skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Single Strand DNA Molecules Translocation through Nanoelectrode Gaps

Abstract

Molecular dynamics simulations were performed to investigate the translocation of single-strand DNA through nanoscale electrode gaps under the action of a constant driving force. The application behind this theoretical study is a proposal to use nanoelectrodes as a screening gap as part of a rapid genomic sequencing device. Preliminary results from a series of simulations using various gap widths and driving forces suggest that the narrowest electrode gap that a single-strand DNA can pass is {approx}1.5 nm. The minimum force required to initiate the translocation within nanoseconds is {approx}0.3 nN. Simulations using DNA segments of various lengths indicate that the minimum initiation force is insensitive to the length of DNA. However, the average threading velocity of DNA varies appreciably from short to long DNA segments. We attribute such variation to the different nature of drag force experienced by the short and long DNA segments in the environment. It is found that DNA molecules deform significantly to fit in the shape of the nanogap during the translocation

Authors:
 [1];  [1];  [1]
  1. ORNL
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
Work for Others (WFO)
OSTI Identifier:
931926
DOE Contract Number:
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nanotechnology; Journal Volume: 18
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; DNA; ELECTRODES; SHAPE; TRANSLOCATION

Citation Formats

Lee, James Weifu, Zhao, Xiongce, and Cummings, Peter T. Single Strand DNA Molecules Translocation through Nanoelectrode Gaps. United States: N. p., 2007. Web.
Lee, James Weifu, Zhao, Xiongce, & Cummings, Peter T. Single Strand DNA Molecules Translocation through Nanoelectrode Gaps. United States.
Lee, James Weifu, Zhao, Xiongce, and Cummings, Peter T. Mon . "Single Strand DNA Molecules Translocation through Nanoelectrode Gaps". United States. doi:.
@article{osti_931926,
title = {Single Strand DNA Molecules Translocation through Nanoelectrode Gaps},
author = {Lee, James Weifu and Zhao, Xiongce and Cummings, Peter T},
abstractNote = {Molecular dynamics simulations were performed to investigate the translocation of single-strand DNA through nanoscale electrode gaps under the action of a constant driving force. The application behind this theoretical study is a proposal to use nanoelectrodes as a screening gap as part of a rapid genomic sequencing device. Preliminary results from a series of simulations using various gap widths and driving forces suggest that the narrowest electrode gap that a single-strand DNA can pass is {approx}1.5 nm. The minimum force required to initiate the translocation within nanoseconds is {approx}0.3 nN. Simulations using DNA segments of various lengths indicate that the minimum initiation force is insensitive to the length of DNA. However, the average threading velocity of DNA varies appreciably from short to long DNA segments. We attribute such variation to the different nature of drag force experienced by the short and long DNA segments in the environment. It is found that DNA molecules deform significantly to fit in the shape of the nanogap during the translocation},
doi = {},
journal = {Nanotechnology},
number = ,
volume = 18,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}
  • Molecular dynamics simulations show that electrophoresis of DNA segments through a nanoscale electrode gap can be controlled by applying appropriate biased voltages in the transmembrane direction. The translocation velocities are dependent on both the DNA molecular weight and nucleotide structure. Application of alternating driving fields results in oscillatory motion of DNA inside the gap. Interruption of the driving field can effectively pause the translocation of DNA segments. Results from this work are useful for designing novel sequencing devices.
  • We report the fabrication of devices in which one single-walled carbon nanotube spans a barrier between two fluid reservoirs, enabling direct electrical measurement of ion transport through the tube. A fraction of the tubes pass anomalously high ionic currents. Electrophoretic transport of small single-stranded DNA oligomers through these tubes is marked by large transient increases in ion current and was confirmed by polymerase chain reaction analysis. Each current pulse contains about 10{sup 7} charges, an enormous amplification of the translocated charge. Carbon nanotubes simplify the construction of nanopores, permit new types of electrical measurements, and may open avenues for controlmore » of DNA translocation.« less
  • The fabrication of sub-micron pores in single crystal diamond membranes, which span the entirety of the membrane, is described for the first time, and the translocation properties of polymeric particles through the pore investigated. The pores are produced using a combination of laser micromachining to form the membrane and electron beam induced etching to form the pore. Single crystal diamond as the membrane material, has the advantages of chemical stability and durability, does not hydrate and swell, has outstanding electrical properties that facilitate fast, low noise current-time measurements and is optically transparent for combined optical-conductance sensing. The resulting pores aremore » characterized individually using both conductance measurements, employing a microcapillary electrochemical setup, and electron microscopy. Proof-of-concept experiments to sense charged polystyrene particles as they are electrophoretically driven through a single diamond pore are performed, and the impact of this new pore material on particle translocation is explored. As a result, these findings reveal the potential of diamond as a platform for pore-based sensing technologies and pave the way for the fabrication of single nanopores which span the entirety of a diamond membrane.« less
  • An apparatus for carrying out the separation, detection, and/or counting of single molecules at nanometer scale. Molecular separation is achieved by driving single molecules through a microfluidic or nanofluidic medium using programmable and coordinated electric fields. In various embodiments, the fluidic medium is a strip of hydrophilic material on nonconductive hydrophobic surface, a trough produced by parallel strips of hydrophobic nonconductive material on a hydrophilic base, or a covered passageway produced by parallel strips of hydrophobic nonconductive material on a hydrophilic base together with a nonconductive cover on the parallel strips of hydrophobic nonconductive material. The molecules are detected andmore » counted using nanoelectrode-gated electron tunneling methods, dielectric monitoring, and other methods.« less