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

TL;DR

This paper uses a microscopic DNA model to distinguish between two competing theories of DNA overstretching, demonstrating that hysteresis behavior supports the existence of S-DNA and depends on loop entropy effects.

Contribution

It provides the first thermodynamic and dynamic evidence favoring the S-DNA model over the molten state in DNA overstretching.

Findings

Hysteresis in DNA stretching cycles supports S-DNA existence.

Unpeeling dynamics generate hysteresis consistent with experiments.

Internal melting effects depend on loop entropy, influencing hysteresis.

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.