Backbone Modification using Methyl Phosphoramidites

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Applicable Products

2050 Ac-dC-Me Phosphoramidite
2051 iPr-Pac-dG-Me Phosphoramidite
2052 Pac-dA-Me Phosphoramidite
2078 dT-Me Phosphoramidite

Physical & Dilution Data

Unit weights are expressed for the methyl triester form. Dilution volumes (in ml) are for 0.1M solutions in dry acetonitrile (4050) 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

2050 C39H49N4O8P 732.81 303.21 3.41 6.82 13.65
2051 C49H59N6O9P 907.21 343.23 2.76 5.51 11.03
2052 C46H53N6O8P 848.93 327.23 2.94 5.89 11.78
2078 C38H48N3O8P 705.79 318.22 3.54 7.08 14.17

Coupling

No changes are required from the standard method recommended by the synthesiser manufacturer. Coupling is as per standard nucleoside amidites. If the oligo contains many dG residues, use phenoxyacetic anhydride in the Cap Mix A (4210) to avoid the exchange of the iPr-Pac group on the dG with acetate from the acetic anhydride capping mix.

Deprotection

Use UltraMILD deprotection with 0.05M potassium carbonate in methanol to leave the methyl triester intact.1

Storage & Stability

Refrigerate the solids at a maximum of 2-8°C. Stability in solution is 2-3 days.

Reference

  1. See also: T. Atkinson and M. Smith in Oligonucleotide synthesis: a Practical Approach, M.J. Gait (editor), IRL Press Limited, Oxford, 1984, pages 68-70.
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