Backbone Modification using Methyl Phosphonamidites


Applicable Products

2073 dT-Me Phosphonamidite
2074 iBu-dG-Me Phosphonamidite
2075 Bz-dA-Me Phosphonamidite
2077 Ac-dC-Me Phosphonamidite

Physical & Dilution Data

Dilution volumes (in ml) are for 0.1M solutions in dry acetonitrile (4050), except for 2074 which is diluted in dry THF. Adjust accordingly for other concentrations. For µmol pack sizes, products should be diluted as 100µmol/ml to achieve 0.1M, regardless of molecular weight.


Mol. Formula

Mol. Wt.

Unit Wt.




2073 C38H48N3O7P 689.79 302.23 3.62 7.25 14.50
2074 C42H53N6O7P 784.89 327.24 3.19 6.37 12.74
2075 C45H51N6O6P 802.91 311.24 3.11 6.23 12.45
2077 C39H49N4O7P 716.81 287.21 3.49 6.98 13.95


dG-Me Phosphonamidite (2074) is dissolved in anhydrous THF prior to use in synthesis. Other monomers are dissolved in anhydrous acetonitrile.


A coupling time of 6min is recommended for syntheses of 1μmol and below. The use of the Ac-dC (2077) monomer is preferred to avoid base modification of dC residues during deprotection with ethylenediamine.1 Trityl monitors may understate the coupling efficiency, presumably due to a difference in the rate of release of the trityl group.

Cleavage & Deprotection

A one-pot procedure for cleavage and deprotection has been described.2 This is preferred to the procedure3 used in the past since it leads to less cleavage of the methyl phosphonate backbone during the ammonium hydroxide solution cleavage step and evaporation of the ethylenediamine.

Typical Protocol

  1. Air-dry the support in the synthesis column, open the column and transfer the support to a deprotection vial.
  2. Add 0.5ml of an ammonium hydroxide solution consisting of acetonitrile/ethanol/ammonium hydroxide (45:45:10) to the support. Seal the vial and leave it at room temperature for 0.5h.
  3. Add 0.5ml of ethylenediamine to the vial and reseal it. Leave it at room temperature for a further 6h.
  4. Filter in a microfilter tube then desalt on a G25 sephadex column and wash the support twice with 0.5ml acetonitrile/water (1:1).
  5. Dilute the combined supernatant and washes to 15ml with water.
  6. Adjust the pH to 7 with 6M hydrochloric acid (1 part) in a 1:1 mix of acetonitrile/water (9 parts) (ca. 2ml).
  7. Desalt using standard procedures.


Regular purification procedures can be used if the oligo contains several phosphodiester linkages. If the oligo contains a very high percentage of Me phosphonate linkages, RP-HPLC purification may work. However, these oligos have poor solubility characteristics and may precipitate in the sample loop, HPLC column, or other surfaces. More detailed descriptions of HPLC purification have been published.2

Note: These procedures have been shown to work well for small scale synthesis (1μmol or below). For larger synthesis scales, changes may be required in the capping and oxidation steps. See reference 3 for more details.

Storage & Stability

All phosphonamidites are stored refrigerated at a maximum of 2-8°C. They are stable in solution for 24h.


  1. (a) Elimination of transamination side product by the use of dC(Ac) methylphosphonamidite in the synthesis of oligonucleotide methylphosphonates, M.P. Reddy, F. Farooqui and N.B. Hanna, Tetrahedron Lett., 37, 8691-8694, 1996; (b) Correction to above, M.P. Reddy, F. Farooqui and N.B. Hanna, Tetrahedron Lett., 38, 1101-1101, 1997.
  2. (a) Deprotection of methylphosphonate oligonucleotides using a novel one- pot procedure, R.I. Hogrefe, M.M. Vaghefi, M.A. Reynolds, K.M. Young and L.J. Arnold, Nucleic Acids Research, 21, 2031-2038, 1993; (b) R.I. Hogrefe, M.A. Reynolds, M.M. Vaghefi, K.M. Young, T.A. Riley, R.E. Klem and L.J. Arnold, Protocols for Oligonucleotides and Analogs, Vol. 20 in the series Methods in Molecular Biology, 143-164, 1993, S. Agrawal, editor, Humana Press Inc., Totowa, NJ.
  3. Oligodeoxynucleoside methylphosphonates–synthesis and enzymatic degradation, S. Agrawal and J. Goodchild, Tetrahedron Lett., 28, 3539-3542, 1987.


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