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Biophysical Journal 84:3212-3217 (2003)
© 2003 The Biophysical Society

Single-Strand Stacking Free Energy from DNA Beacon Kinetics

Daniel P. Aalberts *, John M. Parman * and Noel L. Goddard {dagger}

* Physics Department, Williams College, Williamstown, Massachusetts 01267; and {dagger} Center for Studies in Physics and Biology, Rockefeller University, New York, New York 10021

Correspondence: Address reprint requests to Daniel P. Aalberts, Williams College, 33 Lab Campus Dr., Williamstown, MA 01267. Tel.: 413-597-3520; Fax: 413-597-4116; E-mail: aalberts{at}williams.edu.

DNA beacons are short single-stranded chains which can form closed hairpin shapes through complementary base pairing at their ends. Contrary to the common polymer theory assumption that only their loop length matters, experiments show that their closing kinetics depend on the loop composition. We have modeled the closing kinetics and in so doing have obtained stacking enthalpies and entropies for single-stranded nucleic acids. The resulting change of persistence length with temperature effects the dynamics. With a Monte Carlo study, we answer another polymer question of how the closing time scales with chain length, finding {tau} ~ N2.44±0.02. There is a significant crossover for shorter chains, bringing the effective exponent into good agreement with experiment.




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