Base pair fluctuations in helical models for nucleic acids

TL;DR

This paper introduces a statistical method to estimate maximum base pair fluctuations in nucleic acids, accounting for various conformations and motions, providing insights into DNA and RNA structural dynamics.

Contribution

A novel statistical approach for quantifying base pair fluctuations in 3D nucleic acid models, incorporating twist, bending, and sliding motions.

Findings

Maximum fluctuations estimated for DNA-like helices (~10.5 base pairs per turn)

Untwisting broadens fluctuation range and increases integral cutoff

Sliding motions in RNA shorten helix contour and affect fluctuations

Abstract

A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian motion for a particle embedded in a stable helical structure. The probability to return to the initial position is computed, as a function of time, by integrating over the particle paths consistent with the physical properties of the model potential. The zero time condition for the first-passage probability defines the constraint to select the integral cutoff for various macroscopic helical conformations, obtained by tuning the twist, the bending and the slide motion between adjacent base pairs along the molecule stack. Applying the method to a short homogeneous chain at room temperature, we obtain meaningful estimates for the maximum fluctuations in the twist conformation with $\sim 10.5$ base pairs per helix turn, typical of double stranded DNA helices. Untwisting the double helix, the base pair fluctuations broaden and the integral cutoff grows. The cutoff is found to increase also in the presence of a sliding motion which shortens the helix contour length, a situation peculiar of dsRNA molecules.