Gutenberg Open Science: A Monte Carlo study of knots in long double-stranded DNA chains

Please use this identifier to cite or link to this item: http://doi.org/10.25358/openscience-7143

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DC Field	Value	Language
dc.contributor.author	Rieger, Florian C.	-
dc.contributor.author	Virnau, Peter	-
dc.date.accessioned	2022-06-14T07:47:45Z	-
dc.date.available	2022-06-14T07:47:45Z	-
dc.date.issued	2016
dc.identifier.uri	https://openscience.ub.uni-mainz.de/handle/20.500.12030/7157	-
dc.description.abstract	We develop a coarse-grained model of double-stranded DNA which is solely based on experimentally determined knotting probabilities of short DNA strands. Our analysis is motivated by the emergence of DNA nanopore sequencing technology. The main advantage of nanopore sequencing in comparison to next-generation devices is its capability to sequence rather long DNA strands in a single run, currently up to ≈10,000 base pairs. Unfortunately, long DNA strands easily self-entangle into knotted conformations, and sequencing knotted DNA with nanopores may be subject to error. In our manuscript, the typical extent and likelihood of DNA knots is computed for DNA chains of up to half a million base pairs, and we estimate the abundance of complex and composite knots in relation to DNA length. Our analysis indicates that DNA knots may be a formidable roadblock for the development of devices which support substantially longer read lengths. We also show that structural properties of DNA, like its resistance to bending, are intimately linked to the molecule's tendency to form knots. We demonstrate how this connection can be utilized to introduce mathematical models of DNA which account for the molecule's overall statistical properties.	en_GB
dc.description.sponsorship	DFG, Open Access-Publizieren Universität Mainz / Universitätsmedizin	de
dc.language.iso	eng	de
dc.rights	CC BY	*
dc.rights.uri	https://creativecommons.org/licenses/by/4.0/	*
dc.subject.ddc	530 Physik	de_DE
dc.subject.ddc	530 Physics	en_GB
dc.title	A Monte Carlo study of knots in long double-stranded DNA chains	en_GB
dc.type	Zeitschriftenaufsatz	de
dc.identifier.doi	http://doi.org/10.25358/openscience-7143	-
jgu.type.dinitype	article	en_GB
jgu.type.version	Published version	de
jgu.type.resource	Text	de
jgu.organisation.department	FB 08 Physik, Mathematik u. Informatik	de
jgu.organisation.number	7940	-
jgu.organisation.name	Johannes Gutenberg-Universität Mainz	-
jgu.rights.accessrights	openAccess	-
jgu.journal.title	PLoS Computational Biology	de
jgu.journal.volume	12	de
jgu.journal.issue	9	de
jgu.pages.alternative	e1005029	de
jgu.publisher.year	2016	-
jgu.publisher.name	Public Library of Science	de
jgu.publisher.place	San Francisco, Calif.	de
jgu.publisher.uri	http://dx.doi.org/10.1371/journal.pcbi.1005029	de
jgu.publisher.issn	1553-7358	de
jgu.publisher.issn	1553-734X	de
jgu.organisation.place	Mainz	-
jgu.subject.ddccode	530	de
opus.date.modified	2018-08-22T10:10:26Z
opus.subject.dfgcode	00-000
opus.organisation.string	FB 08: Physik, Mathematik und Informatik: Institut für Physik	de_DE
opus.identifier.opusid	55145
opus.institute.number	0801
opus.metadataonly	false
opus.type.contenttype	Keine	de_DE
opus.type.contenttype	None	en_EN
opus.affiliated	Virnau, Peter
jgu.publisher.doi	10.1371/journal.pcbi.1005029	de
jgu.organisation.ror	https://ror.org/023b0x485
Appears in collections:	DFG-OA-Publizieren (2012 - 2017)

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