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DNA: Working out the knots

Nature Reviews Materials volume 1, Article number: 16072 (2016) Cite this article

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Various experimental techniques have previously been used to investigate DNA knots; however, all of them are bulk methods that are restricted to relatively short (<10 kilobase pairs) and/or circular DNA. By contrast, the nanopore technique reported by Cees Dekker and co-workers in Nature Nanotechnology allows the observation of individual knots in arbitrarily long, double-stranded linear and circular DNA. “Although such knots are most prevalent at long lengths, there was no method to observe knots in long DNA molecules before our technique,” explains Dekker.

Solid-state nanopores are used to study the fundamental properties of biomolecules on a single-molecule level and their interactions (for example, between DNA and proteins), as well as DNA separation and sequencing. The technique involves an electric potential being applied across a membrane that contains a nanopore (typically about 20-nm wide) with an electrolyte-filled reservoir on either side. A charged biomolecule (such as DNA) is driven through the nanopore by an electrophoretic force, where it causes a blockade in the ionic current that depends on the volume of polymer in the pore and, in the case of DNA, on the specific base pairs.

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References

  1. Plesa, C. et al. Direct observation of DNA knots using a solid-state nanopore. Nat. Nanotechnol.http://dx.doi.org/10.1038/nnano.2016.153 (2016)

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Authors
  1. Adam Brotchie
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Brotchie, A. DNA: Working out the knots. Nat Rev Mater 1, 16072 (2016). https://doi.org/10.1038/natrevmats.2016.72

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  • DOI: https://doi.org/10.1038/natrevmats.2016.72

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