title: Single-strand stacking free energy from DNA beacon kinetics.
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 tau approximately N(2.44+/-0.02). There is a significant crossover for shorter chains, bringing the effective exponent into good agreement with experiment.
authors.affiliation: Physics Department, Williams College, 33 Lab Campus Drive, Williamstown, MA 01267, USA. aalberts@williams.edu
authors.forename: Daniel P
authors.initials: DP
authors.lastname: Aalberts
authors.forename: John M
authors.initials: JM
authors.lastname: Parman
authors.forename: Noel L
authors.initials: NL
authors.lastname: Goddard
mesh_terms: D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D004277:DNA, Single-Stranded / Q000737:chemistry*; D004735:Energy Transfer; D007700:Kinetics; D046911:Macromolecular Substances; D008958:Models, Molecular; D015233:Models, Statistical; D009010:Monte Carlo Method; D009038:Motion; D009690:Nucleic Acid Conformation
chemical_list: D001704:Biopolymers; D004277:DNA, Single-Stranded; D046911:Macromolecular Substances