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The nitrogen atom in place of the methine group at position 6 of the uracil ring in 6-Aza-2'-deoxyuridine (6-aza-dU)(1) results in a significant lowering of the pKa of the N3 hydrogen (6.8) vs. that of 2'-deoxyuridine (9.3).(2) Unlike dU, 6-aza-dU is deprotonated at neutral pH, thus bestowing the uracil base with a negative charge. Further, there are significant conformational changes imparted by the presence of the 6-aza substitution: 6-Aza-dU has a high-anti conformation and is present in solution with N-type sugar pucker.
See also 6-Aza-dU CE-Phopshoramidite (BA0303), the phosphoramidite version for incorporation of 6-aza-dU residues into oligonucleotides, the nucleoside 6-Azathymidine (PYA11058), and its phosphoramidite (BA0306).
- (a) Kara, J.; Sorm, F. Coll. Czech. Chem. Commun. 1963, 28, 1441-1448. (b) Holy, A.; Cech, D. Coll. Czech. Chem. Commun. 1974, 39, 3157-3167. (c) Drasar, P.; Hein, L.; Beranek, J. Coll. Czech. Chem. Commun. 1976, 41, 2110-2123. (d) Freskos, J. N. Nucleosides Nucleotides 1989, 8, 549-555.
- Seela, F.; Chittepu, P. J. Org. Chem. 2007, 72, 4358-4366.