Direct observation of DNA knots using a solid-state nanopore

Direct observation of DNA knots using a solid-state nanopore

Plesa, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)
Verschueren, D.V. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)
Pud, S. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)
van der Torre, J. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft)
Ruitenberg, J.W. (TU Delft Education and Student Affairs; Kavli institute of nanoscience Delft)
Witteveen, M.J. (TU Delft Education and Student Affairs; Kavli institute of nanoscience Delft)
Jonsson, P.M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)
Grosberg, Alexander Y. (New York University)
Rabin, Yitzhak (Bar-Ilan University)
Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)

2016-08-15

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).

Nanopores

http://resolver.tudelft.nl/uuid:b0535b8c-d564-4063-8de5-2f126de59dd2

https://doi.org/10.1038/nnano.2016.153

1748-3387

Nature Nanotechnology, 11 (12), 1093-1097

Accepted Author Manuscript

Institutional Repository

journal article

© 2016 C. Plesa, D.V. Verschueren, S. Pud, J. van der Torre, J.W. Ruitenberg, M.J. Witteveen, P.M. Jonsson, Alexander Y. Grosberg, Yitzhak Rabin, C. Dekker