Interaction with Glycine Increases Stability of a Mutagenic Tautomer of Uracil. A Density Functional Theory Study

• Published in: Journal of the American Chemical Society 2005-02, Vol.127 (7), p.2238-2248
• Main Authors: Da̧bkowska, Iwona, Gutowski, Maciej, Rak, Janusz
• Format: Article
• Language: English
• Subjects: 08 HYDROGEN; Biological and medical sciences; DNA - chemistry; DNA - genetics; FREE ENTHALPY; FUNCTIONALS; Fundamental and applied biological sciences. Psychology; GENE MUTATIONS; GLYCINE; Glycine - chemistry; GUANINE; HYDROGEN; INSTABILITY; Interactions. Associations; Intermolecular phenomena; Kinetics; Models, Chemical; Models, Molecular; Molecular biophysics; MONOMERS; Point Mutation; PROTONS; RNA - chemistry; RNA - genetics; STABILITY; STABILIZATION; THERMODYNAMICS; THYMINE; Uracil - chemistry; URACILS
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja048730k

The most stable structures for the gas-phase complexes of minor tautomers of uracil (U) with glycine (G) were characterized at the density functional B3LYP/6-31++G** level of theory. These are cyclic structures stabilized by two hydrogen bonds. The relative stability of isolated tautomers of uracil was rationalized by using thermodynamic and structural arguments. The stabilization energies for complexes between the tautomers of U and G result from interplay between the stabilizing two-body interaction energies and destabilizing one-body terms. The latter are related to the energies of (i) tautomerization of the unperturbed moieties and (ii) distortions of the resulting rare tautomers in the complex. The two-body term describes the interaction energy between distorted tautomers. The two-body interaction energy term correlates with perturbations of length of the proton-donor bonds as well as with deprotonation enthalpies and proton affinities of the appropriate monomer sites. It was demonstrated that the relative instability of rare tautomers of uracil is diminished due to their interactions with glycine. In particular, the instability of the third most stable tautomer (UIII) is decreased from 11.9 kcal/mol for non-interacting uracil to 6.7 kcal/mol for uracil in a complex with the zwitterionic tautomer of glycine. A decrease of instability by 5.2 kcal/mol could result in an increase of concentration of UIII by almost 5 orders of magnitude. This is the tautomer with proton donor and acceptor sites matching guanine rather than adenine. Moreover, kinetic characteristics obtained for the glycine-assisted conversion of the most stable tautomer of uracil (UI) to UIII indicate that the UI↔UIII thermodynamic equilibrium could be easily attained at room temperature. The resulting concentration of this tautomer falls in a mutationally significant range.