Non-Arrhenius Kinetics for the Loop Closure of a DNA Hairpin

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 98; no. 10; pp. 5584 - 5589
• Main Authors: Wallace, Mark I., Ying, Liming, Balasubramanian, Shankar, Klenerman, David
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 08.05.2001; National Acad Sciences; The National Academy of Sciences
• Subjects: Activation energy; Biological Sciences; Biology; Chemistry; Deoxyribonucleic acid; Diffusion; DNA; DNA - chemistry; Energy Transfer; Fluorescence; fluorescence resonance energy transfer; Kinetics; Low temperature; Melting; Molecules; Nucleic Acid Conformation; Physical Sciences; Physics; Temperature dependence; Thermodynamics; Viscosity
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.101523498

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.