The mechanical code of DNA impacts its interaction with DNA gyrase

Abstract

DNA:protein interactions involving large structural deformations of DNA underpin essential biological processes. Although correlative evidence suggests that local, sequence-encoded, mechanical properties of DNA can modulate its interactions with large bent-DNA complexes like nucleosomes, direct high-throughput measurements of programmable mechanical modulation of DNA:protein interactions remain lacking. DNA gyrase is a type II topoisomerase that introduces negative supercoils in bacterial chromosomes via a process that involves extensive, nucleosome-scale, DNA wrapping around its two C-terminal domains (CTDs). Here we combine Systematic Evolution of Ligands by EXponential enrichment (SELEX), neural network predictions of DNA intrinsic cyclizability, and high-throughput DNA-compete binding assays to broadly reveal that sequence-encoded DNA mechanics tunes gyrase:DNA interactions by modulating wrapping of DNA around the CTDs. Further, we find that both genomic gyrase cleavage sites, and SELEX-enriched strong gyrase-binding sequences, display marked mechanical asymmetry: an extended region of flexible DNA facilitating wrapping around only one CTD exists on one half of the enzyme footprint. High throughput binding assays further reveal that strong binding to one CTD alone can compensate for weaker dual binding, suggesting that asymmetric attachment may have evolved to balance the need for stable anchoring with conformational flexibility required for catalytic remodelling. Additionally, we identify key GC-rich motifs that independently enhance gyrase:DNA interactions, also in an asymmetric fashion. Our findings establish sequence-encoded DNA mechanics as a tunable determinant of protein:DNA interactions and illustrate how functional asymmetry within a symmetric enzyme can couple stable substrate association with structural plasticity.