Previously, we reported a novel fluorescence dye, a silylated pyrene derivative, as a DNA labeling agent. In this study, new silylated pyrene derivatives with different linker lengths and different substituents on the silicon atom have been prepared and introduced into oligonucleotides. In particular, when the diphenylsilylpyrene derivative was introduced as a fluorescence dye, the fluorescence intensity of the duplex was enhanced about 20 times compared to the signal in the absence of the target DNA.Fluorescently labeled oligonucleotides have been widely used in the analysis of genetic information.1 Such oligonucleotide probes should exhibit fluorescence emission only in the presence of the fully matched complementary strand, whereas an obvious fluorescent signal will be observed in the presence of the fully matched complementary strand. Various probe DNA and detection systems satisfying this requirement have been developed.2,3 The fluorescence dyes commonly used for fluorescent DNA probes show strong fluorescence intensity and high quantum yield in highly sensitive detection systems that are required for single molecule measurement 4 and in vivo imaging. 5It was reported that the introduction of silyl groups to polyaromatic compounds, such as anthracene and pyrene, induced red shift of the absorption and emission wavelengths, and increased the fluorescence quantum yield. 68 Recently, we reported novel fluorescently labeled oligonucleotides bearing a silylated pyrene derivative at the 5¤-terminus. 9 The silylated pyrene derivative was functionalized by the introduction of a hydroxy group, and the hydroxy group was phosphitylated to give the standard phosphoramidite derivative. The oligonucleotides containing the silylated pyrene derivative showed characteristic spectroscopic properties. While the modified oligonucleotides showed weak emission on the single strand, the presence of the complementary strand induced enhancement of the fluorescent emission. However, the reason for the distinctive spectroscopic behavior is unclear. In this study, in order to elucidate the effect on the fluorescent behavior of the structure, we prepared novel silylated pyrene derivatives, which have different linker lengths to the oligonucleotides and different substituents on the silicon atom instead of the methyl group.First, for elucidation of the relationship between the fluorescent behavior and linker length, we designed various silylated pyrene derivatives having different alkyl linker lengths and different substituents on the silicon atom. Preparation of the silylated pyrene derivatives having different alkyl linker lengths was carried out by the following steps (Scheme 1). The vinyl silane derivative 2a was synthesized from the reaction of 1-bromopyrene with chlorodimethylvinylsilane using the procedure reported previously. 9 The allylsilane derivative 2b was also prepared by the same procedure. The alcohol derivatives 3a and 3b were successfully prepared by using 9-BBN for hydroboration.10