LINKAGE STRUCTURES STRONGLY INFLUENCE THE BINDING COOPERATIVITY OF DNA INTERCALATORS CONJUGATED TO TRIPLER FORMING OLIGONUCLEOTIDES

Conjugation of DNA intercalators to triple helix forming oligodeoxynucleotides (ODN's) can enhance ODN binding properties and consequently their potential ability to modulate gene expression. To test the hypothesis that linkage structure could strongly influence the binding enhancement of intercalator conjugation with tripler forming ODN's, we have used a model system to investigate binding avidity of short oligomers conjugated to DNA intercalators through various linkages. Using a dA(10).T-10 target sequence imbedded in a 20 bp duplex, binding avidities of a T-10 ODN joined to the DNA intercalator 6,9-diamino, 3-methoxy acridine (DAMA) by 8 different 5' linkages were measured using an electrophoretic mobility shift assay. Although unmodified T-10 has a very limited capacity for stable binding under these conditions (apparent K-d >250 mu M at 4 degrees C), conjugation to DAMA using flexible linkers of certain lengths and chemical compositions greatly enhanced binding (K-d Of 1 mu M at 4 degrees C). Other linkers, however, modestly enhanced binding or had no effect on binding at all. Thus, the length, flexibility, and chemical composition of linker structures all substantially influence intercalator conjugated oligodeoxynucleotide binding avidity.