Carbodiimides phosphate groups

Figure 1.72 Cystamine may be used to label phosphate groups, such as at the 5 -end of oligonucleotides, via a carbodiimide reaction using EDC. The resultant phosphoramidate linkage is a common way to modify oligonucleotides at the 5 -end.

DNA or RNA also may be modified with cystamine at the 5 -phosphate group using a carbodiimide reaction. See Chapter 27, Section 2.2 for a complete discussion of the labeling protocol. 

Figure 1.97 Phosphate groups may be modified to possess amines by a carbodiimide reaction in the presence of a diamine.

Molecules containing phosphate groups, such as the 5 phosphate of oligonucleotides, also may be conjugated to amine-containing molecules by using a carbodiimide-mediated reaction (Chapter 27, Section 2.1). The carbodiimide activates the phosphate to an intermediate phosphate ester similar to its reaction with carboxylates (Chapter 3, Section 1). In the presence of an amine, the ester reacts to form a stable phosphoramidate bond (Reaction 13). 

Phosphate-containing carbohydrates that are stable, such as the 5 -phosphate of the ribose derivatives of oligonucleotides, may be targeted for modification using a carbodiimide-facilitated reaction (Section 4.3). The water-soluble carbodiimide EDC can react with the phosphate groups to form highly reactive phospho-ester intermediates. These intermediates can react with amine- or hydrazide-containing molecules to form stable phosphoramidate bonds. 

Carbodiimide-method The partially positively charged carbon atom in carbodiimides rapidly reacts with the partially negatively charged oxygen in the S -phosphate group forming an active phosphodiester. This... 

Deoxyribonucleosides also lack both the adjacent hydroxyls and free phosphate group in this case, the 5 -hydroxyl has been oxidized to a carboxyl group, which is then linked to a synthetic polypeptide carrier with a water-soluble carbodiimide. This procedure has been described in this series (see Vol. 12B [175]). Two other procedures have been used less ex-... 

A d(5 -CCGp)—the 5 end of the trinucleotide is protected as the methyl ester, while the 3 end carries a phosphate group activated by the condensation agent (a carbodiimide). 

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