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Theoretical models of DNA flexibility
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SYSNO ASEP 0428591 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Theoretical models of DNA flexibility Author(s) Dršata, Tomáš (UOCHB-X) RID
Lankaš, Filip (UOCHB-X) RIDNumber of authors 2 Source Title Wiley Interdisciplinary Reviews - Computational Molecular Science - ISSN 1759-0876
Roč. 3, č. 4 (2013), s. 355-363Number of pages 9 s. Language eng - English Country US - United States Keywords molecular dynamics simulations ; base pair level ; indirect readout Subject RIV CF - Physical ; Theoretical Chemistry Institutional support UOCHB-X - RVO:61388963 UT WOS 000334577900003 EID SCOPUS 84879084489 DOI 10.1002/wcms.1144 Annotation 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. Workplace Institute of Organic Chemistry and Biochemistry Contact asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Jana Procházková, Tel.: 220 183 418 Year of Publishing 2015
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