The dynamical behaviour of single stranded DNA plays a key role in a number of biological functions. In particular the appearance of DNA hairpins is suspected to participate in gene expression and DNA recombination. The key experimental method to characterize the dynamics of these hairpins is fluorescence correlation spectroscopy of DNA that has been labeled at its terminal ends with a fluorophore and a quencher. The opening and closing rate kinetics (given by the rate constants k+ and k-, respectively) are determined from fluctuations of the fluorescence signal, which arise when the molecule is not in the hairpin state and the fluo-rophore and quencher are far apart from one another. When the molecule is in the hairpin state the fluorescence is quenched. The opening and closing rates of the hairpins are strongly sequence specific.

In this study, we use Brownian dynamics simulations to directly calculate the rate constants (k+ and k-) for the opening and closing of DNA hairpins using a simulated fluoresence correlation spectroscopy method. We examine the sequence specific kinetics of several DNA. We also characterize the DNA hairpins in terms of their conformation and fluctuations about a ground state hairpin structure. These results have potential implications in understanding the fundamental dynamics of DNA in biological systems and how the structure versus function relationship of DNA dictates its behaviour. on 5-15-2007-->