Theoretical study of collective modes in DNA at ambient temperature

TL;DR

This paper theoretically investigates the collective vibrational modes of DNA at ambient temperature, analyzing their density, dispersion, and coherence, and compares results with experimental spectroscopy data.

Contribution

It introduces an analytical approach to model DNA vibrational modes considering thermal disorder and validates findings against experimental measurements.

Findings

Density of modes agrees with Raman spectroscopy data for nu < 150 cm^{-1}

Radial modes span 50-110 cm^{-1} with high disorder

Angular modes are limited to nu < 25 cm^{-1} and are also highly disordered

Abstract

The instantaneous normal modes corresponding to base pair vibrations (radial modes) and twist angle fluctuations (angular modes) of a DNA molecule model at ambient temperature are theoretically investigated. Due to thermal disorder, normal modes are not plane waves with a single wave number q but have a finite and frequency dependent damping width. The density of modes rho(nu), the average dispersion relation nu(q) as well as the coherence length xi(nu) are analytically calculated. The Gibbs averaged resolvent is computed using a replicated transfer matrix formalism and variational wave functions for the ground and first excited state. Our results for the density of modes are compared to Raman spectroscopy measurements of the collective modes for DNA in solution and show a good agreement with experimental data in the low frequency regime nu < 150 cm^{-1}. Radial modes extend over frequencies ranging from 50 cm^{-1} to 110 cm^{-1}. Angular modes, related to helical axis vibrations are limited to nu < 25 cm^{-1}. Normal modes are highly disordered and coherent over a few base pairs only (xi < 2 nm) in good agreement with neutron scattering experiments.