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Direct observation of DNA knots using a solid-state nanopore
Delft University of Technology, Netherlands.
Delft University of Technology, Netherlands.
Delft University of Technology, Netherlands.
Delft University of Technology, Netherlands.
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2016 (English)In: Nature Nanotechnology, ISSN 1748-3387, E-ISSN 1748-3395, Vol. 11, no 12, 1093-1097 p.Article in journal (Refereed) Published
Abstract [en]

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 LiCI 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).

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP , 2016. Vol. 11, no 12, 1093-1097 p.
National Category
Condensed Matter Physics
Identifiers
URN: urn:nbn:se:liu:diva-133744DOI: 10.1038/NNANO.2016.153ISI: 000389962500020PubMedID: 27525473OAI: oai:DiVA.org:liu-133744DiVA: diva2:1063117
Note

Funding Agencies|Netherlands Organisation for Scientific Research (NWO/OCW), Frontiers of Nanoscience program; European Research Council [247072, 669598]; Koninklijke Nederlandse Akademie van Wetenschappen (KNAW) Academy Assistants Program; Wenner-Gren Foundations; US-Israel Binational Science foundation

Available from: 2017-01-09 Created: 2017-01-09 Last updated: 2017-01-09

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CiteExportLink to record
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Cite
Citation style
  • apa
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