, a site-specific reversion mutation produced improved Cas12a (iCas12a) variants with superior genome editing efficiency at genomic sites that are difficult to edit using wild-type Cas12a. This strategy establishes a pipeline for creating improved genome editing tools by combining structural insights with randomization and selection. The available structures of other CRISPR-Cas enzymes will enable this strategy to be applied to improve the efficacy of other genome-editing proteins.

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