The formation of adjacent triplex-duplex domains in DNA

The ability of single-stranded DNA oligomers to form adjacent tripler and d uplex domains with two DNA structural motifs was examined. Helix-coil trans ition curves and a gel mobility shift assay were used to characterize the i nteraction of single-stranded oligomers 12-20 nt in length with a DNA hairp in and with a DNA duplex that has a dangling end. The 12 nt on the 5'-ends of the oligomers could form a tripler structure with the 12 bp stem of the hairpin or the duplex portion of the DNA with a dangling end. The 3'-ends o f the 17-20 nt strands could form Watson-Crick pairs to the five base loop of the hairpin or the dangling end of the duplex. Complexes of the hairpin DNA with the single-stranded oligomers showed two step transitions consiste nt with unwinding of the tripler strand followed by hairpin denaturation. M elting curve and gel competition results indicated that the complex of the hairpin and the 12 nt oligomer was more stable than the complexes involving the extended single strands. In contrast, results indicated that the exten ded single-stranded oligomers formed Watson-Crick base pairs with the dangl ing end of the duplex DNA and enhanced the stability of the adjacent triple r region.