For the development of the excimer probe responsible for DNA target, the deoxyuridine phosphoramidite derivative bearing the silylated pyrene attached at the C-5 position was prepared and incorporated into oligonucleotides. The modified oligonucleotides showed the excimer emission in the absence of the target DNA, on the other hands, the excimer emission was quenched in the presence of the target DNA. For the utilization of the fluorescence behavior, the novel molecular beacon probe containing the silylated pyrene-modified nucleoside at the stem region was designed and the fluorescence property of the probe found to show the responsibility for DNA target.

Efficient synthesis of a dithymidine dinucleotide analog bearing a diisopropylsilyl linkage instead of a phosphodiester linkage is described with respect to its incorporation into oligonucleotides. The diisopropylsilyl linkage was introduced into the oligonucleotide by preparation of the phosphoramidite derivative of a dithymidine dimer unit. The diisopropylsilyl-modified oligonucleotide exhibited hybridization behavior with both single strand and duplex DNA. The thermal stability of both the duplex and triplex showed a relative instability compared to the corresponding natural phosphodiester DNA, because of the steric hindrance of the isopropyl group on the silicon atom.