DNA hairpin base-flipping dynamics drives APOBEC3A recognition and selectivity

APOBEC3A is a deoxycytidine deaminase which acts preferentially upon a 5'-TC-3' motif, and was recently shown to prefer hairpin loops over unstructured single-stranded DNA. However, the underlying molecular details for its substrate specificity remain unclear. In this work we apply classical molecular dynamics to 212 unique hairpin loops in solvent, with lengths of 3 and 4 nucleotides in the loop, and a representative subset of 23 bound to APOBEC3A. This allows us to gain statistical insight into the types of motions and sequences potentially important for APOBEC3A activity. We demonstrate that base-flipping occurs in solvent before binding to APOBEC3A semi-dependent on the hairpin loop sequence, and that binding does not necessarily require the presence of a cytosine on the hairpin loop. Furthermore, we show measurable physical metrics, such as RMSD and sugar puckering, which may aid in identifying sequences which will exhibit higher rates of base-flipping commensurate with increased APOBEC3A activity.