FRET fluctuation spectroscopy: Exploring the conformational dynamics of a DNA hairpin loop

The motions of a dye-labeled DNA hairpin loop (Cy5-5'-GGGTT-(A)(30)-AACCC-3 '-TMR) have been investigated through the fluctuations in proximity ratio f rom fluorescence resonance energy transfer (FRET). We examine three solutio n conditions: (1) MilliQ water, (2) Tris-EDTA buffer, and (3) Tris-EDTA buf fer plus an excess of DNA complementary to the loop sequence, (T)(30). Corr elations in proximity ratio show submillisecond dynamics. Static heterogene ity is revealed from the distribution of proximity ratio amplitudes. The ob served stretched exponential kinetics are consistent with a model based on the transition between two states over a complex energy landscape.