Autoren:	Rieger, Florian C. Virnau, Peter
Titel:	A Monte Carlo study of knots in long double-stranded DNA chains
Online-Publikationsdatum:	14-Jun-2022
Erscheinungsdatum:	2016
Sprache des Dokuments:	Englisch
Zusammenfassung/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.
DDC-Sachgruppe:	530 Physik 530 Physics
Veröffentlichende Institution:	Johannes Gutenberg-Universität Mainz
Organisationseinheit:	FB 08 Physik, Mathematik u. Informatik
Veröffentlichungsort:	Mainz
ROR:	https://ror.org/023b0x485
DOI:	http://doi.org/10.25358/openscience-7143
Version:	Published version
Publikationstyp:	Zeitschriftenaufsatz
Nutzungsrechte:	CC BY
Informationen zu den Nutzungsrechten:	https://creativecommons.org/licenses/by/4.0/
Zeitschrift:	PLoS Computational Biology 12 9
Seitenzahl oder Artikelnummer:	e1005029
Verlag:	Public Library of Science
Verlagsort:	San Francisco, Calif.
Erscheinungsdatum:	2016
ISSN:	1553-7358 1553-734X
URL der Originalveröffentlichung:	http://dx.doi.org/10.1371/journal.pcbi.1005029
DOI der Originalveröffentlichung:	10.1371/journal.pcbi.1005029
Enthalten in den Sammlungen:	DFG-OA-Publizieren (2012 - 2017)