Temperature-induced swelling and unwinding of double-stranded DNA†

Abstract

We utilized all-atom molecular dynamics simulations to investigate the temperature-induced swelling and unwinding of double-stranded DNA (dsDNA). We adopted three helical parameters, specifically helical twist, helical rise, and diameter, to quantitatively describe the deformations and elastic properties associated with swelling and unwinding processes within an orthogonal cylindrical coordinate system. The results indicate that as temperature increases, dsDNA experiences a weak swelling accompanied by unwinding. This is associated with a slight increase in helical rise, while the helical diameter almost remains unchanged and the helical twist decreases. We evaluated all potential pathways for unwinding and elucidated that twist-diameter coupling drives the unwinding from an entropy perspective. On the other hand, we employed the rigid base pair model to examine the swelling and unwinding elasticities, with a focus on the stiffnesses of twist and diameter. The results suggest that the temperature induces variations in the local twist and diameter elasticities, as well as their couplings of dsDNA, which are closely related to the distance between the base pairs, attributed to its thermal fluctuations and correlations. The global twist elasticity reduces as the temperature rises; nonetheless, the global diameter elasticity and the twist-diameter coupling can be considered as constants, which indicate independence from the increasing temperature.