Modeling Nanopores for Sequencing DNA

  • Jeffrey R. Comer
  • David B. Wells
  • Aleksei Aksimentiev
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 749)

Abstract

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.

Key words

Molecular dynamics Transmembrane transport Nucleic acids Membrane proteins Bionanotechnology Computer simulations 

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Jeffrey R. Comer
  • David B. Wells
  • Aleksei Aksimentiev
    • 1
  1. 1.Department of PhysicsUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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