SEQUENCE-SPECIFIC ARTIFICIAL PHOTO-INDUCED ENDONUCLEASES BASED ON TRIPLE HELIX-FORMING OLIGONUCLEOTIDES

HOMOPYRIMIDINE oligonucleotides bind to homopurine-homopyrimidine sequences of duplex DNA forming a local triple helix1-8. This binding can be demonstrated either directly by a footprinting technique3, gel assays4, or indirectly by inducing irreversible reactions in the target sequence, such as photocrosslinking1,5 or cleavage2,6-8. Binding occurs in the major groove with the homopyrimidine oligonucleotide orientated parallel to the homopurine strand. Thymine and protonated cytosine in the oligonucleotide form Hoogsteen-type hydrogen bonds with A·T and G·C Watson-Crick base pairs, respectively. Here we report that an 11-residue homopyrimidine oligonucleotide covalently attached to an ellipticine derivative by its 3' phosphate photo-induces cleavage of the two strands of a target homopurine-homopyrimidine sequence. To our knowledge, this is the first reported case of a sequence-specific artificial photoendonuclease. In addition we show that a strong binding site for a free ellipticine derivative is induced at the junction between the triplex and duplex structures on the 5' side of the bound oligonucleotide. On irradi-ation, cleavage is observed on both strands of DNA. This opens new possibilities for inducing irreversible reactions on DNA at specific sites by the synergistic action of a triple helix-forming oligonucleotide and an intercalating agent. © 1990 Nature Publishing Group.