Premium
Theoretical models of DNA flexibility
Author(s) -
Dršata Tomáš,
Lankaš Filip
Publication year - 2013
Publication title -
wiley interdisciplinary reviews: computational molecular science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.126
H-Index - 81
eISSN - 1759-0884
pISSN - 1759-0876
DOI - 10.1002/wcms.1144
Subject(s) - nucleosome , base pair , harmonic , dna , anharmonicity , coordinate system , statistical physics , physics , flexibility (engineering) , degrees of freedom (physics and chemistry) , biological system , computer science , algorithm , classical mechanics , mathematics , biology , quantum mechanics , artificial intelligence , genetics , chromatin , statistics
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. This article is categorized under: Electronic Structure Theory > Density Functional Theory