8 December 2006
David Nelson
Lyman Laboratory of Physics
Harvard University
The denaturation of double-stranded DNA as a function of force and temperature is discussed. At room temperature, sequence heterogeneity dominates the physics of single molecule force-extension curves starting about 7 pN below a ~15 pN unzipping transition. The dynamics of the unzipping fork exhibits anomalous drift and diffusion in a similar range above this transition. Energy barriers near the transition scale as the square root of the genome size. We will argue that similar ideas apply to the effect of sequence heterogeneity on molecular motors such as RNA polymerase near the stall force. Instead of simple diffusion with drift, the dynamics is characterized by sequence-dependent jumps and pauses, and the long time displacement grows sublinearly with time, as tμ with μ < 1. The resulting motor velocity is no longer well defined, but depends instead on the time scale of observation.
D R Nelson, "Statistical Physics of Unzipping DNA", arxiv.org/abs/cond-mat/0309559
Y Kafri, D K Lubensky, D R Nelson, "Dynamics of molecular motors and polymer translocation with sequence heterogeneity", Biophys J 86:3373-91 2004. PubMed
Y Kafri, D R Nelson, "Sequence heterogeneity and the dynamics of molecular motors", J Phys: Condens Matter, 17:S3871-86 2005. arxiv.org/abs/cond-mat/0506797