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Issue 9, 2013
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DNA strands with alternating incorporations of LNA and 2′-O-(pyren-1-yl)methyluridine: SNP-discriminating RNA detection probes

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Abstract

Detection of nucleic acids using fluorophore-modified oligonucleotides forms the basis of many important applications in molecular biology, genetics and medical diagnostics. Here we demonstrate that DNA strands with central segments of alternating locked nucleic acid (LNA) and 2′-O-(pyren-1-yl)methyluridine monomers display very large and highly mismatch-sensitive increases in fluorescence emission upon RNA hybridization, whereas corresponding “LNA-free” controls do not. Absorbance spectra strongly suggest that LNA-induced conformational tuning of flanking 2′-O-(pyren-1-yl)methyluridine monomers places the reporter group in the minor groove upon RNA binding, whereby pyrenenucleobase interactions leading to quenching of fluorescence are minimized. Accordingly, these easy-to-synthesize probes are promising SNP-discriminating RNA detection probes.

Graphical abstract: DNA strands with alternating incorporations of LNA and 2′-O-(pyren-1-yl)methyluridine: SNP-discriminating RNA detection probes

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Publication details

The article was received on 15 Mar 2013, accepted on 15 Apr 2013 and first published on 25 Apr 2013


Article type: Edge Article
DOI: 10.1039/C3SC50726B
Citation: Chem. Sci., 2013,4, 3447-3454
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    DNA strands with alternating incorporations of LNA and 2′-O-(pyren-1-yl)methyluridine: SNP-discriminating RNA detection probes

    S. Karmakar and P. J. Hrdlicka, Chem. Sci., 2013, 4, 3447
    DOI: 10.1039/C3SC50726B

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