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3212 Biophysical Journal Volume 84 May 2003 32123217 Single-Strand Stacking Free Energy from DNA Beacon Kinetics
 

Summary: 3212 Biophysical Journal Volume 84 May 2003 32123217
Single-Strand Stacking Free Energy from DNA Beacon Kinetics
Daniel P. Aalberts,* John M. Parman,* and Noel L. Goddardy
*Physics Department, Williams College, Williamstown, Massachusetts 01267; and y
Center for Studies in Physics and Biology, Rockefeller
University, New York, New York 10021
ABSTRACT 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 t ; N 2.4460.02
. There is a significant crossover for shorter chains, bringing the effective
exponent into good agreement with experiment.
INTRODUCTION
Hairpin conformations of single-stranded nucleic acids
dominate secondary structure and have been implicated as
important regulatory elements for transcription and replica-
tion (Lodish et al., 2000). Molecular beacons (see Fig. 1),
self-complementary single-stranded (ss) DNA with fluoro-

  

Source: Aalberts, Daniel P. - Department of Physics, Williams College

 

Collections: Physics