Design and simple routes of synthesis of oligonucleotide conjugates for studies of dna triple helix formation

A series of oligonucleotides conjugated to intercalators, as well as fluore scent and lipophilic substances, minor groove binders and photoactive molec ules were synthesized for studies of their ability to form a stable triple helix. Purine-rich short double stranded DNA fragments from HIV-1 genome an d pyrimidine 16-mer oligodeoxyribonucleotide were used as models. A conjuga te of a dipyrido[3,2-a:2',3'-c]phenazine-ruthenium (II) complex and a tripl e helix-forming oligonucleotide was constructed. Upon sequence-specific dup lex and triplex formation of the conjugate, the ruthenium complex becomes h ighly fluorescent. The attached ruthenium complex induces a stabilization o f the DNA triple helix and a significant increase of the time of residence of the third strand on the duplex.