Final Report AFOSR FA9550-06-1-0408 Studies of single biomolecules, DNA conformational dynamics, and protein binding

Andreas Hanke Department of Physics and Astronomy, University of Texas, 80 Fort Brown, Brownsville Abstract While the Watson-Crick double-strand is the thermodynamically stable state of DNA in a wide range of temperature and salt conditions even at physiological conditions local denaturation bubbles may open up spontaneously due to thermal activation. By rising the ambient temperature, titration, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA. Based on the Poland-Scheraga model we investigate both the equilibrium transition of DNA denaturation and the dynamics of the denaturation bubbles with respect to recent single DNA chain experiments for situations below, at, and above the denaturation transition. We also propose a new single molecule setup based on DNA constructs with two bubble zones to measure the bubble coalescence and extract the physical parameters relevant to DNA breathing. Finally we consider the interplay between denaturation bubbles and selectively single stranded DNA binding proteins.