A mesoscale model of DNA interaction with functionalized nanopore

Yaling Liu; Iqbal, Samir M.
November 2009
Applied Physics Letters;11/30/2009, Vol. 95 Issue 22, p223701
Academic Journal
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.


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