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Topological patterns in two-dimensional gel electrophoresis of DNA knots
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Michieletto , Davide, Marenduzzo , Davide and Orlandini , Enzo (2015) Topological patterns in two-dimensional gel electrophoresis of DNA knots. Proceedings of the National Academy of Sciences of the United States of America, 112 (40). pp. 1-28. doi:10.1073/pnas.1506907112 ISSN 0027-8424.
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Official URL: https://doi.org/10.1073/pnas.1506907112
Abstract
Gel electrophoresis is a powerful experimental method to probe the
topology of DNA and other biopolymers. While there is a large
body of experimental work which allows us to accurately separate
different topoisomers of a molecule, a full theoretical understanding
of these experiments has not yet been achieved. Here we show
that the mobility of DNA knots depends crucially and subtly on
the physical properties of the gel, and in particular on the presence
of dangling ends. The topological interactions between these
and DNA molecules can be described in terms of an “entanglement
number”, and yield a non-monotonic mobility at moderate fields.
Consequently, in two-dimensional electrophoresis, gel bands display
a characteristic arc pattern; this turns into a straight line when the
density of dangling ends vanishes. We also provide a novel framework
to accurately predict the shape of such arcs as a function of
molecule length and topological complexity, which may be used to
inform future experiments.
| Item Type: | Journal Article | ||||||
|---|---|---|---|---|---|---|---|
| Subjects: | Q Science > QD Chemistry | ||||||
| Divisions: | Faculty of Science, Engineering and Medicine > Research Centres > Centre for Complexity Science Faculty of Science, Engineering and Medicine > Science > Physics |
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| Library of Congress Subject Headings (LCSH): | Supramolecular chemistry, DNA | ||||||
| Journal or Publication Title: | Proceedings of the National Academy of Sciences of the United States of America | ||||||
| Publisher: | National Academy of Sciences | ||||||
| ISSN: | 0027-8424 | ||||||
| Official Date: | 6 October 2015 | ||||||
| Dates: |
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| Volume: | 112 | ||||||
| Number: | 40 | ||||||
| Number of Pages: | 28 | ||||||
| Page Range: | pp. 1-28 | ||||||
| DOI: | 10.1073/pnas.1506907112 | ||||||
| Status: | Peer Reviewed | ||||||
| Publication Status: | Published | ||||||
| Access rights to Published version: | Restricted or Subscription Access | ||||||
| Date of first compliant deposit: | 31 December 2015 | ||||||
| Date of first compliant Open Access: | 31 December 2015 |
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