BIOPHYSICAL THEORY AND MODELING |
There and (slowly) back again: Entropy-driven hysteresis in a model of DNA overstretching
Stephen Whitelam 1*, Sander Pronk 1 and Phillip L. Geissler 1
1 University of California at Berkeley
* To whom correspondence should be addressed. E-mail: swhitelam{at}lbl.gov.
Submitted on July 12, 2007
Revised on August 16, 2007
Accepted on 26 September 2007
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Abstract |
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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. 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.
Key Words:
Monte Carlo methods, kinetics of single-molecule experiments, modeling single-molecule experiments, statistical physics
