Detailed Information on Publication Record
2014
Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: A comprehensive quantum chemical approach
YURENKO, Yevgen, Jan NOVOTNÝ, Vladimír SKLENÁŘ and Radek MAREKBasic information
Original name
Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: A comprehensive quantum chemical approach
Authors
YURENKO, Yevgen (804 Ukraine, belonging to the institution), Jan NOVOTNÝ (203 Czech Republic, belonging to the institution), Vladimír SKLENÁŘ (203 Czech Republic, belonging to the institution) and Radek MAREK (203 Czech Republic, guarantor, belonging to the institution)
Edition
Physical Chemistry Chemical Physics, Cambridge, Royal Society of Chemistry, 2014, 1463-9076
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10403 Physical chemistry
Country of publisher
United Kingdom of Great Britain and Northern Ireland
Confidentiality degree
není předmětem státního či obchodního tajemství
References:
Impact factor
Impact factor: 4.493
RIV identification code
RIV/00216224:14740/14:00074812
Organization unit
Central European Institute of Technology
UT WoS
000329175700034
Keywords in English
DNA quadruplex; xanthine; guanine; tetrad; H-bonding; stacking; DFT-D3; Quantum Theory of Atoms in Molecules (QTAIM); Natural Bond Orbital (NBO) analysis; Compliance constant
Tags
Tags
International impact, Reviewed
Změněno: 14/10/2014 16:33, Martina Prášilová
Abstract
V originále
The study aimed to cast light on the structure and internal energetics of guanine- and xanthine-based model DNA quadruplexes and the physico-chemical nature of the non-covalent interactions involved. Several independent approaches were used for this purpose: DFT-D3 calculations, Quantum Theory of Atoms in Molecules, Natural Bond Orbital Analysis, Energy Decomposition Analysis, Compliance Constant Theory, and Non-Covalent Interaction Analysis. The results point to an excellent degree of structural and energetic compatibility between the two types of model quadruplexes. This fact stems from both the structural features (close values of van der Waals volumes, pore radii, geometrical parameters of the H-bonds) and the energetic characteristics (comparable values of the energies of formation). It was established that hydrogen bonding makes the greatest ( about 50 %) contribution to the internal stability of the DNA quadruplexes, whereas the aromatic base stacking and ion coordination terms are commensurable and account for the rest. Energy decomposition analysis performed for guanine (Gua) and xanthine (Xan) quartets B4 and higher-order structures consisting of two or three stacked quartets indicates that whereas Gua structures benefit from a high degree of H-bond cooperativity, Xan models are characterized by more favorable and cooperative pi-pi stacking. The results of electron density topological analysis show that Na+/K+ ion coordination deeply affects the network of non-covalent interactions in Gua models due to the change in the twist angle between the stacked tetrads. For Xan models, ion coordination makes tetrads in stacks more planar without changing the twist angle. Therefore, the presence of the ion seems to be essential for the formation of planar stacks in Xan-based DNA quadruplexes. Detailed study of the nature of ion-base coordination suggests that this interaction has a partially covalent character and cannot be considered as purely electrostatic.
Links
| ED1.1.00/02.0068, research and development project |
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| EE2.3.20.0042, research and development project |
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