Exploring the structural dynamics of DNA using fluorescence polarization microscopy and optical tweezers

Abstract

DNA structural transitions facilitate genomic processes, mediate drug-DNA interactions, and inform the development of emerging DNA-based biotechnology. Here, we use concurrent fluorescence polarization imaging and DNA manipulation experiments to probe the structure of DNA conformations that form under high tension and topological constraints. First, we employ polarization imaging of DNA intercalators (small dye molecules that slide between the DNA base-pairs) to probe the structure of S-DNA, an elongated conformation that can be accessed by mechanical overstretching of (relaxed) B-DNA.