Dynamics of single-base editing: Theoretical analysis

Abstract

Recent experimental advances led to the development of DNA base editors (BEs) with single-nucleotide precision, which is critical for future progress in various scientific and technological fields. The molecular mechanisms of single-base discrimination, however, remain poorly understood. Using a recently developed stochastic approach, we theoretically investigated the dynamics of single-base editing. More specifically, transient and mean times to edit “TC” motifs by cytosine BEs are explicitly evaluated for correct (target) and incorrect (bystander) locations on DNA. In addition, the effect of mutations on the dynamics of the single-base edition is also analyzed. It is found that for most ranges of parameters, it is possible to temporarily separate target and bystander products of base editing, supporting the idea of dynamic selectivity as a method of improving the precision of single-base editing. We conclude that to improve the efficiency of single-base editing, selecting the probability or selecting the time requires different strategies. Physical–chemical arguments to explain the observed dynamic properties are presented. The theoretical analysis clarifies some important aspects of the molecular mechanisms of selective base editing.