title: Modeling nanopores for sequencing DNA.
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.
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Comer
authors.forename: David B
authors.initials: DB
authors.lastname: Wells
authors.forename: Aleksei
authors.initials: A
authors.lastname: Aksimentiev
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000032:analysis* / Q000737:chemistry; D006460:Hemolysin Proteins / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D058608:Nanopores; D036103:Nanotechnology / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D006460:Hemolysin Proteins; D004247:DNA