An NMR structural study of deaminated base pairs in DNA

The structurally aberrant base pairs TG, UG and Tl may occur in DNA as a consequence of deamination of 5-methylcytosine, cytosine and adenine respectively. Results of NMR spectroscopic studies are reported here for these deaminated base pairs in a model seven base pair long oligonucleotide duplex. We find that in all three cases, the DNA helix is a normal B form and both mispaired bases are intrahelical and hydrogen bonded with one another in a wobble geometry. Similarly, in all three cases, all sugars are found to be normal C2′ endo in conformation. Symmetric structural perturbations are observed in the helix twist on the 3′ side of the mispaired pyrimidine and on the 5′ side of the mispaired purine. In all three cases, the amino group of the G residue on the 3′ side of the mispaired pyrimidine shows hindered rotation. Although less thermodynamically stable than helices containing only Watson-Crick base pairs, these helices melt normally from the ends and not from the mispair outwards.