%0 Book Section %B DNA Nanotechnology: Methods and Protocols %D 2011 %T Modeling nanopores for sequencing DNA %A Jeffrey Comer %A David B Wells %A Aleksei Aksimentiev %E Giampaolo Zuccheri %E Bruno Samori %K Base Sequence %K Computer Simulation %K DNA %K Hemolysin Proteins %K Models, Molecular %K Molecular Conformation %K Molecular Dynamics Simulation %K Nanopores %K Nanotechnology %K Sequence Analysis, DNA %X

Using nanopores to sequence DNA rapidly and at a low cost has the potential to radically transform the field of genomic research. However, despite all the exciting developments in the field, sequencing DNA using a nanopore has yet to be demonstrated. Among the many problems that hinder development of the nanopore sequencing methods is the inability of current experimental techniques to visualize DNA conformations in a nanopore and directly relate the microscopic state of the system to the measured signal. We have recently shown that such tasks could be accomplished through computation. This chapter provides step-by-step instructions of how to build atomic scale models of biological and solid-state nanopore systems, use the molecular dynamics method to simulate the electric field-driven transport of ions and DNA through the nanopores, and analyze the results of such computational experiments.

%B DNA Nanotechnology: Methods and Protocols %V 749 %P 317-358 %8 2011 %G eng %R 10.1007/978-1-61779-142-0_22