title: The electromechanics of DNA in a synthetic nanopore.
abstract: We have explored the electromechanical properties of DNA on a nanometer-length scale using an electric field to force single molecules through synthetic nanopores in ultrathin silicon nitride membranes. At low electric fields, E < 200 mV/10 nm, we observed that single-stranded DNA can permeate pores with a diameter >/=1.0 nm, whereas double-stranded DNA only permeates pores with a diameter >/=3 nm. For pores <3.0 nm diameter, we find a threshold for permeation of double-stranded DNA that depends on the electric field and pH. For a 2 nm diameter pore, the electric field threshold is approximately 3.1 V/10 nm at pH = 8.5; the threshold decreases as pH becomes more acidic or the diameter increases. Molecular dynamics indicates that the field threshold originates from a stretching transition in DNA that occurs under the force gradient in a nanopore. Lowering pH destabilizes the double helix, facilitating DNA translocation at lower fields.
authors.affiliation: Department of Electrical and Computer Engineering, Beckman Institute, University of Illinois, Urbana, Illinois 61801, USA.
authors.forename: J B
authors.initials: JB
authors.lastname: Heng
authors.forename: A
authors.initials: A
authors.lastname: Aksimentiev
authors.forename: C
authors.initials: C
authors.lastname: Ho
authors.forename: P
authors.initials: P
authors.lastname: Marks
authors.forename: Y V
authors.initials: YV
authors.lastname: Grinkova
authors.forename: S
authors.initials: S
authors.lastname: Sligar
authors.forename: K
authors.initials: K
authors.lastname: Schulten
authors.forename: G
authors.initials: G
authors.lastname: Timp
mesh_terms: D001703:Biophysics / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004563:Electrochemistry / Q000379:methods; D004574:Electromagnetic Fields; D004586:Electrophoresis; D004587:Electrophoresis, Agar Gel; D006863:Hydrogen-Ion Concentration; D007477:Ions; D008564:Membrane Potentials; D046529:Microscopy, Electron, Transmission; D008958:Models, Molecular; D049329:Nanostructures; D036103:Nanotechnology / Q000379:methods*; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction; D016062:Porosity; D017655:Silicon Compounds; D013997:Time Factors
chemical_list: D007477:Ions; D017655:Silicon Compounds; D004247:DNA; C032734:silicon nitride