So close yet so far apart: Distinct flanking sequence recognition by DNMT3A and DNMT3B

ABSTRACT DNMT3A and DNMT3B are closely related DNA methyltransferases that catalyze de novo CpG methylation yet exhibit distinct preferences for flanking sequences. Despite sharing 91% sequence similarity within their catalytic domains, these paralogs show non-overlapping genomic targeting and divergent biological roles. To uncover the mechanistic basis of this specificity, we performed 16µs of all-atom molecular dynamics simulations on DNMT3A and DNMT3B complexes bound to CpG substrates with varied +2 flanking bases (i.e., CGX). To resolve their base- and shape-readout mechanisms at atomistic detail, we introduce a Comparative Dynamics Analysis (CDA) framework. Our CDA analysis reveals that DNMT3A relies on a rigid, sequence-specific hydrogen bonding network and shape-constrained electrostatic anchoring, whereas DNMT3B employs a more flexible and distributed interface, allowing broader substrate tolerance. This represents the first systematic analysis of shape readout in DNMT3 enzymes and demonstrates how flanking sequence specificity is dynamically encoded by two nearly identical proteins. Our findings not only clarify how closely related DNA-modifying enzymes diverge in recognition strategies, but also lay the foundation for future efforts to engineer paralog-specific protein–DNA interactions.