H-phosphonate monomers are useful for the preparation of internucleotide linkages that are not attainable by phosphoramidite chemistry.⁽¹⁾

Despite being a niche technique, the advantage of this chemistry over phosphoramidite chemistry is that in one reaction the backbone of the entire oligonucleotide is converted to the required form. This is typically oxidation to give a sugar-phosphate backbone or sulphurised to give a thiophosphate-sugar backbone, or conversion to the silyl phosphite triester which provides a useful means of generating a variety of phosphorus analogues.⁽²⁾

The H-phosphonate moiety renders phosphate protection unnecessary and the nucleobases are deprotected using ammonium hydroxide conditions applicable to any unmodified or phosphorothioate oligonucleotide. A popular application of H-phosphonate method is the synthesis of radiolabelled phosphorothioates.⁽³⁾

The ancillary reagents required for H-phosphonate chemistry are different from phosphoramidite chemistry,⁽⁴⁾ and not available through the NAC portfolio. We recommend anyone using this chemistry prepares the ancillary solutions fresh for use.

Ref:

1. Nucleoside H-phosphonates. Chemical synthesis of oligodeoxyribonucleotides by the hydrogenphosphonate approach, P.J. Garegg, I. Lidh, T. Regberg, J. Stawinski and R. Strömberg, Tetrahedron Lett., 27, 4051-4054, 1986.
2. Synthesis of DNA/RNA and their analogs via phosphoramidite and H-phosphonate chemistries, S. Roy and M. Caruthers, Molecules, 18, 14268-14284, 2013.
3. Preparation of 35S-labelled polyphosphorothioate oligodeoxyribonucleotides by the use of H-phosphonate chemistry, C.A.Stein, C.A. Iversen, C. Subashinge, J.S. Cohen, W.J. Stec and G. Zon, Analytical Biochem., 188, 11-16, 1990.
4. Novel activating and capping reagents for improved hydrogenphosphonate DNA synthesis, A. Andrus, J.W. Efcavitch, L.T. McBride and B. Giusti, Tetrahedron Lett., 29, 861-864, 1988.