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Is the kinetoplast DNA a percolating network of linked rings at its critical point?
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Michieletto, Davide, Marenduzzo, Davide and Orlandini, Enzo (2015) Is the kinetoplast DNA a percolating network of linked rings at its critical point? Physical Biology, Volume 12 (Number 3). pp. 1-8. 036001. doi:10.1088/1478-3975/12/3/036001 ISSN 1478-3975.
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Official URL: http://dx.doi.org/10.1088/1478-3975/12/3/036001
Abstract
In this work we present a computational study of the kinetoplast genome, modelled as a large number of semiflexible unknotted loops, which are allowed to link with each other. As the DNA density increases, the systems shows a percolation transition between a gas of unlinked rings and a network of linked loops which spans the whole system. Close to the percolation transition, we find that the mean valency of the network, i.e. the average number of loops which are linked to any one loop, is around three, as found experimentally for the kinetoplast DNA (kDNA). Even more importantly, by simulating the digestion of the network by a restriction enzyme, we show that the distribution of oligomers, i.e. structures formed by a few loops which remain linked after digestion, quantitatively matches experimental data obtained from gel electrophoresis, provided that the density is, once again, close to the percolation transition. With respect to previous work, our analysis builds on a reduced number of assumptions, yet can still fully explain the experimental data. Our findings suggest that the kDNA can be viewed as a network of linked loops positioned very close to the percolation transition, and we discuss the possible biological implications of this remarkable fact.
Item Type: | Journal Article | ||||||||
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Subjects: | Q Science > QR Microbiology | ||||||||
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): | Bacterial genetics | ||||||||
Journal or Publication Title: | Physical Biology | ||||||||
Publisher: | Institute of Physics Publishing Ltd. | ||||||||
ISSN: | 1478-3975 | ||||||||
Official Date: | 13 May 2015 | ||||||||
Dates: |
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Volume: | Volume 12 | ||||||||
Number: | Number 3 | ||||||||
Number of Pages: | 8 | ||||||||
Page Range: | pp. 1-8 | ||||||||
Article Number: | 036001 | ||||||||
DOI: | 10.1088/1478-3975/12/3/036001 | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||
Date of first compliant deposit: | 29 December 2015 | ||||||||
Date of first compliant Open Access: | 29 December 2015 | ||||||||
Funder: | Engineering and Physical Sciences Research Council (EPSRC), Italy. Ministero della pubblica istruzione | ||||||||
Grant number: | EP/E501311 (EPSRC), EP/I034661/1 (EPSRC), PRIN 2010HXAW77 | ||||||||
Open Access Version: |
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