Engineered dual selection for directed evolution of SpCas9 PAM specificity

Gregory W. Goldberg, Jeffrey M. Spencer, David O. Giganti, Brendan R. Camellato, Neta Agmon, David M. Ichikawa, Jef D. Boeke, Marcus B. Noyes

    Research output: Contribution to journalArticlepeer-review

    Abstract

    The widely used Streptococcus pyogenes Cas9 (SpCas9) nuclease derives its DNA targeting specificity from protein-DNA contacts with protospacer adjacent motif (PAM) sequences, in addition to base-pairing interactions between its guide RNA and target DNA. Previous reports have established that the PAM specificity of SpCas9 can be altered via positive selection procedures for directed evolution or other protein engineering strategies. Here we exploit in vivo directed evolution systems that incorporate simultaneous positive and negative selection to evolve SpCas9 variants with commensurate or improved activity on NAG PAMs relative to wild type and reduced activity on NGG PAMs, particularly YGG PAMs. We also show that the PAM preferences of available evolutionary intermediates effectively determine whether similar counterselection PAMs elicit different selection stringencies, and demonstrate that negative selection can be specifically increased in a yeast selection system through the fusion of compensatory zinc fingers to SpCas9.

    Original languageEnglish (US)
    Article number349
    JournalNature communications
    Volume12
    Issue number1
    DOIs
    StatePublished - Dec 2021

    ASJC Scopus subject areas

    • Chemistry(all)
    • Biochemistry, Genetics and Molecular Biology(all)
    • Physics and Astronomy(all)

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