Thermodynamics of Twisted DNA with Solvent Interaction

TL;DR

This paper uses path integral formalism to analyze the thermodynamics of twisted DNA with solvent effects, revealing the equilibrium twist angle that stabilizes the DNA helix against thermal denaturation.

Contribution

It introduces a novel application of path integral methods to model the thermodynamics of heterogeneous DNA with solvent interactions and torsional effects.

Findings

The equilibrium twist angle stabilizes the DNA helix at room temperature.

Thermodynamic properties support the stability of B-DNA configuration.

Large ensemble of base pair paths captures thermal denaturation effects.

Abstract

The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base pairs stacked along the molecule backbone. The base pair displacements are described by an ensemble of temperature dependent paths thus incorporating those fluctuational effects which shape the multisteps thermal denaturation. By summing over $\sim 10^7 - 10^8$ base pair paths, a large number of double helix configurations is taken into account consistently with the physical requirements of the model potential. The partition function is computed as a function of the twist. It is found that the equilibrium twist angle, peculiar of B-DNA at room temperature, yields the stablest helicoidal geometry against thermal disruption of the base pair hydrogen bonds. This result is corroborated by the computation of thermodynamical properties such as fractions of open base pairs and specific heat.