Chemical synthesis of an RNA sequence containing 2-thiocytidine (s2C): the DY647 labelled anticodon stem and loop sequence of Staphylococcus aureus tRNAArg (s2C32, mnm5U34, t6A37)

Incorporation of 2-thiocytidine (s2C) into a DY647 labelled 17-mer RNA sequence corresponding to the anticodon stem loop of Staphylococcus aureus tRNAArg has been achieved by phosphoramidite chemistry. Key to the success was the use of dilute iodine for the P(III) to P(V) oxidation step plus the choice of the trimethylsilylethyl (tse) ester as protection for the threonyl carboxyl group of t6A. In trial experiments with N4-benzoyl-2-thiocytidine, the use of dilute t-BuOOH in toluene as an alternative oxidising agent caused substantial desulfurization.