Document Detail


Analysis of a DNA simulation model through hairpin melting experiments.
MedLine Citation:
PMID:  20886965     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
We compare the predictions of a two-bead Brownian dynamics simulation model to melting experiments of DNA hairpins with complementary AT or GC stems and noninteracting loops in buffer A. This system emphasizes the role of stacking and hydrogen bonding energies, which are characteristics of DNA, rather than backbone bending, stiffness, and excluded volume interactions, which are generic characteristics of semiflexible polymers. By comparing high throughput data on the open-close transition of various DNA hairpins to the corresponding simulation data, we (1) establish a suitable metric to compare the simulations to experiments, (2) find a conversion between the simulation and experimental temperatures, and (3) point out several limitations of the model, including the lack of G-quartets and cross stacking effects. Our approach and experimental data can be used to validate similar coarse-grained simulation models.
Authors:
Margaret C Linak; Kevin D Dorfman
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  The Journal of chemical physics     Volume:  133     ISSN:  1089-7690     ISO Abbreviation:  J Chem Phys     Publication Date:  2010 Sep 
Date Detail:
Created Date:  2010-10-04     Completed Date:  2011-02-09     Revised Date:  2013-07-03    
Medline Journal Info:
Nlm Unique ID:  0375360     Medline TA:  J Chem Phys     Country:  United States    
Other Details:
Languages:  eng     Pagination:  125101     Citation Subset:  IM    
Affiliation:
Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA.
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MeSH Terms
Descriptor/Qualifier:
DNA / chemistry*
Hot Temperature
Hydrogen Bonding
Models, Chemical*
Nucleic Acid Conformation
Nucleic Acid Denaturation*
Phase Transition
Thermodynamics
Grant Support
ID/Acronym/Agency:
5T32GM008347-20/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
9007-49-2/DNA
Comments/Corrections
Erratum In:
J Chem Phys. 2011 Jul 14;135(2):029901

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


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