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Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores

[Image: see text] We investigate by means of molecular dynamics simulations stretch-induced stepwise translocation of single-stranded DNA (ssDNA) through graphene nanopores. The intrinsic stepwise DNA motion, found to be largely independent of size and shape of the graphene nanopore, is brought abou...

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Autores principales: Qiu, Hu, Sarathy, Aditya, Leburton, Jean-Pierre, Schulten, Klaus
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2015
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676420/
https://www.ncbi.nlm.nih.gov/pubmed/26581231
http://dx.doi.org/10.1021/acs.nanolett.5b03963
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author Qiu, Hu
Sarathy, Aditya
Leburton, Jean-Pierre
Schulten, Klaus
author_facet Qiu, Hu
Sarathy, Aditya
Leburton, Jean-Pierre
Schulten, Klaus
author_sort Qiu, Hu
collection PubMed
description [Image: see text] We investigate by means of molecular dynamics simulations stretch-induced stepwise translocation of single-stranded DNA (ssDNA) through graphene nanopores. The intrinsic stepwise DNA motion, found to be largely independent of size and shape of the graphene nanopore, is brought about through alternating conformational changes between spontaneous adhesion of DNA bases to the rim of the graphene nanopore and unbinding due to mechanical force or electric field. The adhesion reduces the DNA bases’ vertical conformational fluctuations, facilitating base detection and recognition. A graphene membrane shaped as a quantum point contact permits, by means of transverse electronic conductance measurement, detection of the stepwise translocation of the DNA as predicted through quantum mechanical Green’s function-based transport calculations. The measurement scheme described opens a route to enhance the signal-to-noise ratio not only by slowing down DNA translocation to provide sufficient time for base recognition but also by stabilizing single DNA bases and, thereby, reducing thermal noise.
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spelling pubmed-46764202016-11-19 Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores Qiu, Hu Sarathy, Aditya Leburton, Jean-Pierre Schulten, Klaus Nano Lett [Image: see text] We investigate by means of molecular dynamics simulations stretch-induced stepwise translocation of single-stranded DNA (ssDNA) through graphene nanopores. The intrinsic stepwise DNA motion, found to be largely independent of size and shape of the graphene nanopore, is brought about through alternating conformational changes between spontaneous adhesion of DNA bases to the rim of the graphene nanopore and unbinding due to mechanical force or electric field. The adhesion reduces the DNA bases’ vertical conformational fluctuations, facilitating base detection and recognition. A graphene membrane shaped as a quantum point contact permits, by means of transverse electronic conductance measurement, detection of the stepwise translocation of the DNA as predicted through quantum mechanical Green’s function-based transport calculations. The measurement scheme described opens a route to enhance the signal-to-noise ratio not only by slowing down DNA translocation to provide sufficient time for base recognition but also by stabilizing single DNA bases and, thereby, reducing thermal noise. American Chemical Society 2015-11-19 2015-12-09 /pmc/articles/PMC4676420/ /pubmed/26581231 http://dx.doi.org/10.1021/acs.nanolett.5b03963 Text en Copyright © 2015 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes.
spellingShingle Qiu, Hu
Sarathy, Aditya
Leburton, Jean-Pierre
Schulten, Klaus
Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores
title Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores
title_full Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores
title_fullStr Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores
title_full_unstemmed Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores
title_short Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores
title_sort intrinsic stepwise translocation of stretched ssdna in graphene nanopores
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676420/
https://www.ncbi.nlm.nih.gov/pubmed/26581231
http://dx.doi.org/10.1021/acs.nanolett.5b03963
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