Modeling nanopores for sequencing DNA.

Jeffrey R. Comer, David B. Wells, Aleksei Aksimentiev

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)317-358
Number of pages42
JournalMethods in molecular biology (Clifton, N.J.)
StatePublished - 2011

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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