Modeling DNA Dynamics by Path Integrals

TL;DR

This paper uses path integral methods to model the thermodynamics of DNA breathing, linking microscopic hydrogen bond fluctuations to macroscopic DNA denaturation and topology.

Contribution

It introduces a novel application of imaginary time path integrals to a mesoscopic DNA model considering helicoidal geometry and thermodynamic constraints.

Findings

Helical geometry influences DNA denaturation thermodynamics.

Path integral approach captures hydrogen bond fluctuations.

Nonlinear interactions relate to DNA topology.

Abstract

Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the breathing of DNA, are generally localized and, microscopically, are due to the breaking of the hydrogen bonds linking the base pairs (\emph{bps}). I apply imaginary time path integral techniques to a mesoscopic Hamiltonian which accounts for the helicoidal geometry of a short circular DNA molecule. The \emph{bps} displacements with respect to the ground state are interpreted as time dependent paths whose amplitudes are consistent with the model potential for the hydrogen bonds. The portion of the paths configuration space contributing to the partition function is determined by selecting the ensemble of paths which fulfill the second law of thermodynamics. Computations of the thermodynamics in the denaturation range show the energetic advantage for the equilibrium helicoidal geometry peculiar of B-DNA. I discuss the interplay between twisting of the double helix and anharmonic stacking along the molecule backbone suggesting an interesting relation between intrinsic nonlinear character of the microscopic interactions and molecular topology.