Direct observation of DNA knots using a solid-state nanopore

Calin Plesa, Daniel Verschueren, Sergii Pud, Jaco van der Torre, Justus W. Ruitenberg, Menno J. Witteveen, Magnus P. Jonsson, Alexander Y. Grosberg, Yitzhak Rabin, Cees Dekker

    Research output: Contribution to journalArticle

    Abstract

    Long DNA molecules can self-entangle into knots. Experimental techniques for observing such DNA knots (primarily gel electrophoresis) are limited to bulk methods and circular molecules below 10 kilobase pairs in length. Here, we show that solid-state nanopores can be used to directly observe individual knots in both linear and circular single DNA molecules of arbitrary length. The DNA knots are observed as short spikes in the nanopore current traces of the traversing DNA molecules and their detection is dependent on a sufficiently high measurement resolution, which can be achieved using high-concentration LiCl buffers. We study the percentage of molecules with knots for DNA molecules of up to 166 kilobase pairs in length and find that the knotting occurrence rises with the length of the DNA molecule, consistent with a constant knotting probability per unit length. Our experimental data compare favourably with previous simulation-based predictions for long polymers. From the translocation time of the knot through the nanopore, we estimate that the majority of the DNA knots are tight, with remarkably small sizes below 100 nm. In the case of linear molecules, we also observe that knots are able to slide out on application of high driving forces (voltage).

    Original languageEnglish (US)
    JournalNature Nanotechnology
    DOIs
    StateAccepted/In press - Aug 15 2016

    Fingerprint

    Nanopores
    DNA
    deoxyribonucleic acid
    solid state
    Molecules
    molecules
    electrophoresis
    Electrophoresis
    chutes
    spikes
    Buffers
    Polymers
    Gels
    buffers
    gels
    occurrences
    polymers
    Electric potential
    electric potential
    estimates

    ASJC Scopus subject areas

    • Bioengineering
    • Biomedical Engineering
    • Materials Science(all)
    • Electrical and Electronic Engineering
    • Condensed Matter Physics
    • Atomic and Molecular Physics, and Optics

    Cite this

    Plesa, C., Verschueren, D., Pud, S., van der Torre, J., Ruitenberg, J. W., Witteveen, M. J., ... Dekker, C. (Accepted/In press). Direct observation of DNA knots using a solid-state nanopore. Nature Nanotechnology. https://doi.org/10.1038/nnano.2016.153

    Direct observation of DNA knots using a solid-state nanopore. / Plesa, Calin; Verschueren, Daniel; Pud, Sergii; van der Torre, Jaco; Ruitenberg, Justus W.; Witteveen, Menno J.; Jonsson, Magnus P.; Grosberg, Alexander Y.; Rabin, Yitzhak; Dekker, Cees.

    In: Nature Nanotechnology, 15.08.2016.

    Research output: Contribution to journalArticle

    Plesa, C, Verschueren, D, Pud, S, van der Torre, J, Ruitenberg, JW, Witteveen, MJ, Jonsson, MP, Grosberg, AY, Rabin, Y & Dekker, C 2016, 'Direct observation of DNA knots using a solid-state nanopore', Nature Nanotechnology. https://doi.org/10.1038/nnano.2016.153
    Plesa C, Verschueren D, Pud S, van der Torre J, Ruitenberg JW, Witteveen MJ et al. Direct observation of DNA knots using a solid-state nanopore. Nature Nanotechnology. 2016 Aug 15. https://doi.org/10.1038/nnano.2016.153
    Plesa, Calin ; Verschueren, Daniel ; Pud, Sergii ; van der Torre, Jaco ; Ruitenberg, Justus W. ; Witteveen, Menno J. ; Jonsson, Magnus P. ; Grosberg, Alexander Y. ; Rabin, Yitzhak ; Dekker, Cees. / Direct observation of DNA knots using a solid-state nanopore. In: Nature Nanotechnology. 2016.
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