Base-by-Base Dynamics in DNA Hybridization Probed by Fluorescence Correlation Spectroscopy

Thermodynamics and dynamics of DNA hybridization/dehybridization at a terminal of a DNA duplex are investigated using steady-state fluorescence and fluorescence correlation spectroscopy (FCS). We introduce two pairs of dyes with different characteristic distances in fluorescence resonance energy transfer (FRET) to investigate the same process. The phenomenal discrepancy in the experimental observations between our two FRET pairs is incompatible with the traditional two-state model. We propose a so-called stretched exponential zipper (SEZ) model to successfully analyze the experimental data, through which the fundamental behavior of base-by-base hybridization/dehybridization is revealed. The dynamic parameters of the activation energy of single base-pair reaction derived from the two FRET pairs are consistent. The enthalpy change and entropy change of single base-pair formation are in agreement with theoretical prediction.