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The nitrogen atom in place of the methine group at position 6 of the thymine ring in 6-Azathymidine(1) results in a significant lowering of the pKa of the N3 hydrogen (7.0)(2) vs. that of thymidine (10.0). Hence, 6-azathymidine will be significantly deprotonated at neutral pH.
The phosphoramidite of this nucleoside (BA0306) has been incorporated into oligonucleotides,1 where it imparts nuclease resistance when installed at the 5'-position. Duplexes with DNA or RNA are only slightly destabilized, and heteroduplexes with RNA support RNase-H cleavage.
See also the nucleoside 6-Aza-2'-deoxyuridine (PYA11057) and its phosphoramidite (BA0303).
- Sanghvi, Y.; Hoke, G. D.; Freier, S. M.; Zounes, M. C.; Gonzalez, C.; Cummins, L.; Sasmor, H.; Cook, P. D. Nucleic Acids Res. 1993, 21, 3197-3203.
- Seela, F.; Chittepu, P. J. Org. Chem. 2007, 72, 4358-4366.
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