H-1-NMR CHARACTERIZATION OF A DUPLEX OLIGODEOXYNUCLEOTIDE CONTAINING PROPANODEOXYGUANOSINE OPPOSITE A 2-BASE DELETION IN THE (CPG)(3) FRAMESHIFT HOTSPOT OF SALMONELLA-TYPHIMURIUM HISD3052

The exocyclic lesion 1,N-2-propano-2'-deoxyguanosine (PdG) was incorpo rated into 5'-d[ATCGC(PdG)CGGCATG]-3', derived from the hisD3052 gene of Salmonella typhimurium. The modified oligodeoxynucleotide was annea led with the complementary strand 5'-d[CATGCCGCGAT]-3' which contained a CpG deletion. The resulting duplex 5'-d[ATCGC(PdG)-CGGCATG]-3'-5'-d [CATGCCGCGAT]-3' required PdG and one adjacent cytosine to be unpaired . Four thymine imino H-1 NMR resonances were observed at temperatures below 25 degrees C, which demonstrated formation of a stable duplex wi th a two-base bulge. PdG was accommodated within the DNA helix, wherea s the 3'-neighbor cytosine was poorly stacked and appeared to be extra helical. The sequential nuclear Overhauser enhancement connectivities between aromatic and H1' protons along the modified strand were interr upted between PdG and the 3'-neighboring unpaired cytosine. On the com plementary strand no interruptions were observed. An NOE was observed between the PdG methylene protons H8(a,b) and the imino proton of the 5'-neighbor base pair. Weaker NOEs were observed between the PdG H8(a, b) protons and the imino proton from guanine two nucleotides removed i n the 3'-direction, and to the amino proton of cytosine located in the complementary strand two nucleotides removed in the 3'-direction. Che mical shift perturbations were also observed for the latter cytosine a s Compared to the corresponding cytosine in the unmodified fully compl ementary duplex. These observations provided evidence for a poorly sta cked or an extrahelical conformation of this unpaired cytosine. The am ino proton resonances of the 3'-neighbor cytosine were not observed, p resumably due to increased exchange with solvent. The methylene proton s from PdG were shifted upfield relative to the monomer PdG, probably as a result of aromatic ring current shielding, consistent with an int rahelical location. Multimeric derivative oligonucleotides containing the PdG bulge migrated anomalously on nondenaturing polyacrylamide gel s, consistent with a structure in which the unpaired nucleotides induc ed a bend in the DNA.