Sequence dependent rigidity of single stranded DNA

Single stranded DNA (ssDNA) equilibrium dynamics are investigated using a f luorophore/quencher-labeled hairpin structure which thermally fluctuates be tween open and closed states. Temporal correlations of the fluorescence flu ctuations are used to determine the energy barrier tu conformational change . We find that ssDNA distortion is purely entropic for poly(T) but requires an additional enthalpy of +0.5 kcal . mol(-1) base(-1) for poly(A), consis tent with the disruption of base stacking. Such sequence dependent dynamics challenge the classical model of ssDNA as a completely flexible coil.