Twist-stretch profiles of DNA chains

Abstract

Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are applied to generate a large ensemble of possible configurations for the base pairs of the sequence. The model also accounts for the bending and twisting fluctuations between adjacent base pairs along the molecules stack. Simulating a broad range of twisting conformation, we compute the helix structural parameters by averaging over the ensemble of base pairs configurations. The method selects, for any applied force, the average twist angle which minimizes the molecule's free energy. It is found that the chains generally over-twist under an applied stretching and the over-twisting is physically associated to the contraction of the average helix diameter, i.e. to the damping of the base pair fluctuations. Instead, assuming that the maximum amplitude of the bending fluctuations may decrease against the external load, the DNA molecule first over-twists for weak applied forces and then untwists above a characteristic force value. Our results are discussed in relation to available experimental information albeit for kilo-base long molecules.

References in corpus (23)

• Theory of High-Force DNA Stretching and Overstretching
• Wringing out DNA
• Length scale dependence of DNA mechanical properties
• Probing the elastic limit of DNA bending
• Flexibility of short DNA helices with finite-length effect: from base pairs to tens of base pairs
• The Electrostatic Persistence Length Calculated from Monte Carlo, Variational and Perturbation Methods
• Thermodynamics of Twisted DNA with Solvent Interaction
• DNA flexibility on short length scales probed by atomic force microscopy
• Healing Length and Bubble Formation in DNA
• Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of wire model vs. extended ladder model
• Path Integral Method for DNA Denaturation
• Unbiased charge oscillations in DNA monomer-polymers and dimer-polymers
• Denaturation Patterns in Heterogeneous DNA
• Stacking Interactions in Denaturation of DNA Fragments
• Helix untwisting and bubble formation in circular DNA
• Twist versus Nonlinear Stacking in Short DNA Molecules
• J-factors of short DNA molecules
• Flexibility of short DNA helices under mechanical stretching
• Dynamical versus statistical mesoscopic models for DNA denaturation
• Path Integral Description of a Semiclassical Su-Schrieffer-Heeger Model
• Extreme bendability of DNA double helix due to bending asymmetry
• Anharmonic stacking in supercoiled DNA
• Force distribution in a semiflexible loop

Cited by in corpus (5)

• End-to-end distance and contour length distribution functions of DNA helices
• Base pair fluctuations in helical models for nucleic acids
• Periodic polymers with increasing repetition unit: Energy structure and carrier transfer
• Twisting short dsDNA with applied tension
• Stretching DNA in hard-wall potential channels