Applications of Fluorescence Correlation Spectroscopy to the Study of Nucleic Acid Conformational Dynamics

Fluorescence correlation spectroscopy (FCS) is a quantitative technique where temporal fluctuations in fluorescence intensity are analyzed to yield information about physical processes that contribute to the fluctuations, These include diffusion through the observation volume, conformational dynamics, and chemical or photophysical reactions. To date, FCS applications in biochemistry and biophysics have been mostly focused on the investigation of molecular diffusion. In this chapter, we present a look into the recent applications of FCS to the study of conformational dynamics of nucleic acids. We first survey the basic theoretical and experimental aspects of the technique and then focus oil the results obtained in studies with DNA hairpins, nucleosomes, and single-stranded and duplex DNA.