Twist-diameter coupling drives DNA twist changes by salt and temperature

TL;DR

This study uncovers a strong negative coupling between DNA diameter and twist angle, driven by salt concentration and temperature, using experiments, simulations, and theoretical analysis to explain the physical mechanism.

Contribution

The paper reveals a previously unrecognized strong negative twist-diameter coupling in DNA, supported by experimental, simulation, and theoretical evidence, explaining salt and temperature effects.

Findings

DNA twist increases with salt concentration.

Reduction in DNA diameter causes increase in twist angle.

Predicted temperature dependence of DNA twist matches experimental data.

Abstract

DNA deformations play crucial roles in many biological processes and material applications. During DNA deformation, DNA structural parameters often exhibit non-trivial and counterintuitive couplings, such as the twist-stretch and twist-bending couplings. Here, we reveal an unexpectedly strong negative twist-diameter coupling through the synergy of magnetic-tweezers experiments, atomistic molecular dynamics simulations, and theoretical calculations. In experiments, the DNA twist angle always increases with the concentration of NaCl, KCl, or RbCl. Our simulations quantitatively reproduce salt-induced twist changes and reveal the underlying physical mechanism: the reduction of DNA diameter under a high salt concentration leads to the increase in DNA twist angle through a strong negative twist-diameter coupling. The twist-diameter coupling is mediated by two dihedral angles in DNA structure and the coupling constant is 4.5 kBT/(deg nm) for one base-pair. Based on this coupling constant, we predict the temperature-dependence of DNA twist -0.0102 deg/K per bp, which agrees with our and previous experimental results. Our analysis suggests that the twist-diameter coupling is a common driving force for salt- and temperature-induced DNA twist changes.