title: The flexibility of the nucleic acids: (II). The calculation of internal energy and applications to mononucleotide repeat DNA.
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.
authors.affiliation: Institut de Biologie Physico-Chimique, Laboratoire de Biochemie Théorique associé au C.N.R.S., Paris, France.
authors.forename: R
authors.initials: R
authors.lastname: Lavery
authors.forename: H
authors.initials: H
authors.lastname: Sklenar
authors.forename: K
authors.initials: K
authors.lastname: Zakrzewska
authors.forename: B
authors.initials: B
authors.lastname: Pullman
mesh_terms: D004247:DNA / Q000648:ultrastructure; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011089:Polydeoxyribonucleotides; D012399:Rotation; D013816:Thermodynamics
chemical_list: D011089:Polydeoxyribonucleotides; D004247:DNA