Design of 2′-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters. Issue 23 (8th June 2017)

• Record Type: Journal Article
• Authors: Astakhova, Kira; Golovin, Andrey V.; Prokhorenko, Igor A.; Ustinov, Alexey V.; Stepanova, Irina A.; Zatsepin, Timofei S.; Korshun, Vladimir A.
• Is Part Of: Tetrahedron. Volume 73:Issue 23(2017)
• Page Start: 3220
• Page End: 3230
• Publication Date: 2017-06-08
• Subjects: Oligonucleotide -- Single nucleotide polymorphism -- Phenylethynylpyrene -- Hybridization -- Fluorescence; Chemistry, Organic -- Periodicals; 547.005
• DOI: 10.1016/j.tet.2017.04.045
• Languages: English
• ISSNs: 0040-4020

Abstract

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 … NNXX NN … 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. Graphical abstract: