A mesoscale model of DNA interaction with functionalized nanopore
Abstract
Functionalized nanopores have been used recently for the detection of specific DNA. The
interactions between the DNA and the nanopore are not well understood due to the small size of
DNA/nanopore and dynamic translocation process. Various chemical modifications have also been
applied on nanopore surfaces for improved signal yield and selective detection. This paper
develops an understanding of the interactions between translocating DNA and chemically modified
nanopore surfaces. An energy-based mesoscale computational model is used to elucidate critical
interrelationships between physical properties of the nanopore, electric field strength, and
translocation kinetics. We report a nonlinear increase in DNA translocation speed with increasing
electric field strength. The model predicts a transition in translocation from hybridization-driven to
electric field-driven, in agreement with experimental data. This work advances the molecule-level
understanding of the DNA-nanopore interface, and can help in designing optimized lab-on-chip
devices for molecule based diagnosis. © 2009 American Institute of Physics.
doi:10.1063/1.3240400