SpringerProtocols: Abstract: Phenylethynylpyrene Excimer Forming Hybridization Probes for Fluorescence SNP Detection

13. Phenylethynylpyrene Excimer Forming Hybridization Probes for Fluorescence SNP Detection

By: Igor A. Prokhorenko¹, Irina V. Astakhova¹, Kuvat T. Momynaliev², Timofei S. Zatsepin³, Vladimir A. Korshun¹

Abstract

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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.

Affiliation(s): (1) Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya, Moscow, Russia
(2) Research Institute of Physico-Chemical Medicine, Miklukho-Maklaya, Moscow, Russia
(3) Department of Chemistry, M. V. Lomonosov Moscow State University; Central Research Institute of Epidemiology, Novogireevskaya, Moscow, Russia

Book Title: Single Nucleotide Polymorphisms: Methods and Protocols

Series: Methods in Molecular Biology | Volume: 578 | Pub. Date: Sep-01-2008 | Page Range: 209-222 | DOI: 10.1007/978-1-60327-411-1_13

Subject: Genetics/Genomics

Key Words: DNA probes - single nucleotide polymorphism detection - excimer fluorescence - pyrene - 1-phenylethynylpyrene - Helicobacter pylori

References

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