USE OF A STILBENEDICARBOXAMIDE BRIDGE IN STABILIZING, MONITORING, AND PHOTOCHEMICALLY ALTERING FOLDED CONFORMATIONS OF OLIGONUCLEOTIDES

A stilbenedicarboxamide bridge (-Sigma-) is shown to serve as a unique and unusually effective cap for stabilizing and characterizing short oligonucleotide double and triple stranded structures. As representative of the stability of a family of oligomers studied, T-m values for the thermal transitions in 0.1 M NaCl of the hairpin forms of dTTT-Sigma-dAAA and dGCG-Sigma-dCGC are similar to 42 degrees C and >80 degrees C, respectively, and T-m for unfolding of the triple-stranded, double-hairpin conformation of d(TTTTTT-Sigma-)(2)dAAAAAA is 69 degrees C. The intercalating dye, ethidium, binds efficiently to the mini-hairpin structures formed by these conjugates, even to dTT-Sigma-dAA, which has a single four-nucleotide pocket; and the DNA groove binding agent, Hoechst 33258, interacts with dTTT-Sigma-dAAA as well as with longer conjugates. The distinctive monomer and excimer fluorescence bands for the stilbenedicarboxamide moiety provide useful information on the structures of these small organized domains, and photoinduced isomerization permits postsynthetic alteration of the geometry of the bridge and therefore alteration of the hybridization properties of the conjugate. The sensitivity to light depends on the nucleotides abutting the linker. When stability to light is desired, it can be achieved by incorporating a dG-dC pair in this position.