THE PURINE-RICH TRINUCLEOTIDE REPEAT SEQUENCES D(CAG)(15) AND D(GAC)(15) FORM HAIRPINS

The structures of single-stranded (ss) oligonucleotides containing (CAG)(15) [ss(CAG)(15)] or (GAC)(15) [ss(GAC)(15)] were examined. At 10 degrees C, the electrophoretic mobilites of the two DNAs were similar to ss(CTG)(15), a DNA that forms a hairpin containing base paired and/or stacked thymines. At 37 degrees C in 50 mM NaCl, single-strand-specific P1 nuclease cleaved the G33-G36 phosphodiesters of ss(GAC)(15), and the G32-A34, G35-C36 phosphodiesters of ss(CAG)(15) (where the loop apex of both DNAs = A34). Electrophoretic mobility melting profiles indicated that the melting temperature (T-m) of ss(CAG)(15) in low (similar to 1 mM Na+) ionic strength was 38 degrees C. In contrast, the T-m of ss(GAC)(15) was 49 degrees C a value similar to the T-m of ss(CTG)(15). These results provide evidence that ss(GAC)(15) and ss(CAG)(15) form similar, but distinguishable hairpin structures.