The structures of nucleic acids composed exclusively of non-standard base pairs

We have reported that d(GGAGGAA) forms a new type of quadruplex in the presence of K+. Here we report that in the absence of K+ it forms another kind of new structure composed of non-standard base pairs exclusively. The structure is neither a quadruplex nor a hairpin. The structure gives three clear imino proton signals of G at 10.0, 13.0 and 13.8 ppm, indicating the formation of G:A and/or G:G base pairs. The two signals at 13.0 and 13.8 ppm indicate that there are two base pairs in which the imino protons of G are hydrogen bonded. All residues take anti conformation, which imposes the restriction on the combination of a mutual direction of strands and types of base pairs. Phosphorus signals of the second and fifth residues appear at higher field, while that of the seventh residue at lower field, when compared with those of A and B form structures, suggesting deviations of a backbone conformation from the standard one. Replacement of the second or fifth G by I results in destabilization of the structure, which implies the involvement of amino groups of these residues in base pairing. On the basis of these results, the structure of d(GGAGGAA) is discussed.