Document Detail


Sequence-dependent thermodynamics of a coarse-grained DNA model.
MedLine Citation:
PMID:  23039613     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes. By developing a histogram reweighting technique, we are able to fit our parameters to the melting temperatures of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its melting point, (c) the effects of stacking strength in the loop on the melting temperature of hairpins, (d) the force-extension properties of single strands, and (e) the structure of a kissing-loop complex. Where possible, we compare our results with experimental data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as a free software.
Authors:
Petr Šulc; Flavio Romano; Thomas E Ouldridge; Lorenzo Rovigatti; Jonathan P K Doye; Ard A Louis
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Publication Detail:
Type:  JOURNAL ARTICLE    
Journal Detail:
Title:  The Journal of chemical physics     Volume:  137     ISSN:  1089-7690     ISO Abbreviation:  J Chem Phys     Publication Date:  2012 Oct 
Date Detail:
Created Date:  2012-10-8     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  0375360     Medline TA:  J Chem Phys     Country:  -    
Other Details:
Languages:  ENG     Pagination:  135101     Citation Subset:  -    
Affiliation:
Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford, OX1 3NP, United Kingdom.
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