Sequence dependence of DNA translocation through a Nanopore

    Authors

    K. F. Luo; T. Ala-Nissila; S. C. Ying;A. Bhattacharya

    Comments

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    Abbreviated Journal Title

    Phys. Rev. Lett.

    Keywords

    MONTE-CARLO-SIMULATION; POLYMER TRANSLOCATION; POLYNUCLEOTIDE MOLECULES; MEMBRANE; DYNAMICS; DRIVEN; DISCRIMINATION; TRANSPORT; PORE; Physics, Multidisciplinary

    Abstract

    We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases A and C, which have been shown previously to have different interactions with the pore. We study DNA with repeating blocks A(n)C(n) for various values of n and find that the translocation time depends strongly on the block length 2n as well as on the orientation of which base enters the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through a nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences is contained in the periodicity of the residence time of the individual nucleotides inside the pore.

    Journal Title

    Physical Review Letters

    Volume

    100

    Issue/Number

    5

    Publication Date

    1-1-2008

    Document Type

    Article

    Language

    English

    First Page

    4

    WOS Identifier

    WOS:000253019600091

    ISSN

    0031-9007

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