Dynamics of RNA Translocation through a Nanopore

Details Dynamics of RNA Translocation through a Nanopore Dynamics of RNA Translocation through a Nanopore

2007-03-12

arxiv.org/abs/q-bio/0703028v1

Biology

Quantitative Biology

Biomolecules

17 Pages, 12 Figures

Scientific paper

We present a simplified model of the dynamics of translocation of RNA through a nanopore which only allows the passage of unbound nucleotides. In particular, we consider the disorder averaged translocation dynamics of random, two-component, single-stranded nucleotides, by reducing the dynamics to the motion of a random walker on a one-dimensional free energy landscape of translocation. These translocation landscapes are calculated from the folds of the RNA sequences and the voltage bias applied across the nanopore. We compute these landscapes for 1500 randomly drawn two-letter sequences of length 4000. Simulations of the dynamics on these landscapes display anomalous characteristics, similar to random forcing energy landscapes, where the translocation process proceeds slower than linearly in time for sufficiently small voltage biases across the nanopore, but moves linearly in time at large voltage biases. We argue that our simplified model provides an upper bound to the more realistic translocation dynamics, and thus we expect that all RNA translocation models will exhibit anomalous regimes.

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