Document Detail


Multiscale modeling of double-helical DNA and RNA: a unification through Lie groups.
MedLine Citation:
PMID:  22676719     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Several different mechanical models of double-helical nucleic-acid structures that have been presented in the literature are reviewed here together with a new analysis method that provides a reconciliation between these disparate models. In all cases, terminology and basic results from the theory of Lie groups are used to describe rigid-body motions in a coordinate-free way, and when necessary, coordinates are introduced in a way in which simple equations result. We consider double-helical DNAs and RNAs which, in their unstressed referential state, have backbones that are either straight, slightly precurved, or bent by the action of a protein or other bound molecule. At the coarsest level, we consider worm-like chains with anisotropic bending stiffness. Then, we show how bi-rod models converge to this for sufficiently long filament lengths. At a finer level, we examine elastic networks of rigid bases and show how these relate to the coarser models. Finally, we show how results from molecular dynamics simulation at full atomic resolution (which is the finest scale considered here) and AFM experimental measurements (which is at the coarsest scale) relate to these models.
Authors:
Kevin C Wolfe; Whitney A Hastings; Samrat Dutta; Andrew Long; Bruce A Shapiro; Thomas B Woolf; Martin Guthold; Gregory S Chirikjian
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Intramural; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2012-06-07
Journal Detail:
Title:  The journal of physical chemistry. B     Volume:  116     ISSN:  1520-5207     ISO Abbreviation:  J Phys Chem B     Publication Date:  2012 Jul 
Date Detail:
Created Date:  2012-07-26     Completed Date:  2012-11-27     Revised Date:  2014-03-06    
Medline Journal Info:
Nlm Unique ID:  101157530     Medline TA:  J Phys Chem B     Country:  United States    
Other Details:
Languages:  eng     Pagination:  8556-72     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Anisotropy
DNA / chemistry*
Elasticity
Molecular Dynamics Simulation*
Nucleic Acid Conformation
RNA / chemistry*
Grant Support
ID/Acronym/Agency:
R01 GM064746/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
63231-63-0/RNA; 9007-49-2/DNA

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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