title: Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix.
abstract: It is now possible to slow and trap a single molecule of double-stranded DNA (dsDNA), by stretching it using a nanopore, smaller in diameter than the double helix, in a solid-state membrane. By applying an electric force larger than the threshold for stretching, dsDNA can be impelled through the pore. Once a current blockade associated with a translocating molecule is detected, the electric field in the pore is switched in an interval less than the translocation time to a value below the threshold for stretching. According to molecular dynamics (MD) simulations, this leaves the dsDNA stretched in the pore constriction with the base-pairs tilted, while the B-form canonical structure is preserved outside the pore. In this configuration, the translocation velocity is substantially reduced from 1 bp/10 ns to approximately 1 bp/2 ms in the extreme, potentially facilitating high fidelity reads for sequencing, precise sorting, and high resolution (force) spectroscopy.
authors.affiliation: Beckman Institute, University of Illinois, Urbana, IL 61801, USA.
authors.forename: Utkur
authors.initials: U
authors.lastname: Mirsaidov
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Comer
authors.forename: Valentin
authors.initials: V
authors.lastname: Dimitrov
authors.forename: Aleksei
authors.initials: A
authors.lastname: Aksimentiev
authors.forename: Gregory
authors.initials: G
authors.lastname: Timp
mesh_terms: D010582:Bacteriophage lambda; D004247:DNA / Q000737:chemistry*; D004279:DNA, Viral; D055664:Electrochemical Techniques; D046529:Microscopy, Electron, Transmission; D056004:Molecular Dynamics Simulation; D058608:Nanopores / Q000648:ultrastructure*; D036103:Nanotechnology / Q000379:methods*; D009690:Nucleic Acid Conformation; D010316:Particle Size
chemical_list: D004279:DNA, Viral; D004247:DNA
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