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dG (iBu) H-Phosphonate TEA salt

dG (iBu) H-Phosphonate TEA salt

Monomer for H-phosphonate nucleic acid synthesis.
  • Allows alternative approach to nucleic acid synthesis, difficult by phosphoramidite method.
  • Provided in stable salt form.
  • Note that additional ancillary reagents are required for use.
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Product information

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.

Applicable Products

LK2005 dT-H Phosphonate, TEA Salt
LK2006 dG-H Phosphonate, TEA Salt
LK2007 dA-H Phosphonate, TEA Salt
LK2035 dC-H Phosphonate, DBU Salt

Please note that the liquid reagents used in H-phosphonate synthesis are unfortunately not available from Link Technologies.

Physical & Dilution Data

Dilution volumes (in ml) are for 0.1M solutions in dry acetonitrile/pyridine (1:1). Adjust accordingly for other concentrations. For µmol pack sizes, products should be diluted as 100µmol/ml to achieve 0.1M, regardless of molecular weight.

Item

Mol. Formula

Mol. Wt.

Unit Wt.

250mg

500mg

1g

LK2005 C37H48N3O9P 707.79 304.20 3.52 7.04 14.09
LK2006 C41H53N6O9P 804.89 329.21 3.11 6.21 12.42
LK2007 C44H51N6O8P 822.90 313.21 3.04 6.08 12.15
LK2035 C43H51N4O9P 849.93 289.18 2.94 5.88 11.77

Dissolution

All monomers must be dissolved in acetonitrile/ pyridine (1:1).

Coupling & Capping1

Normal deblock is used, however activation is carried out with 1-adamantane carbonyl chloride dissolved in acetonitrile/pyridine (95:5). Capping is carried out with the TEA salt of isopropyl phosphite.

Oxidation

There are two oxidation steps and they need only be carried out at the end of the synthesis. The first is accomplished using 0.1M iodine in pyridine/ N-methylimidazole/water/THF (5:1:5:89), and the second with 0.1M iodine in triethylamine/water/ THF (5:5:90).

Deprotection

Standard oligonucleotide deprotection conditions can be applied when deprotecting an oligo synthesised using these products.

Storage & Stability

Refrigerate monomers. Stability in solution is approximately 1 week.

Reference

  1. 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.

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