DNA TRIPLE-HELIX SPECIFIC INTERCALATORS AS ANTIGENE ENHANCERS - UNFUSED AROMATIC CATIONS

Triple-helical structures involving the interaction of an oligonucleot ide third strand with a duplex nucleic acid sequence have recently gai ned attention as a therapeutic strategy in the ''antigene'' approach [ cf. Helene, C. (1991) Eur. J. Cancer 27, 1466-1471]. This method utili zes the triple helix formed from the cellular duplex and an added thir d strand to directly regulate the activity of a selected gene. The lim ited stability of nucleic acid triple-helical interactions, particular ly if the third strand has backbone modifications such as methylphosph onate or phosphorothioate substitutions, is a limiting condition for t he use of this approach. We have designed and synthesized compounds, o n the basis of the following three criteria, that we feel should provi de selective interactions and significant stabilization of triplexes: appropriate aromatic surface area for stacking with triplex bases in a n intercalation complex, positive charge, and limited torsional freedo m in the aromatic system to match the propeller twist of the triple-ba se interactions in the triplex. A series of quinoline derivatives with an alkylamine side chain at the 4-position and with different aryl su bstituents at the 2-position has been synthesized as our first compoun ds. A 2-naphthyl derivative provides significant and selective stabili zation of the triplex. In a 0.2 M NaCl buffer, the naphthyl derivative increased the T(m) for the triplex (triplex to duplex and third stran d transition) by approximately 30-degrees-C more than the T(m) increas e for the duplex (duplex to single strands transition). Spectral chang es and energy-transfer results indicate that the naphthyl compound and related derivatives bind to the triplex by intercalation. Molecular m odeling results indicate very good stacking of the naphthylquinoline r ing system with the bases at a triplex intercalation site, but the res ults also indicate that the ring system is too large to stack optimall y with base pairs at a duplex intercalation site.