Hydrogen-bonded trimers of DNA bases and their interaction with metal cations: ab initio quantum-chemical and empirical potential study.
Neutral (G.GC, A.AT, G.AT, T.AT, and C(imino).GC) and protonated (CH+.GC and AH+.GC) hydrogen-bonded trimers of nucleic acid bases were characterized by ab initio methods with the inclusion of electron correlation. In addition, the influence of metal cations on the third-strand binding in Purine-Purine-Pyrimidine (Pu.PuPy) reverse-Hoogsteen triplets has been studied. The ab initio calculations were compared with those from recently introduced force fields (AMBER4.1, CHARMM23, and CFF95). The three-body term in neutral trimers is mostly negligible, and the use of empirical potentials is justified. The only exception is the neutral G.GC Hoogsteen trimer with a three-body term of -4 kcal/mol. Protonated trimers are stabilized by molecular ion-molecular dipole attraction and the interaction within the complex is nonadditive, with the three-body term on the order of -3 kcal/mol. There is a significant induction interaction between the third-strand protonated base and guanine. The calculations indicate an enhancement of the third-strand binding in the G.GC reverse-Hoogsteen trimer due to-metal cation coordination to the N7/O6 position of the third-strand guanine. Interactions between metal cations and complexes of DNA bases are in general highly non-additive; the three-body term is above-10 kcal/mol in a complex of a divalent cation (Ca2+) with the GG reverse-Hoogsteen pair. The pairwise additive empirical potentials qualitatively underestimate the binding energy between cation and base.
Sponer
J
J
J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague. sponer@indy.jh-inst.cas.cz
Burda
J V
JV
Mejzlík
P
P
Leszczynski
J
J
Hobza
P
P
D000225:Adenine / Q000737:chemistry*; D001482:Base Composition; D002151:Calorimetry; D002412:Cations; D003198:Computer Simulation; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D006147:Guanine / Q000737:chemistry*; D006860:Hydrogen Bonding; D008670:Metals; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D012984:Software; D013941:Thymine / Q000737:chemistry*
D002412:Cations; D008670:Metals; D006147:Guanine; D003596:Cytosine; D004247:DNA; D000225:Adenine; D013941:Thymine