Twisting short dsDNA with applied tension

TL;DR

This paper presents a computational model to analyze how short DNA molecules twist and stretch under external forces, predicting over-twisting followed by untwisting and changes in helix parameters, aligning with experimental observations.

Contribution

A novel coarse-grained Hamiltonian model and computational method for predicting the elastic response of short DNA fragments under tension and torsion.

Findings

Short DNA over-twists then untwists under increasing tension.

Helix diameter shrinks while elongating under torsional strain.

Quantitative relation between elongation and superhelical density derived.

Abstract

The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair fluctuations. The latter are all the more important at short length scales in which DNA fragments maintain an intrinsic flexibility. The presented computational method simulates a broad ensemble of possible molecule conformations characterized by a specific average twist and determines the energetically most convenient helical twist by free energy minimization. As this is done for any external load, the method yields the characteristic twist-stretch profile of the molecule and also computes the changes in the macroscopic helix parameters i.e. average diameter and rise distance. It is predicted that short molecules under stretching should first over-twist and then untwist by increasing the external load. Moreover, applying a constant load and simulating a torsional strain which over-twists the helix, it is found that the average helix diameter shrinks while the molecule elongates, in agreement with the experimental trend observed in kilo-base long sequences. The quantitative relation between percent relative elongation and superhelical density at fixed load is derived. The proposed theoretical model and computational method offer a general approach to characterize specific DNA fragments and predict their macroscopic elastic response as a function of the effective potential parameters of the mesoscopic Hamiltonian.