Branching out: new methods and applications for single-molecule spectroscopy

Abstract: I will present some of our recent work using single-molecule fluorescence techniques to study branched DNA. These molecules play critical roles in replication, repair and recombination; they are also key building blocks for the self-assembly of DNA nanostructures and nanomechanical devices. We have combined single-molecule multi-parameter fluorescence detection of FRET and molecular dynamics simulations to determine the global structure of a branched DNA molecule in solution, free of interference from sample heterogeneity and surface effects. These structures serve as the benchmark for our ongoing studies of forked DNA and their interactions with repair enzymes and accessory proteins. Results for the related three-way DNA junctions, which provided both global and local structural information, will also be presented. I will also describe more recent work aimed at developing new tools and methods for single-molecule analyses, including the use of ultrafast lasers for multiphoton excitation.