title: Structure and Binding Energy of Double-Stranded A-DNA Mini-helices: Quantum-Chemical Study.
abstract: A-DNA is thought to play a significant biological role in gene expression due to its specific conformation and binding features. In this study, double-stranded mini-helices (dA:dT)3 and (dG:dC)3 in A-like DNA conformation were investigated. M06-2X/6-31G(d,p) method has been utilized to identify the optimal geometries and predict physicochemical parameters of these systems. The results show the ability of the corresponding mini-helices to preserve their A-like conformation under the influences of solvent, charge, and Na(+) counterions. Presented structural and energetic data offer evidence that two steps of GG/CC or AA/TT are already enough to turn the DNA helix to generate different forms by favoring specific values of roll and slide at a local level. Our calculations support the experimentally known fact that AA/TT steps prefer the B-form over the A-ones, whereas GG/CC steps may be found in either the B- or A-form. The stability of mini-helices at the level of total energy analysis, ΔEtotal((A–B)), is discussed.
authors.affiliation: Division of Functional Materials Chemistry, SSI "Institute for Single Crystals", National Academy of Science of Ukraine , Kharkiv 61001, Ukraine.
authors.forename: Tetiana
authors.initials: T
authors.lastname: Zubatiuk
authors.affiliation: Division of Functional Materials Chemistry, SSI "Institute for Single Crystals", National Academy of Science of Ukraine , Kharkiv 61001, Ukraine.
authors.forename: Maxim A
authors.initials: MA
authors.lastname: Kukuev
authors.affiliation: Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv , Kyiv 03022, Ukraine.
authors.forename: Alexandra S
authors.initials: AS
authors.lastname: Korolyova
authors.affiliation: Department of Molecular Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv 03143, Ukraine.
authors.forename: Leonid
authors.initials: L
authors.lastname: Gorb
authors.affiliation: Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv , Kyiv 03022, Ukraine.
authors.forename: Alexey
authors.initials: A
authors.lastname: Nyporko
authors.affiliation: Department of Molecular Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv 03143, Ukraine.
authors.forename: Dmytro
authors.initials: D
authors.lastname: Hovorun
authors.affiliation: Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University , Jackson, Mississippi 39217, United States.
authors.forename: Jerzy
authors.initials: J
authors.lastname: Leszczynski
mesh_terms: D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D011789:Quantum Theory
chemical_list: D004247:DNA