DIFFERENT CONFORMATIONAL FAMILIES OF PYRIMIDINE-CENTER-DOT-PURINE-CENTER-DOT-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 cle avage analysis. Synthetic methods were developed to attach EDTA Fe to a single nucleotide on RNA as well as DNA oligonucleotides. Cleavage p atterns generated by a localized diffusible oxidant in the major groov e on the pyrimidine strand of four purine pyrimidine double helices co nsisting of all DNA, all RNA, and the corresponding hybrids reveal tha t the relative cleavage intensity shifts to the 5' end of the purine s trand increasingly in the order: DD < DR < RD < RR. These results are consistent with models derived from structural studies. In six pyrimid ine purine pyrimidine triple helices, the altered cleavage patterns of the Watson - Crick pyrimidine strands reveal at least two conformatio nal families: (i) D + DD, R + DD, D + DR, and R + DR and (ii) R + RD a nd R + RR.