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

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

2006-07-22

arxiv.org/abs/cond-mat/0607572v2

Biophysical Journal 94:2452-2469 (2008)

Physics

Condensed Matter

Statistical Mechanics

18 pages, 10 figures

Scientific paper

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.

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