Thiophosphoramidites

Replacing two non-bridging oxygen atoms with sulfur atoms in a DNA phosphodiester linkage creates a phosphorodithioate (PS2) linkage.1 Like natural DNA, the phosphorodithioate linkage is achiral at phosphorus. This analog is completely resistant to nuclease degradation and forms complexes with DNA and RNA with somewhat reduced stabilities.2 Moreover, it has been found that PS2-ODNs bind proteins with a higher affinity than their phosphodiester analogues2-6 suggesting that PS2-ODNs may have additional utility in the form of sulfur-modified phosphate ester aptamers (thioaptamers)3,6-8 for therapeutic and diagnostic applications. Thiophosphoramidites are now commercially available after recent work at AM Biotechnologies

(www.thioaptamer.com).

1. Thiophosphoramidites (ThioPAs) are not soluble in anhydrous acetonitrile diluent. Rather, 10% DCM (v/v) in acetonitrile is an ideal diluent for all four of the thioPAs for a final amidite concentration of 0.15 M.
2. ThioPAs are somewhat less stable than normal DNA phosphoramidites in anhydrous acetonitrile containing 10% DCM; however, the coupling efficiency of all four thioPAs is not reduced after two days in solution at room temperature.
3. After synthesis, the thioPA bottle on the synthesizer should be replaced with one containing acetonitrile diluent and the synthesizer line flushed with acetonitrile.

A typical cycle for the solid-phase synthesis of a PS2 linkage is different from a standard cycle for the synthesis of normal phosphate linkages. After coupling, the resulting thiophosphite triester is then sulfurized with DDTT. Capping is carried out AFTER sulfurization.

Upon completion of the automated synthesis, deprotection is carried out using a concentrated ammonia:ethanol (3:1, v:v) mix containing 20 mM DTT at 55 °C for 15-16 h.

REFERENCES

(1) J. Nielsen, W.K.D. Brill, and M.H. Caruthers, Tetrahedron Letters, 1988, 29, 2911-2914.
(2) L. Cummins, D. Graff, G. Beaton, W.S. Marshall, and M.H. Caruthers, Biochemistry, 1996, 35, 8734-41.
(3) X. Yang, and D.G. Gorenstein, Curr Drug Targets, 2004, 5, 705-15.
(4) W.S. Marshall, and M.H. Caruthers, Science, 1993, 259, 1564-70.
(5) J.L. Tonkinson, et al., Antisense Research and Development, 1994, 4, 269-278.
(6) X. Yang, et al., Bioorg Med Chem Lett, 1999, 9, 3357-62.
(7) X. Yang, et al., Ann N Y Acad Sci, 2006, 1082, 116-9.
(8) X. Yang, et al., Nucleic Acids Res, 2002, 30, e132.

2’-OMe-Thiophosphoramidites

The phosphorodithioate linkage (PS2) is both achiral and essentially resistant to nucleases. Previous studies have shown very interesting results which include observations that DNA with PS2 linkages activates RNase H in vitro, strongly inhibits human immunodeficiency virus (HIV) reverse transcriptase, induces B-cell proliferation and differentiation, and is completely resistant to hydrolysis by various nucleases. 2’-OMe- RNA Thiophosphoramidites are RNA monomers designed to produce oligos combining the PS2 linkage with the 2’-O-methyl ribose modification. These PS2-modified RNA oligos have potential for use in siRNAs and dithiophosphate aptamers (thioaptamers).