title: Mutual relationship between stacking and hydrogen bonding in DNA. Theoretical study of guanine-cytosine, guanine-5-methylcytosine, and their dimers.
abstract: The mutual relationship between stacking and hydrogen-bonding and the possible influence of stacking in the different behavior of cytosine (C) and 5-methylcytosine (C') in DNA have been studied through complete DFT optimization of different structures of G-C and G-C' dimers (i.e., G-C/C-G and G-C'/C'-G), using four different functionals. Our results show that stacking leads to an increase of the O(6)...H-N(4) hydrogen bond length and to a simultaneous decrease of the N(2)-H...O(2) one, in such a way that both lengths approach each other and, in some cases, an inversion occurs. These results suggest that stacking can be a factor to explain the disparity between theory and experiment on the relative strength of the two lateral hydrogen bonds. Regarding the difference between cytosine and 5-methylcytosine, we have shown that methylation enhances the stacking interactions, mainly due to the increase of polarizability. Methylation also favors the existence of slid structures which can produce local distortions of DNA.
authors.affiliation: Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193 Spain.
authors.forename: Carles
authors.initials: C
authors.lastname: Acosta-Silva
authors.forename: Vicenç
authors.initials: V
authors.lastname: Branchadell
authors.forename: Joan
authors.initials: J
authors.lastname: Bertran
authors.forename: Antoni
authors.initials: A
authors.lastname: Oliva
mesh_terms: D044503:5-Methylcytosine / Q000737:chemistry*; D020029:Base Pairing; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D019281:Dimerization; D006147:Guanine / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D006147:Guanine; D044503:5-Methylcytosine; D003596:Cytosine; D004247:DNA