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Nature Protocols 2, 3122–3135 (1 December 2007) | doi:10.1038/nprot.2007.451

Synthesis of the 3|[prime]|-thio-nucleosides and subsequent automated synthesis of oligodeoxynucleotides containing a 3|[prime]|-S-phosphorothiolate linkage

James W Gaynor , Joanne Bentley & Richard Cosstick

Oligodeoxynucleotides containing 3|[prime]|-S-phosphorothiolate (3|[prime]|-PS) linkages have become useful tools for probing enzyme-catalyzed cleavage processes in DNA. This protocol describes the synthesis of the phosphorothioamidite monomers derived from thymidine and 2|[prime]|-deoxycytidine, and their application to a fully automated procedure for synthesising oligodeoxynucleotides containing 3|[prime]|-PS linkages. The synthesis of the 5|[prime]|-protected-3|[prime]|-amidites is achievable in 2 weeks with the DNA synthesis and purification taking another 1 week.