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Direct observation of DNA knots using a solid-state nanopore

Overview of attention for article published in Nature Nanotechnology, August 2016
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About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (94th percentile)
  • Above-average Attention Score compared to outputs of the same age and source (63rd percentile)

Mentioned by

news
2 news outlets
blogs
1 blog
twitter
23 tweeters
q&a
1 Q&A thread

Readers on

mendeley
102 Mendeley
Title
Direct observation of DNA knots using a solid-state nanopore
Published in
Nature Nanotechnology, August 2016
DOI 10.1038/nnano.2016.153
Pubmed ID
Authors

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, 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

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).

Twitter Demographics

The data shown below were collected from the profiles of 23 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 102 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 <1%
Belgium 1 <1%
Korea, Republic of 1 <1%
Unknown 99 97%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 40 39%
Researcher 16 16%
Student > Master 15 15%
Student > Bachelor 9 9%
Unspecified 6 6%
Other 16 16%
Readers by discipline Count As %
Physics and Astronomy 25 25%
Chemistry 23 23%
Engineering 18 18%
Agricultural and Biological Sciences 10 10%
Unspecified 6 6%
Other 20 20%

Attention Score in Context

This research output has an Altmetric Attention Score of 38. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 14 March 2017.
All research outputs
#321,657
of 11,309,368 outputs
Outputs from Nature Nanotechnology
#453
of 2,311 outputs
Outputs of similar age
#14,578
of 262,729 outputs
Outputs of similar age from Nature Nanotechnology
#19
of 52 outputs
Altmetric has tracked 11,309,368 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 97th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 2,311 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 30.1. This one has done well, scoring higher than 80% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 262,729 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 94% of its contemporaries.
We're also able to compare this research output to 52 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 63% of its contemporaries.