Parts | Days | Selection | Search | Updates | Downloads | Help

BP: Fachverband Biologische Physik

BP 15: Single-Molecule Biophysics I

BP 15.2: Talk

Tuesday, March 15, 2011, 10:45–11:00, ZEU 250

A versatile first passage framework for the theoretical analysis of nanopore translocation experiments with structured polynucleotides — •Severin Schink¹, Karen Alim², and Ulrich Gerland¹ — ¹ASC and CeNS, Ludwig-Maximilians-Universität Munich, Germany — ²Harvard School of Engineering and Applied Sciences, Harvard University, USA

Probing the structures and folding dynamics of DNA or RNA molecules by translocation through nanopores is an emerging new experimental approach of single-molecule biophysics. The nanopore allows single- but not double-strands to pass and thereby couples translocation to unfolding (and refolding) of the molecule. For the quantitative interpretation of these measurements, analysis based on theoretical models for the translocation process is required. The spectrum of available theoretical approaches ranges from generic Kramers rate theory to detailed simulations of both the basepairing and translocation dynamics. Here, we present a versatile mesoscopic framework, which is based on the construction of squence-dependent one-dimensional free energy landscapes starting from the known free energy parameters for RNA and DNA secondary structure formation. This approach has only a small number of adjustable parameters which can be calibrated using translocation experiments with simple sequences. The model then yields a baseline prediction for other sequences, based on which the corresponding experiments can be interpreted, both for constant force measurements as well as nanopore force spectroscopy data. We illustrate the use of our framework with several examples.