title: How the intercalation of phenanthroline affects the structure, energetics, and bond properties of DNA base pairs: theoretical study applied to adenine-thymine and guanine-cytosine tetramers.
abstract: The effects of phenanthroline (phen) intercalation on the structure, energetics, and bonding of adenine-thymine and guanine-cytosine tetramers (A-T/T-A and G-C/C-G) were studied through density functional theory (DFT) using functionals that were recently improved to consider the effect of dispersion forces. Our results given by energy decomposition analysis show that the dispersion contribution, ΔEdisp, is the most important contribution to the interaction energy, ΔEint. However, it is not enough to compensate the Pauli repulsion term, ΔEPauli, and the roles of the orbital contribution, ΔEorb, and, in particular, the electrostatic contribution, ΔEelstat, become crucial for the stabilization of the structures in the intercalation process. On the other hand, for G-C/C-G systems, hydrogen-bonding (HB) interactions are more important than stacking (S) interactions, whereas for A-T/T-A systems, HB and S become competitive. Moreover, intercalation produces important changes not only in the hydrogen bonds of base pairs, because S and HB are deeply connected, but also in other characteristic geometric parameters of the base pairs.
authors.affiliation: Centro de Química e Bioquímica, DQB, Faculdade de Ciências, Universidade de Lisboa , Campo Grande, 1749-016 Lisboa, Portugal.
authors.forename: Adrià
authors.initials: A
authors.lastname: Gil
authors.affiliation: Centro ALGORITMI, Universidade do Minho , 4710-057 Braga, Portugal.
authors.forename: Manuel
authors.initials: M
authors.lastname: Melle-Franco
authors.affiliation: Departament de Química, Universitat Autònoma de Barcelona , 08193 Bellaterra, Barcelona, Spain.
authors.forename: Vicenç
authors.initials: V
authors.lastname: Branchadell
authors.affiliation: Centro de Química e Bioquímica, DQB, Faculdade de Ciências, Universidade de Lisboa , Campo Grande, 1749-016 Lisboa, Portugal.
authors.forename: Maria José
authors.initials: MJ
authors.lastname: Calhorda
mesh_terms: D000225:Adenine / Q000737:chemistry; D020029:Base Pairing / Q000187:drug effects*; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000737:chemistry* / Q000187:drug effects*; D006147:Guanine / Q000737:chemistry; D015394:Molecular Structure; D010618:Phenanthrolines / Q000737:chemistry* / Q000494:pharmacology*; D011789:Quantum Theory; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry
chemical_list: D010618:Phenanthrolines; D006147:Guanine; D003596:Cytosine; D004247:DNA; D000225:Adenine; D013941:Thymine