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Toward detection of DNA‐bound proteins using solid‐state nanopores: Insights from computer simulations
Author(s) -
Comer Jeffrey,
Ho Anthony,
Aksimentiev Aleksei
Publication year - 2012
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.201200164
Subject(s) - nanopore , dna , biophysics , molecular dynamics , chemistry , electrophoresis , static electricity , linker , ionic bonding , nanopore sequencing , nanotechnology , materials science , biochemistry , dna sequencing , biology , ion , computational chemistry , physics , organic chemistry , quantum mechanics , computer science , operating system
Through all‐atom molecular dynamics simulations, we explore the use of nanopores in thin synthetic membranes for detection and identification of DNA binding proteins. Reproducing the setup of a typical experiment, we simulate electric field driven transport of DNA‐bound proteins through nanopores smaller in diameter than the proteins. As model systems, we use restriction enzymes Eco RI and Bam HI specifically and nonspecifically bound to a fragment of dsDNA, and streptavidin and NeutrAvidin proteins bound to dsDNA and ssDNA via a biotin linker. Our simulations elucidate the molecular mechanics of nanopore‐induced rupture of a protein–DNA complex, the effective force applied to the DNA–protein bond by the electrophoretic force in a nanopore, and the role of DNA–surface interactions in the rupture process. We evaluate the ability of the nanopore ionic current and the local electrostatic potential measured by an embedded electrode to report capture of DNA, capture of a DNA‐bound protein, and rupture of the DNA–protein bond. We find that changes in the strain on dsDNA can reveal the rupture of a protein–DNA complex by altering both the nanopore ionic current and the potential of the embedded electrode. Based on the results of our simulations, we suggest a new method for detection of DNA binding proteins that utilizes peeling of a nicked double strand under the electrophoretic force in a nanopore.