Triple helix-directed psoralen crosslinks are recognized by Uvr(A)BC excinuclease

Pyrimidine oligonucleotides bind to the major groove of an oligopyrimidine-oligopurine DNA sequence by triple helix formation. A 14-mer oligopyrimidine 3'-psoralen-conjugate (P) and a doubly modified 5'-acridine/3'-psoralen-oligonucleotide (PA) were photo-crosslinked to their target site. The crosslinked complexes were tested regarding their sensitivity to Uvr(A)BC excinuclease/DNA complex formation and excision, and compared to free psoralen crosslinked to the same site (M). An electrophoretic mobility-shift assay showed that the crosslinked triple-helix did not hamper formation of the (A)2B complex under conditions where the third strand was bound to its target. In vitro excision experiments performed on damaged DNA fragments containing crosslinked 5-methoxypsoralen (M-target) confirmed that the psoralen photoadduct was recognized by Uvr(A)BC and that excision occurred at the crosslinked site. The major cleavage reaction took place on the 5'-side of oligopurine strand. The excision was less efficient on the 5'-side of the pyrimidine strand. The 3'-side incision either on the purine or pyrimidine strand was even weaker. With optimal Uvr(A) concentrations, it was observed that the incision reaction on (P)- and (PA)-modified targets was clearly inhibited compared to the (M)-modified target, reflecting an effect of the oligonucleotide on the recognition/excision process. These results demonstrate that a triple helix is efficient in promoting inhibition of Uvr(A)BC excision nuclease activity. These results could account for divergent findings concerning the effects of triple helix-forming oligonucleotides on repair systems and open new perspectives to study DNA repair processes through the use of bi-substituted triple helix-forming oligonucleotides.