TRIPLEX-FORMING OLIGONUCLEOTIDES TRIGGER CONFORMATION CHANGES OF A TARGET HAIRPIN SEQUENCE

We used a DNA duplex formed between the 5' end of a 69mer (69T) and an 11mer (OL7) as a substrate for BamHI. The former oligonucleotide fold s into a hairpin structure, the stem of which contains a stretch of py rimidines in one strand and consequently a stretch of purines in the o ther strand. The oligomer 69T was used as a target for complementary o ligodeoxypyrimidines made of 10 nt (OL1), 16 nt (OL5) or 26 nt (OL2) w hich can engage the same 10 pyrimidine-purine-pyrimidine triplets with the 69T hairpin stem. Although the binding site of OL7 did not overla p that OL1, OL2 or OL5, the BamHI activity on 69T-OL7 complexes was dr astically modified in the presence of these triplex-forming oligomers: OL1 abolished the cleavage by BamHI whereas OL5 and OL2 strongly incr eased it. Using footprinting assays and point-mutated oligonucleotides we demonstrated that these variations were due to different conformat ions of the 69T-OL7 complex induced by the binding of oligomers OL1, O L2 or OL5. Therefore, oligonucleotides can act as structural switchers , offering one additional mode for modulating gene expression.