Theoretical models of DNA flexibility

0428591 - ÚOCHB 2015 RIV US eng J - Journal Article
Dršata, Tomáš - Lankaš, Filip
Theoretical models of DNA flexibility.
Wiley Interdisciplinary Reviews - Computational Molecular Science. Roč. 3, č. 4 (2013), s. 355-363. ISSN 1759-0876. E-ISSN 1759-0884
Institutional support: RVO:61388963
Keywords : molecular dynamics simulations * base pair level * indirect readout
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 9.041, year: 2013

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.
Permanent Link: http://hdl.handle.net/11104/0233923