DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA 'breathing') play a central role in such processes. Here we review the development and application of novel spectroscopic methods and analyses - both at the ensemble and single-molecule levels - to study structural and dynamic properties of exciton-coupled cyanine and fluorescent nucleobase analogue dimer-labeled DNA constructs at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as 'sensors' of the local conformations adopted by the sugar-phosphate backbones and bases immediately surrounding the dimer probes. These methods can be used to study the mechanisms of protein binding and function at these sites.
Keywords: DNA ‘breathing’; Fourier transform spectroscopy; exciton-coupled dimer probe; exciton-coupled probe spectroscopy; fluorescent base analogue; free energy surface; polarization-sweep single-molecule fluorescence (PS-SMF) microscopy; protein-DNA interactions; two-dimensional coherent spectroscopy; two-dimensional fluorescence spectroscopy (2DFS); two-photon excitation.