The Flexibility of the Nucleic Acids: (II) The Calculation of Internal Energy and Applications to Mononucleotide Repeat DNA |
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| Authors: | Richard Lavery Heinz Sklenar Krystyna Zakrzewska Bernard Pullman |
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| Affiliation: | 1. Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Théorique associé au C.N.R.S. , 13 rue Pierre et Marie Curie, Paris , 75005 , France;2. Central Institute of Molecular Biology, Academy of Sciences of the GDR , DDR-1115 Berlin-Buch, Robert-Rossie Str. 10, German Democratic Republic |
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| Abstract: | Abstract Results concerning the flexibility of mononucleotide repeat DNA are presented using a novel methodology, denoted “SIR”, to describe continuous changes in the structure of the nucleic acid. This methodology, combined with internal energy calculations and analytical energy gradients allows us to determine optimal conformations of poly(dG)?poly(dC) and poly (dA)?poly(dT) in both the A and B forms, taking into account the influence of the solvent medium and explicit counterions. Subsequently, several different types of distorsion of these optimal structures are investigated. It is shown that excellent correlation with experimental results concerning coupled changes in structural variables is obtained and several new correlations are also detected. |
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