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@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, roč.~16, č.~5, s.~2072-2084. ISSN~1463-9076. doi:10.1039/C3CP53875C. 2014.
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