NMR studies of abasic sites in DNA duplexes: Deoxyadenosine stacks into the helix opposite acyclic lesions

Proton and phosphorus NMR studies are reported for two complementary nonanucleotide duplexes containing acyclic abasic sites. The first duplex, d(C-A-T-G-A-G-T-A-C).d(G-T-A-C-P-C-A-T-G), contains an acyclic propanyl moiety, P, located opposite a deoxyadenosine at the center of the helix (designated AP_P 9-mer duplex). The second duplex, d(C-A-T-G-A-G-T-A-C)·d(G-T-A-C-£'-C-A-T-G), contains a similarly located acyclic ethanyl moiety, E (designated AP_E 9-mer duplex). The ethanyl moiety is one carbon shorter than the natural carbon-phosphodiester backbone of a single nucleotide unit of DNA. The majority of the exchangeable and nonexchangeable base and sugar protons in both the AP_P9-mer and AP_E 9-mer duplexes, including those at the abasic site, have been assigned by recording and analyzing two-dimensional phasesensitive NOESY data sets in H₂O and D₂O solution between-5 and 5 °C. These spectroscopic observations establish that A5 inserts into the helix opposite the abasic site (PI4 and El4) and stacks between the flanking G4·C15 and G6·C13 Watson-Crick base pairs in both the AP_P9-mer and AP_E 9-mer duplexes. The helix is right-handed at and adjacent to the abasic site, and all glycosidic torsion angles are anti in both 9-mer duplexes. Proton NMR parameters for the AP_P9-mer and AP_E 9-mer duplexes are similar to those reported previously for the AP_F 9-mer duplex (F = furan) in which a cyclic analogue of deoxyribose was embedded in an otherwise identical DNA sequence [Kalnik, M. W., Chang, C. N., Grollman, A. P., & Patel, D. J. (1988) Biochemistry 27, 924–931]. These proton NMR experiments demonstrate that the structures at abasic sites are very similar whether the five-membered ring is open or closed or whether the phosphodiester backbone is shortened by one carbon atom. Phosphorus spectra of the AP_P9-mer and AP_E 9-mer duplexes (5 °C) indicate that the backbone conformation is similarly perturbed at three phosphodiester backbone torsion angles. These same torsion angles are also distorted in the AP_F 9-mer but assume a different conformation than those in the AP_P9-mer and AP_E 9-mer duplexes.