Solution conformation of the N-(deoxyguanosin-8-yl)aminofluorene adduct opposite deoxyinosine and deoxyguanosine in DNA by NMR and computational characterization.

Two-dimensional proton NMR and energy minimization computations have been employed to characterize the conformations of the N-(deoxyguanosin-8-yl)aminofluorene adduct [(AF)G] positioned opposite deoxyguanosine in one, and opposite deoxyinosine in another DNA undecamer duplex in aqueous solution. The two oligomer duplexes used in this study are d[C1-C2-A3-T4-C5-(AF)G6-C7-T8-A9-C10-C11].[G12-G13-T14 -A15-G16-X17-G18- A19-T20-G21-G22], where X17 was deoxyinosine in one duplex and deoxyguanosine in another. The exchangeable and nonexchangeable protons of the DNA are well resolved and narrow in the NMR spectra of the duplexes, and the base and sugar nucleic acid protons were assigned by NOESY and COSY data sets. All nine of the nonexchangeable aminofluorene ring protons were also assigned for the duplex that has deoxyinosine across from the modification site, and the (AF)G-I structure was employed to model the (AF)G-G one. The NOE distance restraints establish that the glycosidic torsion angle at (AF)G6 is syn. All other glycosidic torsion angles are anti, Watson-Crick type A.T and G-C base pairing is intact throughout the duplex except at the site of modification, and the helix maintains an overall B-DNA conformation. The syn orientation at the (AF)G6 places the aminofluorene ring in the B-DNA minor groove in a conformation similar to that found previously when the (AF)G was positioned opposite deoxyadenosine [Norman et al. (1989) Biochemistry 28, 7462-7476].