Exploring non-covalent interactions in guanine- and
xanthine-based model DNA quadruplex structures: A comprehensive
quantum chemical approach

J 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 a Radek MAREK

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

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

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

Změněno: 14. 10. 2014 16:33, Martina Prášilová

Anotace

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

EE2.3.20.0042, projekt VaV

Název: Internacionalizace programu Strukturní biologie s důrazem na rozvoj nových směrů výzkumu

Přiložené soubory

PCCP14_16_2072.pdf

Požádat o autorskou verzi souboru

Citovat

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. Dostupné z: https://dx.doi.org/10.1039/C3CP53875C.

@article{1129502,
   author = {Yurenko, Yevgen and Novotný, Jan and Sklenář, Vladimír and Marek, Radek},
   article_location = {Cambridge},
   article_number = {5},
   doi = {http://dx.doi.org/10.1039/C3CP53875C},
   keywords = {DNA quadruplex; xanthine; guanine; tetrad; H-bonding; stacking; DFT-D3; Quantum Theory of Atoms in Molecules (QTAIM); Natural Bond Orbital (NBO) analysis; Compliance constant},
   language = {eng},
   issn = {1463-9076},
   journal = {Physical Chemistry Chemical Physics},
   title = {Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: A comprehensive quantum chemical approach},
   url = {http://dx.doi.org/10.1039/C3CP53875C},
   volume = {16},
   year = {2014}
}

TY  - JOUR
ID  - 1129502
AU  - Yurenko, Yevgen - Novotný, Jan - Sklenář, Vladimír - Marek, Radek
PY  - 2014
TI  - Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: A comprehensive quantum chemical approach
JF  - Physical Chemistry Chemical Physics
VL  - 16
IS  - 5
SP  - 2072-2084
EP  - 2072-2084
PB  - Royal Society of Chemistry
SN  - 14639076
KW  - DNA quadruplex
KW  - xanthine
KW  - guanine
KW  - tetrad
KW  - H-bonding
KW  - stacking
KW  - DFT-D3
KW  - Quantum Theory of Atoms in Molecules (QTAIM)
KW  - Natural Bond Orbital (NBO) analysis
KW  - Compliance constant
UR  - http://dx.doi.org/10.1039/C3CP53875C
L2  - http://dx.doi.org/10.1039/C3CP53875C
N2  - 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.
ER  -

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. \textit{Physical Chemistry Chemical Physics}. Cambridge: Royal Society of Chemistry, 2014, roč.~16, č.~5, s.~2072-2084. ISSN~1463-9076. Dostupné z: https://dx.doi.org/10.1039/C3CP53875C.

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