title: Theoretical Characterization of the H-Bonding and Stacking Potential of Two Nonstandard Nucleobases Expanding the Genetic Alphabet.
abstract: We report a quantum chemical characterization of the non-natural (synthetic) H-bonded base pair formed by 6-amino-5-nitro-2(1H)-pyridone (Z) and 2-aminoimidazo[1,2-a]-1,3,5-triazin-4(8H)-one (P). The Z:P base pair, orthogonal to the classical G:C base pair, has been introduced into DNA molecules to expand the genetic code. Our results indicate that the Z:P base pair closely mimics the G:C base pair in terms of both structure and stability. To clarify the role of the NO2 group on the C5 position of the Z base, we compared the stability of the Z:P base pair with that of base pairs having different functional groups at the C5 position of Z. Our results indicate that the electron-donating/-withdrawing properties of the group on C5 have a clear impact on the stability of the Z:P base pair, with the strong electron-withdrawing nitro group achieving the largest stabilizing effect on the H-bonding interaction and the strong electron-donating NH2 group destabilizing the Z:P pair by almost 4 kcal/mol. Finally, our gas-phase and in-water calculations confirm that the Z-nitro group reinforces the stacking interaction with its adjacent purine or pyrimidine ring.
authors.affiliation: Physical Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia.
authors.forename: Mohit
authors.initials: M
authors.lastname: Chawla
authors.affiliation: Physical Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia.
authors.forename: Raffaele
authors.initials: R
authors.lastname: Credendino
authors.affiliation: Physical Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia.
authors.forename: Edrisse
authors.initials: E
authors.lastname: Chermak
authors.affiliation: Department of Sciences and Technologies, University Parthenope of Naples , Centro Direzionale Isola C4, I-80143 Naples, Italy.
authors.forename: Romina
authors.initials: R
authors.lastname: Oliva
authors.affiliation: Physical Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia.
authors.forename: Luigi
authors.initials: L
authors.lastname: Cavallo
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA; D004247:DNA