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Statements

Subject Item
n2:RIV%2F00216208%3A11320%2F14%3A10286287%21RIV15-MSM-11320___
rdf:type
skos:Concept n13:Vysledek
rdfs:seeAlso
http://dx.doi.org/10.1088/0953-8984/26/20/205102
dcterms:description
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as a function of the number of open base pairs and applied mechanical force. Using a commonly employed model, we first analyze for which types of sequences a particularly simple landscape structure is predicted, where forward and backward energy barriers between partly unfolded states are decreasing linearly with force. Stochastic unfolding trajectories for such molecules with simple FEL are subsequently generated by kinetic Monte Carlo simulations. Introducing probabilities that can be sampled from these trajectories, it is shown how the parameters characterizing the FEL can be estimated. Already 300 trajectories, as typically generated in experiments, provide faithful results for the FEL parameters. DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as a function of the number of open base pairs and applied mechanical force. Using a commonly employed model, we first analyze for which types of sequences a particularly simple landscape structure is predicted, where forward and backward energy barriers between partly unfolded states are decreasing linearly with force. Stochastic unfolding trajectories for such molecules with simple FEL are subsequently generated by kinetic Monte Carlo simulations. Introducing probabilities that can be sampled from these trajectories, it is shown how the parameters characterizing the FEL can be estimated. Already 300 trajectories, as typically generated in experiments, provide faithful results for the FEL parameters.
dcterms:title
Unfolding kinetics of periodic DNA hairpins Unfolding kinetics of periodic DNA hairpins
skos:prefLabel
Unfolding kinetics of periodic DNA hairpins Unfolding kinetics of periodic DNA hairpins
skos:notation
RIV/00216208:11320/14:10286287!RIV15-MSM-11320___
n4:aktivita
n19:S
n4:aktivity
S
n4:cisloPeriodika
20
n4:dodaniDat
n10:2015
n4:domaciTvurceVysledku
n9:7814631 n9:4990552
n4:druhVysledku
n5:J
n4:duvernostUdaju
n16:S
n4:entitaPredkladatele
n18:predkladatel
n4:idSjednocenehoVysledku
51938
n4:idVysledku
RIV/00216208:11320/14:10286287
n4:jazykVysledku
n7:eng
n4:klicovaSlova
DNA sequences; free energy landscape; DNA unfolding; single molecule experiment; nonequilibrium kinetics
n4:klicoveSlovo
n6:DNA%20unfolding n6:single%20molecule%20experiment n6:nonequilibrium%20kinetics n6:DNA%20sequences n6:free%20energy%20landscape
n4:kodStatuVydavatele
GB - Spojené království Velké Británie a Severního Irska
n4:kontrolniKodProRIV
[0221EDF65892]
n4:nazevZdroje
Journal of Physics Condensed Matter
n4:obor
n15:BE
n4:pocetDomacichTvurcuVysledku
2
n4:pocetTvurcuVysledku
4
n4:rokUplatneniVysledku
n10:2014
n4:svazekPeriodika
26
n4:tvurceVysledku
Holubec, Viktor Chvosta, Petr Nostheide, Sandra Maass, Philipp
n4:wos
000336244900004
s:issn
0953-8984
s:numberOfPages
11
n14:doi
10.1088/0953-8984/26/20/205102
n3:organizacniJednotka
11320