1H NMR of an oligodeoxynucleotide containing a propanodeoxyguanosine adduct positioned in a (CG)3 frameshift hotspot of Salmonella typhimurium hisD3052: Hoogsteen base-pairing at pH 5.8.

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The exocyclic DNA adduct 1,N2-propano-2'-deoxyguanosine (PdG) was inserted into the oligodeoxynucleotide 5'-CGC(PdG)CGGCATG-3' and annealed to the complementary oligodeoxynucleotide 5'-CATGCCGCGCG-3'. This sequence is derived from a spontaneous revertant of the hisD3052 gene in a frameshift-sensitive tester strain of Salmonella typhimurium and is a hotspot for two-base pair deletions. The solution structure of the modified duplex was examined by 1H NMR spectroscopy. The exocyclic lesions resulted in loss of Watson-Crick base-pairing capability. Modification resulted in an approximately 24 degrees C decrease in Tm of the duplex. NMR experiments revealed pH-dependent conformational equilibria, which involved the modified base pair and its 3'-neighbor base pair. At pH 5.8, the lesion resulted in a localized perturbation of the B-form helix. PdG was rotated about the glycosyl bond from the anti to the syn conformation, thus placing the propano moiety into the major groove. This resulted in the observation of a strong NOE between the imidazole proton of PdG and the anomeric proton of the attached deoxyribose. Additional NOEs were observed between the methylene protons of the propano moiety and H5 and H6 of the 5'-neighbor cytosine. An imino proton resonance from the cytosine complementary to PdG and protonated at N3, characteristic of a Hoogsteen base pair, was observed at 15 ppm, but was broadened due to exchange with water. The amino protons of the complementary cytosine were shifted downfield from the other cytosine amino protons, characteristic of a Hoogsteen-like conformation at the site of modification. A second equilibrium involved the 3'-neighbor base pair, which alternated between Watson-Crick and Hoogsteen pairing, also via rotation of the guanosine glycosyl bond from the anti to the syn conformer. The conformational exchange of the 3'-neighbor base pair was sufficiently slow on the NMR time scale to allow simultaneous observation of resonances from the Watson-Crick and the Hoogsteen conformers.