Incorporating Halogenated Nucleosides

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Applicable Products

2009 5-I-dC-CE Phosphoramidite
2010 5-F-dU-CE Phosphoramidite
2011 5-Br-dC-CE Phosphoramidite
2012 5-Br-dU-CE Phosphoramidite
2014 5-I-dU-CE Phosphoramidite
2054 8-Br-dA-CE Phosphoramidite
2055 8-Br-dG-CE Phosphoramidite
2325 5-Br-dU SynBase™ CPG 1000/110

Physical & Dilution Data

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

2009 C46H51N5O8PI 959.83 415.08 2.60 5.21 10.42
2010 C39H46N4O8PF 748.79 308.16 3.34 6.68 13.35
2011 C46H51N5O8PBr 912.82 368.08 2.74 5.48 10.96
2012 C39H46N4O8PBr 809.69 369.07 3.09 6.18 12.35
2014 C39H46N4O8PI 856.69 416.07 2.92 5.84 11.67
2054 C43H52N8O6PBr 887.81 392.11 2.82 5.63 11.26
2055 C43H52N8O7PBr 903.90 408.10 2.77 5.53 11.06
2325 - - 369.07 - - -

Coupling

No changes are required from the standard method recommended by the synthesiser manufacturer. Coupling is as per standard nucleoside amidites and supports.

Deprotection

To avoid ammonolysis at the halogenated site, a mild deprotection step is recommended using ammonium hydroxide for 24h at room temperature, or AMA for 2h at room temperature provided dmf-dG and Ac-dC are used. Bz-protected C amidites are not compatible with AMA deprotection.

Storage & Stability

Store the solid phosphoramidites refrigerated, dry, at a maximum of 2-8°C. Store the monomers in solution for no longer than 24h, although 8-Br-dG (2055) and 5-Br-dU (2012) are stable for 2-3 days. Halogenated nucleosides tend to be photosensitive therefore retain the amidites in amber vials.

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