About: Theoretical models of DNA flexibility

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	DNA sequence-dependent three-dimensional structure and mechanical deformability play a large role in biological processes such as protein-DNA interactions, nucleosome positioning, promoter identification, and drug-DNA recognition. On the important scale of 10-100 base pairs, models where DNA bases are represented by interacting rigid bodies have proved useful. We focus on a recently proposed rigid base model with nonlocal, harmonic interaction energy. We discuss the choice of internal coordinates and a method to obtain model parameters from coordinate fluctuations. Parameter transformation upon change of reference strand, coordinate constraints, and models with reduced number of degrees of freedom are described. Relation to traditional local harmonic models is clarified. We outline recent attempts to include anharmonic effects. A rigid base model of a DNA oligomer containing A-tract is presented as an example. Perspectives of model development and application are discussed. DNA sequence-dependent three-dimensional structure and mechanical deformability play a large role in biological processes such as protein-DNA interactions, nucleosome positioning, promoter identification, and drug-DNA recognition. On the important scale of 10-100 base pairs, models where DNA bases are represented by interacting rigid bodies have proved useful. We focus on a recently proposed rigid base model with nonlocal, harmonic interaction energy. We discuss the choice of internal coordinates and a method to obtain model parameters from coordinate fluctuations. Parameter transformation upon change of reference strand, coordinate constraints, and models with reduced number of degrees of freedom are described. Relation to traditional local harmonic models is clarified. We outline recent attempts to include anharmonic effects. A rigid base model of a DNA oligomer containing A-tract is presented as an example. Perspectives of model development and application are discussed. (en)
Title	Theoretical models of DNA flexibility Theoretical models of DNA flexibility (en)
skos:prefLabel	Theoretical models of DNA flexibility Theoretical models of DNA flexibility (en)
skos:notation	RIV/61388963:_____/13:00428591!RIV15-AV0-61388963
http://linked.open...avai/riv/aktivita	I
http://linked.open...avai/riv/aktivity	I
http://linked.open...iv/cisloPeriodika	4
http://linked.open...vai/riv/dodaniDat	2015
http://linked.open...aciTvurceVysledku	Dršata, Tomáš Lankaš, Filip
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Ústav organické chemie a biochemie AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	110831
http://linked.open...ai/riv/idVysledku	RIV/61388963:_____/13:00428591
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	molecular dynamics simulations; base pair level; indirect readout (en)
http://linked.open.../riv/klicoveSlovo	molecular dynamics simulations base pair level indirect readout
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[7C409F0E5955]
http://linked.open...i/riv/nazevZdroje	Wiley Interdisciplinary Reviews - Computational Molecular Science
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	2 (xsd:int)
http://linked.open...cetTvurcuVysledku	2 (xsd:int)
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	3
http://linked.open...iv/tvurceVysledku	Lankaš, Filip Dršata, Tomáš
http://linked.open...ain/vavai/riv/wos	000334577900003
issn	1759-0876
number of pages	9 (xsd:int)
http://bibframe.org/vocab/doi	10.1002/wcms.1144

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