Different conformational families of pyrimidine·purine·pyrimidine triple helices depending on backbone composition

Different helical conformations of DNA (D), RNA (R), and DNA-RNA (DR) hybrid double and triple helices have been detected using affinity cleavage analysis. Synthetic methods were developed to attach EDTA Fe to a single nucleotide on RNA as well as DNA oligonucleotides. Cleavage patterns generated by a localized diffusible oxidant in the major groove on the pyrimidine strand of four purine-pyrimidine double helices consisting of all DNA, all RNA, and the corresponding hybrids reveal that the relative cleavage intensity shifts to the 5′ end of the purine strand increasingly in the order: DD<DR<RD<RR. These results are consistent with models derived from structural studies. In six pyrimidine·purine·pyrimidine triple helices, the altered cleavage patterns of the Watson-Crick pyrimidine strands reveal at least two conformational families: (i) D + DD, R + DD, D + DR, and R + DR and (ii) R + RD and R + RR.