title: Optimal configuration of pyrene excimer induced by the excimer-forming two-probe nucleic acid hybridization method.
abstract: 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.
authors.affiliation: Tsukuba Research Laboratory, Hamamatsu Photonics K. K., Japan.
authors.forename: M
authors.initials: M
authors.lastname: Masuko
authors.forename: S
authors.initials: S
authors.lastname: Toyoda
authors.forename: M
authors.initials: M
authors.lastname: Suwa
authors.forename: S
authors.initials: S
authors.lastname: Mitaku
authors.forename: A
authors.initials: A
authors.lastname: Shimazu
authors.forename: H
authors.initials: H
authors.lastname: Ohtani
mesh_terms: D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes; D007460:Iodoacetamide / Q000031:analogs & derivatives; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D015345:Oligonucleotide Probes; D011721:Pyrenes; D013816:Thermodynamics
chemical_list: D005456:Fluorescent Dyes; C110226:N-(1-pyrenemethyl)iodoacetamide; D015345:Oligonucleotide Probes; D011721:Pyrenes; D004247:DNA; D007460:Iodoacetamide