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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}
}