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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. (en)
Title
  • Unfolding kinetics of periodic DNA hairpins
  • Unfolding kinetics of periodic DNA hairpins (en)
skos:prefLabel
  • Unfolding kinetics of periodic DNA hairpins
  • Unfolding kinetics of periodic DNA hairpins (en)
skos:notation
  • RIV/00216208:11320/14:10286287!RIV15-MSM-11320___
http://linked.open...avai/riv/aktivita
http://linked.open...avai/riv/aktivity
  • S
http://linked.open...iv/cisloPeriodika
  • 20
http://linked.open...vai/riv/dodaniDat
http://linked.open...aciTvurceVysledku
http://linked.open.../riv/druhVysledku
http://linked.open...iv/duvernostUdaju
http://linked.open...titaPredkladatele
http://linked.open...dnocenehoVysledku
  • 51938
http://linked.open...ai/riv/idVysledku
  • RIV/00216208:11320/14:10286287
http://linked.open...riv/jazykVysledku
http://linked.open.../riv/klicovaSlova
  • DNA sequences; free energy landscape; DNA unfolding; single molecule experiment; nonequilibrium kinetics (en)
http://linked.open.../riv/klicoveSlovo
http://linked.open...odStatuVydavatele
  • GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV
  • [0221EDF65892]
http://linked.open...i/riv/nazevZdroje
  • Journal of Physics Condensed Matter
http://linked.open...in/vavai/riv/obor
http://linked.open...ichTvurcuVysledku
http://linked.open...cetTvurcuVysledku
http://linked.open...UplatneniVysledku
http://linked.open...v/svazekPeriodika
  • 26
http://linked.open...iv/tvurceVysledku
  • Chvosta, Petr
  • Holubec, Viktor
  • Maass, Philipp
  • Nostheide, Sandra
http://linked.open...ain/vavai/riv/wos
  • 000336244900004
issn
  • 0953-8984
number of pages
http://bibframe.org/vocab/doi
  • 10.1088/0953-8984/26/20/205102
http://localhost/t...ganizacniJednotka
  • 11320
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