Conformational energies of DNA sugar-phosphate backbone: Reference QM calculations and a comparison with density functional theory and molecular mechanics

0356082 - BFÚ 2011 RIV US eng J - Journal Article
Mládek, Arnošt - Šponer, Judit E. - Jurečka, P. - Banáš, P. - Otyepka, M. - Svozil, D. - Šponer, Jiří
Conformational energies of DNA sugar-phosphate backbone: Reference QM calculations and a comparison with density functional theory and molecular mechanics.
Journal of Chemical Theory and Computation. Roč. 6, č. 12 (2010), s. 3817-3835. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/10/2302
Grant - others:GA ČR(CZ) GD203/09/H046; GA MŠk(CZ) LC06030; GA MŠk(CZ) LC512
Program: GD; LC; LC
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : intramolecular hydrogen-bonds * main-group thermochemistry * set superposition error
Subject RIV: BO - Biophysics
Impact factor: 5.138, year: 2010

The study investigates electronic structure and gas-phase energetics of the DNA sugar-phosphate backbone via advanced quantum chemical (QM) methods. The analysis has been carried out on biologically relevant backbone conformations composed of 11 canonical BI-DNA structures, 8 pathological structures with R/γ torsion angles in the g+/t region, and 3 real noncanonical γ-trans structures occurring in the loop region of guanine quadruplex DNA. The influence of backbone conformation on the intrinsic energetics was primarily studied using a model system consisting of two sugar moieties linked together via a phosphodiester bond (SPSOM model). To get the conformation of the studied system fully under control, for each calculation we have frozen majority of the dihedral angles to their target values. CCSD(T) energies extrapolated to the complete basis set were utilized as reference values.
Permanent Link: http://hdl.handle.net/11104/0194699