Enone as TFO Linker: Synthesis and Parallel DNA Triplex Stability Evaluation

Two new intercalated nucleic acid monomers, X and Y, possessing enone as linker have been synthesized. The monomers were incorporated into 14-mer polypyrimidine strand to act as triplex-forming oligonucleotide (TFO). The thermal stabilities of the formed parallel triplexes, parallel and antiparallel duplexes were evaluated to show high stability of its parallel triplexes at pH 5.0 and pH 7.2, while limited stability at pH 6.0 compared to unmodified triplex. The architectures of enone linker are shown to disturb the planarity of its parallel and antiparallel duplexes and consequently the pi-pi stacking ability with the neighboring nucleobases. The data was confirmed by molecular dynamics simulation and binding energy calculations. Characteristic fluorescence spectra were also investigated to show the ability of X and Y containing TFO to discriminate parallel triplex from parallel and antiparallel duplex.