Spectroscopic Approaches for Studies of Site-Specific DNA Base and Backbone “Breathing” Using Exciton-Coupled Dimer-Labeled DNA
摘要
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 analog 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.