title: Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA.
abstract: With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanopore sequencing can be extended to detection of DNA modifications and RNA characterization.
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
authors.forename: Maxim
authors.initials: M
authors.lastname: Belkin
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
authors.forename: Shu-Han
authors.initials: SH
authors.lastname: Chao
authors.affiliation: Organic Electronics, Department of Science and Technology (ITN), Linköping University , SE-58183 Linköping, Sweden.|Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology , 2628 CJ Delft, The Netherlands.
authors.forename: Magnus P
authors.initials: MP
authors.lastname: Jonsson
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology , 2628 CJ Delft, The Netherlands.
authors.forename: Cees
authors.initials: C
authors.lastname: Dekker
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
authors.forename: Aleksei
authors.initials: A
authors.lastname: Aksimentiev
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000235:genetics*; D004277:DNA, Single-Stranded / Q000235:genetics; D056004:Molecular Dynamics Simulation; D058608:Nanopores; D017422:Sequence Analysis, DNA; D013059:Spectrum Analysis, Raman
chemical_list: D004277:DNA, Single-Stranded; D004247:DNA
keywords: DNA sequencing; molecular dynamics; nanoplasmonics; nanopore; plasmonic tweezers