There and (slowly) back again: Entropy-driven hysteresis in a model of DNA overstretching

Abstract

When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to a molten state consisting of unhybridized single strands. The second picture instead introduces an elongated hybridized phase, called S-DNA, structurally and thermodynamically distinct from standard B-DNA. Little thermodynamic evidence exists to discriminate directly between these competing pictures. Here we show that within a microscopic model of DNA we can distinguish between the dynamics associated with each. In experiment, considerable hysteresis in a cycle of stretching and shortening develops as temperature is increased. Since there are few possible causes of hysteresis in a system whose extent is appreciable in only one dimension, such behavior offers a discriminating test of the two pictures of overstretching. Most experiments are performed upon nicked DNA, permitting the detachment (`unpeeling') of strands. We show that the long-wavelength progression of the unpeeled front generates hysteresis, the character of which agrees with experiment only if we assume the existence of S-DNA. We also show that internal melting (distinct from unpeeling) can generate hysteresis, the degree of which is strongly dependent upon the nonextensive loop entropy of single-stranded DNA.

18 pages, 10 figures

References in corpus (5)

• Why is the DNA Denaturation Transition First Order?
• Theory of High-Force DNA Stretching and Overstretching
• Localization of Denaturation Bubbles in Random DNA Sequences
• Loop Dynamics in DNA Denaturation
• Probability distribution of bubble lengths in DNA

Cited by in corpus (12)

• Coarse-grained simulations of DNA overstretching
• Path Integral Method for DNA Denaturation
• Dependence on temperature and GC content of bubble length distributions in DNA
• Stretching chimeric DNA: a test for the putative S-form
• Melting of persistent double-stranded polymers
• Mesoscopic models for DNA stretching under force: new results and comparison to experiments
• Dynamical model for the full stretching curve of DNA
• A three-state model with loop entropy for the over-stretching transition of DNA
• Hysteresis curves reveal the microscopic origin of cooperative CO${}_2$ adsorption in diamine-appended metal-organic frameworks
• Remembering the work of Phillip L. Geissler: A coda to his scientific trajectory
• Mechanical response to tension and torque of molecular chains via statistically interacting particles associated with extension, contraction, twist, and supercoiling
• Microscopic implications of S-DNA