title: Phenylethynylpyrene excimer forming hybridization probes for fluorescence SNP detection.
abstract: Excimer formation is a unique feature of some fluorescent dyes (e.g., pyrene) which can be used for probing the proximity of biomolecules. Pyrene excimer fluorescence has previously been used for homogeneous detection of single nucleotide polymorphism (SNP) on DNA. 1-Phenylethynylpyrene (1-1-PEPy), a photostable pyrene derivative with redshifted fluorescence, is able to form excimers (emission maximum about 500-510 nm) and is well suitable for nucleic acid labeling. We have shown the utility of 1-1-PEPy in the excimer-forming DNA probes for detection of 2144A/G and 2143A/G transitions, and 2143A/C substitution in the 23S ribosomal RNA gene of Helicobacter pylori strains resistant to clarithromycin. The phenylethynylpyrene pair can be generated either from 1-1-PEPy pseudonucleoside 4-[4-(pyren-1-ylethynyl)phenyl]-1,3-butanediol or from 2'-O-(1-PEPy) modified nucleosides--2'-O-[3-(pyren-1-ylethynyl)benzyl]uridine and 2'-O-[4-(pyren-1-ylethynyl)benzyl]uridine.
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya, Moscow, Russia.
authors.forename: Igor A
authors.initials: IA
authors.lastname: Prokhorenko
authors.forename: Irina V
authors.initials: IV
authors.lastname: Astakhova
authors.forename: Kuvat T
authors.initials: KT
authors.lastname: Momynaliev
authors.forename: Timofei S
authors.initials: TS
authors.lastname: Zatsepin
authors.forename: Vladimir A
authors.initials: VA
authors.lastname: Korshun
mesh_terms: D001483:Base Sequence; D005456:Fluorescent Dyes / Q000737:chemistry*; D016480:Helicobacter pylori / Q000235:genetics; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation / Q000235:genetics; D009692:Nucleic Acid Heteroduplexes / Q000235:genetics; D009693:Nucleic Acid Hybridization / Q000379:methods*; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011721:Pyrenes / Q000737:chemistry*; D012338:RNA, Ribosomal, 23S / Q000235:genetics; D013050:Spectrometry, Fluorescence; D013696:Temperature
chemical_list: C525966:1-phenylethynylpyrene; D005456:Fluorescent Dyes; D009692:Nucleic Acid Heteroduplexes; D011721:Pyrenes; D012338:RNA, Ribosomal, 23S