Stacking heterogeneity: A model for the sequence dependent melting cooperativity of duplex DNA

A microscopic Potts-like one-dimensional model with many particle interactions [referred as the generalized model of polypeptide chains (GMPCs)] is developed to investigate cooperativity of DNA sequence dependent melting. For modeling sequence, regular homogeneous sequences were arranged in heteroge...

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Bibliographic Details
Published in:The Journal of chemical physics 2007-04, Vol.126 (16), p.165101-165101-9
Main Authors: Grigoryan, A. V., Mamasakhlisov, E. Sh, Buryakina, T. Yu, Tsarukyan, A. V., Benight, A. S., Morozov, V. F.
Format: Article
Language:English
Subjects:
DNA - chemistry
Models, Theoretical
Nucleic Acid Conformation
Nucleic Acid Denaturation
Sequence Analysis, DNA - methods
Thermodynamics
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Summary:A microscopic Potts-like one-dimensional model with many particle interactions [referred as the generalized model of polypeptide chains (GMPCs)] is developed to investigate cooperativity of DNA sequence dependent melting. For modeling sequence, regular homogeneous sequences were arranged in heterogeneous blocks of various lengths. Within the framework of the GMPC the authors show that the inclusion of stacking interaction heterogeneity relative to homogeneous hydrogen bond interactions leads to an unexpected and quite remarkable increase in melting cooperativity for small blocks. In some cases this tendency persists for long blocks having sharp sequence heterogeneity.
ISSN:0021-9606
1089-7690
DOI:10.1063/1.2727456