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Molecular dynamics simulations of DNA sequencing with graphene nanopores indicate that DNA bases can be identified by their translocation times
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Department of Chemistry, Soft Matter Research Center, Zhejiang University, China .
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2015 (English)In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 5, no 13, 9389-9395 p.Article in journal (Refereed) Published
Abstract [en]

The improvement of the resolution of DNA sequencing by nanopore technology is very important for its real-life application. In this paper, we report our work on using molecular dynamics simulation to study the dependence of DNA sequencing on the translocation time of DNA through a graphene nanopore, using the single-strand DNA fragment translocation through graphene nanopores with diameters down to similar to 2 nm as examples. We found that A, T, C, and G could be identified by the difference in the translocation time between different types of nucleotides through 2 nm graphene nanopores. In particular, the recognition of the graphene nanopore for different nucleotides can be greatly enhanced in a low electric field. Our study suggests that the recognition of a graphene nanopore by different nucleotides is the key factor for sequencing DNA by translocation time. Our study also indicates that the surface of a graphene nanopore can be modified to increase the recognition of nucleotides and to improve the resolution of DNA sequencing based on the DNA translocation time with a suitable electric field.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2015. Vol. 5, no 13, 9389-9395 p.
Keyword [en]
DNA, DNA sequences, Electric fields, Gene encoding, Graphene, Molecular dynamics, Nanopores, Nucleotides, DNA basis, DNA Sequencing, DNA translocation, Key factors, Molecular dynamics simulations, Real-life applications, Single strand DNA
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-160405DOI: 10.1039/c4ra12530dISI: 000347976500011Scopus ID: 2-s2.0-84921318920OAI: oai:DiVA.org:kth-160405DiVA: diva2:790373
Note

QC 20150224

Available from: 2015-02-24 Created: 2015-02-19 Last updated: 2017-12-04Bibliographically approved

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Ågren, HansTu, Yaoquan

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