OligoDNA possessing consecutive modified nucleotide residues bearing silylated pyrene at C-2¤ position was synthesized. The fluorescent oligoDNA exhibited marked excimer fluorescent signal upon binding to a fully matched complementary DNA strand, however, the signal was effectively quenched in the single-stranded form as well as in the mismatched base pair duplex.Sensitive and sequence specific detection of certain gene fragments are key technology for diagnostics and genetic studies. Fluorescent oligonucleotide probes have been intensively studied for the past decades as a tool to meet these demands and substituting conventional radio-labeled probes.1 As a feasible gene-detecting tool, however, it is highly desirable that the probe exhibits a specific fluorescent signal only when it binds to the target oligonucleotide. To avoid false results, the probe should also have the capability of recognizing uncomplementary dissimilarities of the target, including single-nucleotide mismatches (SNPs). A probe possessing such ability would greatly simplify the detection process because of the abridgment of tedious separation and washing steps after the binding of the probe to the sample to be examined. Meanwhile, a common fluorescent material pyrene is known to form a characteristic excimer in an appropriate condition to emit bright fluorescence at around 460 nm. Several modified oligonucleotide probes utilizing pyrene to exhibit excimer fluorescence upon hybridization to their complementary oligonucleotides have been reported.2 On the other hand, silylated pyrene bearing a modifiable functional group is a recently developed new derivative of pyrene capable of introduction into biological molecules such as nucleic acids and lipids.3,4 The compound exhibits enhanced fluorescent quantum yield along with a bathochromic shift in absorption and emission, due to the specific ·³ interaction. 5,6 Thus, the compound is more advantageous as a fluorescent labeling agent compared to original pyrene. During the course of our study to investigate the utilities of silylated pyrene derivatives, we have found that a modified oligonucleotide having silylated pyrene moieties at the C-2¤ position of neighboring uridine residues exhibits bright excimer-based fluorescent signal in the presence of fully complementary oligoDNA strand. 7 The signal was, however, strongly quenched in the single-stranded form and in the duplexes having mismatched base pairs.To synthesize a modified oligonucleotide, we have applied C2¤-functionalization via a carbamate function 8 utilizing 1,1¤-carbonyldiimidazole (CDI) and a silylated pyrene derivative bearing primary amine function. The outline of the synthesis of the key compound, a modified uridine phosphoramidite bearing silylated pyrene at 2¤-position through carbamate function (9), is summarized in Scheme 1.1-Bromopyrene (1) was treated with n-BuLi in dry THF (¹78°C) under argon atmosphere followed by the addition of vinyldimethylsilyl chloride. The mixture was allowed to reach room temperature to give the cor...