Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins.
Elucidating the mechanism of folding of polynucleotides depends on accurate estimates of free energy surfaces and a quantitative description of the kinetics of structure formation. Here, the kinetics of hairpin formation in single-stranded DNA are measured after a laser temperature jump. The kinetics are modeled as configurational diffusion on a free energy surface obtained from a statistical mechanical description of equilibrium melting profiles. The effective diffusion coefficient is found to be strongly temperature-dependent in the nucleation step as a result of formation of misfolded loops that do not lead to subsequent zipping. This simple system exhibits many of the features predicted from theoretical studies of protein folding, including a funnel-like energy surface with many folding pathways, trapping in misfolded conformations, and non-Arrhenius folding rates.
Ansari
A
A
Department of Physics (M/C 273), University of Illinois, 845 West Taylor Street, Chicago, IL 60607, USA. ansari@uic.edu
Kuznetsov
S V
SV
Shen
Y
Y
D004247:DNA / Q000737:chemistry*; D007700:Kinetics; D008956:Models, Chemical; D009690:Nucleic Acid Conformation
D004247:DNA