Colloquium on April 11th, 2005

David Nelson
Department of Physics
Division of Engineering and Applied Science
Harvard University

DNA unzipping and motor proteins: Effect of the genetic code

The inluence of the base pair sequence on DNA unzipping and on molecular motors such as helicases and RNA polymerases is described. When DNA is denatured by an applied force, sequence heterogeneity dominates single molecule force-extension curves starting about 7 piconewtons below a 15 pN unzipping transition. The dynamics of the unzipping fork exhibits anomalous pauses and jumps in a similar range above the transition. The molecular motors essential for cell division and function are not usually biased by an explicit force, but instead by a coupling to chemical energy. However, an externally applied force can oppose these biases. We argue that anomalous dynamics also occurs in these systems near the stall force, characterized by an average displacement which grows sublinearly in time, as t^mu with mu<1. This is the characterstic behavior of a one dimensional Brownian particle diffusing in a random force field. In this regime, the observed "velocity" of a DNA unzipping fork or a molecular motor will depend in a precise way on the time scale of the experiment.