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As compared to dU residues, 6-aza-dU nucleotides are deprotonated at neutral pH, have enhanced 3'-exonuclease stability, and exhibit a high-anti glycosidic bond conformation and N-type sugar pucker.(1) DNA duplexes containing 6-aza-dU-dA base pairs have been studied and are less stable than T-dA base pairs at neutral pH due to deprotonation of the N3 hydrogen on 6-aza-dU. However, at lower pH, duplex stability increases as N3 becomes protonated and therefore able to hydrogen bond to dA. Metal-DNA (M-DNA) complexes are formed at neutral pH rather than at higher pH as is the case for canonical DNA.
See also 6-Aza-dU nucleoside (PYA11057), the nucleoside 6-Azathymidine (PYA11058), and its phosphoramidite (BA0306).
- Seela, F.; Chittepu, P. J. Org. Chem. 2007, 72, 4358-4366.
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