YURENKO, Yevgen, Jan NOVOTNÝ, Vladimír SKLENÁŘ a Radek MAREK. Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: A comprehensive quantum chemical approach. Physical Chemistry Chemical Physics. Cambridge: Royal Society of Chemistry, 2014, roč. 16, č. 5, s. 2072-2084. ISSN 1463-9076. doi:10.1039/C3CP53875C.
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Základní údaje
Originální název Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: A comprehensive quantum chemical approach
Autoři YURENKO, Yevgen (804 Ukrajina, domácí), Jan NOVOTNÝ (203 Česká republika, domácí), Vladimír SKLENÁŘ (203 Česká republika, domácí) a Radek MAREK (203 Česká republika, garant, domácí).
Vydání Physical Chemistry Chemical Physics, Cambridge, Royal Society of Chemistry, 2014, 1463-9076.
Další údaje
Originální jazyk angličtina
Typ výsledku Článek v odborném periodiku
Obor 10403 Physical chemistry
Stát vydavatele Velká Británie
Utajení není předmětem státního či obchodního tajemství
WWW DOI: 10.1039/C3CP53875C
Impakt faktor Impact factor: 4.493
Kód RIV RIV/00216224:14740/14:00074812
Organizační jednotka Středoevropský technologický institut
Doi http://dx.doi.org/10.1039/C3CP53875C
UT WoS 000329175700034
Klíčová slova anglicky DNA quadruplex; xanthine; guanine; tetrad; H-bonding; stacking; DFT-D3; Quantum Theory of Atoms in Molecules (QTAIM); Natural Bond Orbital (NBO) analysis; Compliance constant
Štítky kontrola MP, rivok
Příznaky Mezinárodní význam, Recenzováno
Změnil Změnila: Martina Prášilová, učo 342282. Změněno: 14. 10. 2014 16:33.
Anotace
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.
Návaznosti
ED1.1.00/02.0068, projekt VaVNázev: CEITEC - central european institute of technology
EE2.3.20.0042, projekt VaVNázev: Internacionalizace programu Strukturní biologie s důrazem na rozvoj nových směrů výzkumu
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