SIMA is an analog of HEX with improved stability. 5-SIMA phosphoramidite is a fluorescent dye for oligonucleotide labeling.
Reference Reading
1. 5-Fluoro-4-thiouridine phosphoramidite: new synthon for introducing photoaffinity label into oligodeoxynucleotides
Jan Milecki, Joanna Nowak, Bohdan Skalski, Stefan Franzen. Bioorg Med Chem. 2011 Oct 15;19(20):6098-106. doi: 10.1016/j.bmc.2011.08.035.
The synthesis of phosphoramidite of 5-fluoro-4-thio-2'-O-methyluridine is described. An appropriate set of protecting groups was optimized including the 4-thio function introduced via 4-triazolyl as the 4-(2-cyanoethyl)thio derivative, and the t-butyldimethyl silyl for 2' and 3' hydroxyl protection, enabling efficient synthesis of the phosphoramidite. These protecting groups prevented unwanted side reactions during oligonucleotide synthesis. The utility of the proposed synthetic route was proven by the preparation of several oligonucleotides via automated synthesis. Photochemical experiments confirmed the utility of the synthon.
2. Synthesis of 5'-Thio-3'-O-ribonucleoside Phosphoramidites
Nan-Sheng Li, Jun Lu, Joseph A Piccirilli. J Org Chem. 2017 Dec 1;82(23):12003-12013. doi: 10.1021/acs.joc.7b01484.
The chemical synthesis of phosphoramidite derivatives of all four 5'-deoxy-5'-thioribonucleosides is described. These phosphoramidites contained trityl (A, G, C, and U), dimethoxytrityl (A and G), or tert-butyldisulfanyl (G) as the 5'-S-protecting group. The application of several of these phosphoramidites for solid-phase synthesis of oligoribonucleotides containing a 2'-O-photocaged 5'-S-phosphorothiolate linkage or 5'-thiol-labeled RNAs is also further investigated.
3. On-demand synthesis of phosphoramidites
Alexander F Sandahl, Thuy J D Nguyen, Rikke A Hansen, Martin B Johansen, Troels Skrydstrup, Kurt V Gothelf. Nat Commun. 2021 May 12;12(1):2760. doi: 10.1038/s41467-021-22945-z.
Automated chemical synthesis of oligonucleotides is of fundamental importance for the production of primers for the polymerase chain reaction (PCR), for oligonucleotide-based drugs, and for numerous other medical and biotechnological applications. The highly optimised automised chemical oligonucleotide synthesis relies upon phosphoramidites as the phosphate precursors and one of the drawbacks of this technology is the poor bench stability of phosphoramidites. Here, we report on the development of an on-demand flow synthesis of phosphoramidites from their corresponding alcohols, which is accomplished with short reaction times, near-quantitative yields and without the need of purification before being submitted directly to automated oligonucleotide synthesis. Sterically hindered as well as redox unstable phosphoramidites are synthesised using this methodology and the subsequent couplings are near-quantitative for all substrates. The vision for this technology is direct integration into DNA synthesisers thereby omitting manual synthesis and storage of phosphoramidites.
