A versatile, chemically-controlled DNA binding switch enables temporal modulation of Cas9-based effectors

CRISPR-Cas9s RNA-guided genome targeting ability has been leveraged to develop a plethora of effectors including targeted transcriptional activators, DNA base editors, and DNA prime editors. Although systems for inducibly modulating Cas9 activity have been developed, current approaches for conferring temporal control require extensive screening of functional protein components. A simpler and general strategy for conferring temporal control over diverse Cas9-based effector activities is needed. Here we describe a versatile chemically-controlled and rapidly-activated DNA binding Cas9 module (ciCas9) that is able to confer temporal control over a variety of Cas9-based effectors. Using the ciCas9 module, we engineer temporally-controlled cytidine and adenine DNA base editors. We employ the ciCas9 base editors to reveal that in vivo bystander editing kinetics occurs via a dependent process where editing at a preferred nucleotide position increases the frequency of edits at a second nucleotide within a target site. Finally, we demonstrate the versatility of the ciCas9 module by creating a temporally-controlled transcriptional activator, a dual cytidine and adenine base editor, and a prime editor.