Sequence Dependent Rigidity of Single Stranded DNA

Abstract

Single stranded DNA (ssDNA) equilibrium dynamics are investigated using a fluorophore/quencher-labeled hairpin structure which thermally fluctuates between open and closed states. Temporal correlations of the fluorescence fluctuations are used to determine the energy barrier to conformational change. We find that ssDNA distortion is purely entropic for $\mathrm{poly}\left(T\right)$ but requires an additional enthalpy of $+0.5\mathrm{kcal}̇\mathrm{mol}{}^{-1\mathrm{}}̇\mathrm{base}{}^{-1\mathrm{}}$ for $\mathrm{poly}\left(A\right)$, consistent with the disruption of base stacking. Such sequence dependent dynamics challenge the classical model of ssDNA as a completely flexible coil.