Key featuresShow Hide
- Introduces a carboxylate functionality for conjugation to amines.
- Incorporates a dT nucleobase internally.
- Methyl ester is hydrolysed during deprotection and can be coupled directly to a molecule containing a primary amino group by via a peptide coupling reaction.
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The use of the 5'-carboxylate modifier (BA0012 / LK2057) (1) allows the introduction of a carboxylic acid function at the 5'-end of an oligonucleotide that is available for conjugation to amines whilst still on the solid support. This strategy avoids the problems of low yields, long reaction times and the need for excess reactants often encountered by other post-cleavage solution methods.
The 2'-chlorotrityl protecting group is stable during coupling, capping and oxidation or sulphurisation but is easily removed during the deblock step; typically 3% TCA in DCM. At this stage the 5'-carboxylate oligonucleotide can be cleaved and deprotected or further modified by on-column conjugation. Alternatively the 2-chlorotrityl protection can be retained until after cleavage and deprotection.
If the conjugation step has already been completed, provided the label is stable, most deprotection conditions are applicable. Otherwise it is best to use 0.4 M NaOH in methanol/water (4:1) overnight at room temperature. This will avoid the formation of an amide as would be the case using ammonium hydroxide or AMA deprotection conditions.
Subsequent conjugation of the 5'-carboxylic acid function to a range of primary and secondary aliphatic amines can be achieved through amide bond formation on the solid support. We have demonstrated the flexibility of this modifier through reactions with the diene furfurylamine, an aminocaproic ester spacer and ß-casomorphin-5-amide, the latter providing a simple and expedient synthesis of an oligonucleotide-peptide conjugate.
The analogous 5'-Carboxy-C10 CE-Phosphoramidite product (LK2531) is used in the same way as LK2057, but offers the flexibility of an elongated C10 spacer.
Internal carboxylate functions can be achieved using Carboxy-dT-CE Phosphoramidite (LK2142). The methyl ester is hydrolysed during deprotection and can be coupled directly to a molecule containing a primary amino group by via a peptide coupling reaction.
- A new and efficient method for the synthesis of 5'-conjugates of oligonucleotides through amide-bond formation on solid phase, A.V. Kachalova, D.A. Stetsenko, E.A. Romanova, V.N. Tashlitsky, M.J. Gait and T.S. Oretskaya, Helvetica Chimica Acta, 85, 2409-2416, 2002.