Design of 2′-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters

Kira Astakhova, Andrey V. Golovin, Igor A. Prokhorenko, Alexey V. Ustinov, Irina A. Stepanova, Timofei S. Zatsepin, Vladimir A. Korshun

    Research output: Contribution to journalArticlepeer-review

    8 Citations (Scopus)

    Abstract

    1-Phenylethynylpyrene fluorophore (1-PEPy) has long-wavelength shifted emission and higher photostability compared to pyrene, retaining, however, pyrene's ability to form excimers. Here we report the synthesis of 2′-O-[3(and 4)-(pyren-1-ylethynyl)benzyl]-uridines and their tandem incorporation into deoxyribo- and 2′-O-Me-ribo-oligonucleotide probes. Excimer forming probes of type NN … NNXXNN … NN (X = 2′-O-[meta(or para)-(pyren-1-ylethynyl)-benzyl]uridine) containing two adjacent fluorescent nucleosides within an oligonucleotide are available in four types (meta-meta; para-meta; meta-para; para-para). Both DNA (N = deoxyribonucleotides) and 2′-O-Me-RNA (N = 2′-O-Me-ribo-nucleotides) probes were synthesized and their hybridization with complementary and singly mismatched DNA and RNA was studied. Several probes show a dramatic response of their excimer-to-monomer intensity ratio upon hybridization. Remarkably, most spectacular fluorescence changes were demonstrated for probes with para-meta and meta-para combination within 2′-O-Me-ribo-oligonucleotides. Using excimer forming probes, three natural SNP in Helicobacter pylori 23S RNA gene (A2144G, A2143G, A2143C) and the wild type gene can be distinguished.

    Original languageEnglish
    Pages (from-to)3220-3230
    Number of pages11
    JournalTetrahedron
    Volume73
    Issue number23
    DOIs
    Publication statusPublished - 2017

    Keywords

    • Fluorescence
    • Hybridization
    • Oligonucleotide
    • Phenylethynylpyrene
    • Single nucleotide polymorphism

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