Coupled dynamics of RNA folding and nanopore translocation

Preprint

1 August 2005

preprint
Published by arXiv in arXiv

Abstract

The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base-pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte Carlo simulations and analytical methods. We find that (i) the formation of non-native basepairs can significantly speed up translocation, and (ii) the crossover between slow and fast translocation can be described by a simple phenomenological model.

Keywords

MONTE CARLO SIMULATIONS
NANOPORE TRANSLOCATION
ANALYTICAL METHODS
COUPLED DYNAMICS
STRUCTURED RNA
BASE PAIRING
RNA FOLDING
KINETIC

All Related Versions

Version 1, 2005-08-01, ArXiv
Version 2, 2005-09-29, ArXiv
Published version: Physical Review Letters, 95 (20), 208104.

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