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

• DOI: 10.1073/pnas.101523498
• Publication Date: 2002-07-26T14:37:36Z
• Authors: Mark I. Wallace; Liming Ying; Shankar Balasubra...; David Klenerman
• Keywords: Diffusion; 0301 basic medicine; Kinetics; 03 medical and health sciences; Energy Transfer; Viscosity; Nucleic Acid Conformation; Thermodynamics; DNA; Fluorescence

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 (β = 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.