  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.
