Naphthalene- and perylene-based linkers for the stabilization of hairpin triplexes

Planar perylene- and naphthalene-based diimide linkers can be employed to tether the Watson-Crick and the Hoogsteen strands of a DNA triplex, thus providing conjugates capable of targeting single-stranded nucleic acids with the formation of hairpin triplexes. The planar linkers are designed to bridge the terminal base triplet of the three-stranded complex and provide base-stacking interactions with all three residues. Sixteen complexes have been prepared, eight with each linker, half with RNA (R) targets and half with DNA (D) targets. The conjugate sequences are composed of two strands of DNA, two of 2'-O-methyl RNA (M), or one of each. In comparison to similar complexes formed with a hexa(ethylene glycol) linker, the planar linkers enhance the T-M values for the complexes by as much as 28 degrees C with Delta G values indicating as much as 12.3 kcal/mol of stabilization relative to the simple glycol linker. All sixteen complexes have been characterized by T-M measurements and Delta G determinations. That pi-stacking interactions are present between the linkers, and the nucleobases can be inferred from the quenching of the perylene fluorescence upon complex formation, and the observation of an absorbance vs temperature transition for the naphthalene-based linker at 383 nm and for the perylene-based linker monitored at 537 nm.