title: Non-Arrhenius kinetics for the loop closure of a DNA hairpin.
abstract: Intramolecular chain diffusion is an elementary process in the conformational fluctuations of the DNA hairpin-loop. We have studied the temperature and viscosity dependence of a model DNA hairpin-loop by FRET (fluorescence resonance energy transfer) fluctuation spectroscopy (FRETfs). Apparent thermodynamic parameters were obtained by analyzing the correlation amplitude through a two-state model and are consistent with steady-state fluorescence measurements. The kinetics of closing the loop show non-Arrhenius behavior, in agreement with theoretical prediction and other experimental measurements on peptide folding. The fluctuation rates show a fractional power dependence (beta = 0.83) on the solution viscosity. A much slower intrachain diffusion coefficient in comparison to that of polypeptides was derived based on the first passage time theory of SSS [Szabo, A., Schulten, K. & Schulten, Z. (1980) J. Chem. Phys. 72, 4350-4357], suggesting that intrachain interactions, especially stacking interaction in the loop, might increase the roughness of the free energy surface of the DNA hairpin-loop.
authors.affiliation: Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
authors.forename: M I
authors.initials: MI
authors.lastname: Wallace
authors.forename: L
authors.initials: L
authors.lastname: Ying
authors.forename: S
authors.initials: S
authors.lastname: Balasubramanian
authors.forename: D
authors.initials: D
authors.lastname: Klenerman
mesh_terms: D004247:DNA / Q000737:chemistry*; D004058:Diffusion; D004735:Energy Transfer; D005453:Fluorescence; D007700:Kinetics; D009690:Nucleic Acid Conformation; D013816:Thermodynamics; D014783:Viscosity
chemical_list: D004247:DNA