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.
Masuko
M
M
Tsukuba Research Laboratory, Hamamatsu Photonics K. K., Japan.
Toyoda
S
S
Suwa
M
M
Mitaku
S
S
Shimazu
A
A
Ohtani
H
H
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
D005456:Fluorescent Dyes; C110226:N-(1-pyrenemethyl)iodoacetamide; D015345:Oligonucleotide Probes; D011721:Pyrenes; D004247:DNA; D007460:Iodoacetamide