title: Velocity of DNA during translocation through a solid-state nanopore.
abstract: While understanding translocation of DNA through a solid-state nanopore is vital for exploiting its potential for sensing and sequencing at the single-molecule level, surprisingly little is known about the dynamics of the propagation of DNA through the nanopore. Here we use linear double-stranded DNA molecules, assembled by the DNA origami technique, with markers at known positions in order to determine for the first time the local velocity of different segments along the length of the molecule. We observe large intramolecular velocity fluctuations, likely related to changes in the drag force as the DNA blob unfolds. Furthermore, we observe an increase in the local translocation velocity toward the end of the translocation process, consistent with a speeding up due to unfolding of the last part of the DNA blob. We use the velocity profile to estimate the uncertainty in determining the position of a feature along the DNA given its temporal location and demonstrate the error introduced by assuming a constant translocation velocity.
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology , Lorentzweg 1, 2628 CJ Delft, The Netherlands.
authors.forename: Calin
authors.initials: C
authors.lastname: Plesa
authors.forename: Nick
authors.initials: N
authors.lastname: van Loo
authors.forename: Philip
authors.initials: P
authors.lastname: Ketterer
authors.forename: Hendrik
authors.initials: H
authors.lastname: Dietz
authors.forename: Cees
authors.initials: C
authors.lastname: Dekker
mesh_terms: D004247:DNA / Q000737:chemistry*; D009038:Motion; D058608:Nanopores; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA
keywords: DNA; DNA origami; Nanopore; translocation; velocity