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A new phosphoramidite enables orthogonal double labelling to form combination oligonucleotide probes.

Chunsen BaiPiotr KlimkowskiCheng JinJagannath KuchlyanAfaf H El-SagheerTom Brown
Published in: Organic & biomolecular chemistry (2022)
Oligonucleotides labelled with thiazole orange intercalator and a reporter dye on the same thymine base have been synthesized. The key phosphoramidite (AP-C3 dT) contains an alkyne and amine, enabling dual orthogonal labelling of the nucleobase. Multiple monomers can be added to produce heavily functionalised oligonucleotides. In their DNA and 2'-OMe RNA formats these combination probes display high duplex stability and fluorescence when bound to complementary DNA and RNA.
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