Berlin 2005 – scientific programme
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AKB: Biologische Physik
AKB 45: Single Molecule Biophysics
AKB 45.2: Talk
Monday, March 7, 2005, 15:00–15:15, TU H2013
Kinetics of driven RNA translocation through nanopores — •Ulrich Gerland1 and Ralf Bundschuh2 — 1Department Physik and CENS, LMU München, Germany — 2Department of Physics, The Ohio State University, Columbus, Ohio
Motivated by recent experiments, we study the translocation of structured RNA molecules through narrow pores that allow single but not double strands to pass. The translocation dynamics is coupled to the base pairing dynamics of the RNA molecules, which we incorporate explicitly in kinetic Monte Carlo simulations. For a number of exemplary molecules as well as for random sequences, we characterize the translocation dynamics as a function of the driving force. For strongly driven translocation, we find a narrow distribution of translocation times with a mean that scales linearly with the RNA length. In contrast, for weakly driven translocation we observe a pronounced sequence-dependence in the distribution of translocation times. Simple physical arguments can explain these two limiting regimes. Furthermore, we identify the sequence-specific properties of RNA molecules that are reflected in the translocation times.