Three-State DNA Hairpin Conformational Dynamics Revealed by Higher-Order Fluorescence Correlation Spectroscopy

Previous fluorescence correlation spectroscopy (FCS) measurements of DNA hairpin folding dynamics revealed at least three conformational states of the DNA are present, distinguished by the brightness of fluorescent dye-quencher labels. Rapid fluctuations between two of the states occurred on time scales observable by FCS. A third state that was static on the FCS time scale was also observed. In this study, we investigate these conformational states using newly developed higher-order FCS techniques. It is shown that conventional FCS alone cannot uniquely distinguish the conformational states or assign their roles in the observed mechanism. The additional information offered by higher-order FCS makes it possible (i) to uniquely identify the static and rapidly fluctuating states and (ii) to directly measure the brightnesses and populations of all three observed states. The rapid fluctuations occurring on the FCS time scale are due to a reversible reaction between the two lowest brightness levels, attributed to the folded and random-coil conformations of the DNA. Evidence is presented that the third state, which is the brightest, may be associated with spatially extended unfolded conformations that are isolated from the more compact conformations by a substantial barrier. These conformations attain a maximum equilibrium population of nearly 10% near physiological temperatures and salt concentrations.