Optimal configuration of pyrene excimer induced by the excimer-forming two-probe nucleic acid hybridization method

Excimer-forming two-probe nucleic acid hybridization (ETPH) method with pyrene as a fluorophore enables homogeneous hybridization assays. We examined the effect of linker length between a pyrene residue and a terminal sugar moiety on Tm of hybrids in the presence of 20% dimethylformamide (DMF). The results including those of CD measurements indicated no interaction of pyrene residues with the duplex formed between a target 32-mer and a pyrenemethyliodoacetamide-introduced 16-mer probe (PMIA-P5)/a pyrenebutanoic acid-introduced 16-mer probe (PBuA-P3), which is the best pair of probes for intense excimer emission. This was also supported by a computer-assisted molecular modeling using Insight II and Discover software.