Non-Arrhenius kinetics for the loop closure of a DNA hairpin

Intramolecular chain diffusion is an elementary process in the conformation al fluctuations of the DNA hairpin-loop. We have studied the temperature an d viscosity dependence of a model DNA hairpin-loop by FRET (fluorescence re sonance energy transfer) fluctuation spectroscopy (FRETfs). Apparent thermo dynamic parameters were obtained by analyzing the correlation amplitude thr ough a two-state model and are consistent with steady-state fluorescence me asurements. The kinetics of closing the loop show non-Arrhenius behavior, i n agreement with theoretical prediction and other experimental measurements on peptide folding. The fluctuation rates show a fractional power dependen ce (beta = 0.83) on the solution viscosity. A much slower intrachain diffus ion 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 interact ions, especially stacking interaction in the loop, might increase the rough ness of the free energy surface of the DNA hairpin-loop.