Pergamon Tetrahedron Letters 39 (1998) 8361-8364 TETRAHEDRON LETTERS Phosphoramidites Derived from Tertiary Alcohols. Why Do They Sometimes Couple with Low Efficiency? Claus Scheuer-Larsen, Britta M. Dahl, Jesper Wengel, and Otto Dahl* Department of Chemistry, University of Copenhagen, The H. C. Orsted Institute, Universitetsparken 5, DK-2 llXl Copenhagen, Denmark Received 7 July 1998; accepted 1 September 1998 Abstract. tert-Alkyl phosphoramidites are somewhat stet-ically hindered, but give phosphites in good yields with tetrazole catalysis when the coupling time with alcohols is prolonged. Low yields of phosphotriesters are caused by elimination of the tertiary alkyl group during the subsequent oxidation of the phosphite with iodine/water/pyridine, and can he avoided by the use of tert-butyl hydroperoxide as the oxidant. © 1998 ElsevierScienceLtd. All rights reserved. One of the main methods to prepare DNA and RNA oligomers uses nucleoside phosphoramidites as the monomers, and phosphoramidite methods are often chosen to prepare a variety of other biologically interesting phosphomonoesters and phosphodiesters. 1 In this method, the phosphoramidite reacts with an alcohol in the presence of a catalyst, most often tetrazole, to give a phosphite, which subsequently is oxidized to a phosphotriester, usually with a mixture of iodine, water, and pyridine. Finally, protective groups are removed to give the desired phosphomonoester or phosphodiester. In the solid phase synthesis of DNA and RNA oligomers the 5'-hydroxy group is usually protected with dimethoxytfityl, and the yield of each coupling is estimated from the amount of dimethoxytrityl cations liberated after a coupling cycle. Provided the water content is kept low, such "DMT efficiencies" can be above 99%, which m~es this method so attractive for the preparation of longer phosphodiester oligomers. The phosphoramidite method has also been popular to prepare modified oligonucleotides for antisense purposes. 2 In connection with studies of sugar modified oligonucleotides we observed that 3'-0- phosphoramidites derived from 3'-C-alkyl nucleosides, e.g. 1 - 3 (Fig. 1), coupled with very low DMT efficiencies (< 5% to about 40%), even alter repeated couplings and prolonged reaction times. 3-5 However, some bicyclic analogues gave varying results. Thus, 4 gave satisfactory DMT efficiencies "after 2 x 12 min coupling (ca. 95%), 6 5 gave medium (50%) and 6 quite low efficiency (30%). 7 Other groups have published similar results, e.g. Herdewijn et al. reported that 7 failed completely to couple, 8 whereas Leuman et al. obtained high DMT-efficiencies (>98% for 6 min couplings) for the bicyclic phosphoramidites 8. 9 These phosphoramidites are all derived from tertiary alcohols and are expected to react more slowly than phosphoramidites derived from primary or secondary alcohols due to stefic hindrance, but this effect is not large, l(I and does not explain the varying results described above. We show here that phosphoramidites derived from tertiary alcohols react efficiently with alcohols to give phosphites, but the phosphites are cleaved in the subsequent oxidation step by the usual oxidation reagent, iodine/water/pyridine, if elimination of the tertiary alkyl group is facile. Good yields of phosphotriesters can be obtained by simply replacing iodine/water/pyridine with tert-butyl hydroperoxide as the oxidant. 0040-4039/98/$ - see front matter © 1998 Elsevier Science Ltd. All rights reserved. PII: S0040-4039(98)01844-9