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There and (Slowly) Back Again: Entropy-Driven Hysteresis in a Model of DNA Overstretching

Department of Chemistry, University of California at Berkeley, and Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, California

Correspondence: Address reprint requests to Stephen Whitelam, Tel.: 44-24-7615-0243; E-mail: s.b.whitelam{at}warwick.ac.uk.

When pulled along its axis, double-stranded DNA elongates abruptly at a force of 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 introduces an elongated hybridized phase called S-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 can generate hysteresis, the degree of which depends upon the nonextensive loop entropy of single-stranded DNA.