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 journalArticlepeer-review

206 Scopus citations

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 100nm. 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
Pages (from-to)1093-1097
Number of pages5
JournalNature Nanotechnology
Volume11
Issue number12
DOIs
StatePublished - 1 Dec 2016

Bibliographical note

Publisher Copyright:
© 2016 Macmillan Publishers Limited, part of Springer Nature.

Funding

The authors would like to thank C. Micheletti, M. Di Stefano and P. Virnau for discussions, M.-Y. Wu for TEM drilling of nanopores and R. Joseph and S. W. Kowalczyk for early experiments. This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the Frontiers of Nanoscience program, and by the European Research Council under research grant NanoforBio (no. 247072) and SynDiv (no. 669598), the Koninklijke Nederlandse Akademie van Wetenschappen (KNAW) Academy Assistants Program and by the Wenner-Gren Foundations. Y.R. and A.Y.G. would like to acknowledge support from the US–Israel Binational Science foundation. This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the Frontiers of Nanoscience program, and by the European Research Council under research grant NanoforBio (no. 247072) and SynDiv (no. 669598), the Koninklijke Nederlandse Akademie van Wetenschappen (KNAW) Academy Assistants Program and by the Wenner-Gren Foundations. Y.R. and A.Y.G. would like to acknowledge support from the US'Israel Binational Science foundation.

FundersFunder number
NWO/OCW
SynDiv
National Human Genome Research InstituteR01HG007406
Wenner-Gren Stiftelserna
European Research Council669598, 247072
Koninklijke Nederlandse Akademie van Wetenschappen
United States-Israel Binational Science Foundation
Ministerie van Onderwijs, Cultuur en Wetenschap
Nederlandse Organisatie voor Wetenschappelijk Onderzoek

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