A universal twist-slide coupling mechanism governs deformations of DNA, RNA, and RNA-DNA hybrid duplexes

Abstract

Nucleic acid duplexes, including DNA, RNA, and RNA–DNA hybrid (RDH), undergo structural deformations that are essential for genome replication, transcription, and RNA-mediated regulation. However, quantitative measurements and mechanistic understanding of these deformations remain limited. Here, we probe nucleic acid deformations by measuring helical twist changes using single-molecule magnetic tweezers, where minute twist variations ( ~ 0.01° per base pair) accumulate over kilobase-length duplexes and become experimentally detectable. Unexpectedly, we find that RDHs do not behave as a simple intermediate between DNA and RNA. Instead, RDHs exhibit markedly attenuated twist responses to salt and temperature, together with nearly vanishing twist–stretch coupling. Despite these distinct mechanical behaviors, all-atom molecular dynamics simulations reveal a common deformation pathway shared by all three duplex types: external perturbations first modulate base-pair slide, which is subsequently transduced into twist changes through a universal twist–slide coupling. Building on this mechanism, we derive approximate theoretical predictions that quantitatively reproduce the salt- and temperature-dependent twist responses of RDH. We further show that protein-induced RDH deformations also occur predominantly along the twist–slide coupling pathway. Together, our results establish twist–slide coupling as a universal framework governing nucleic acid deformations across duplex types and environmental conditions. Helical twist is a fundamental mechanical property of nucleic acids that governs genome stability, gene expression, and gene editing. Here, using single-molecule experiments and molecular simulations, the authors show that RNA–DNA hybrid exhibit strongly attenuated twist responses and nearly vanishing twist-stretch coupling.