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

SYSNO ASEP	0356082
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	Conformational energies of DNA sugar-phosphate backbone: Reference QM calculations and a comparison with density functional theory and molecular mechanics
Author(s)	Mládek, Arnošt (BFU-R) Šponer, Judit E. (BFU-R)_{RID, ORCID} Jurečka, P. (CZ) Banáš, P. (CZ) Otyepka, M. (CZ) Svozil, D. (CZ) Šponer, Jiří (BFU-R)_{RID, ORCID}
Number of authors	7
Source Title	Journal of Chemical Theory and Computation . - : American Chemical Society - ISSN 1549-9618 Roč. 6, č. 12 (2010), s. 3817-3835
Number of pages	19 s.
Language	eng - English
Country	US - United States
Keywords	intramolecular hydrogen-bonds ; main-group thermochemistry ; set superposition error
Subject RIV	BO - Biophysics
R&D Projects	IAA400040802 GA AV ČR - Academy of Sciences of the Czech Republic (AV ČR)
	GA203/09/1476 GA ČR - Czech Science Foundation (CSF)
	GAP208/10/2302 GA ČR - Czech Science Foundation (CSF)
CEZ	AV0Z50040507 - BFU-R (2005-2011)
	AV0Z50040702 - BFU-R (2007-2013)
UT WOS	000285217000018
DOI	10.1021/ct1004593
Annotation	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.
Workplace	Institute of Biophysics
Contact	Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244
Year of Publishing	2011

Number of the records: 1