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

Chunsen Bai, Piotr Klimkowski, Cheng Jin, Jagannath Kuchlyan, Afaf H. El-Sagheer* and Tom Brown*. Org. Biomol. Chem. 20, 8618-8622, 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.