Bicyclononyne (BCN) is a stable and one of the most reactive cyclooctynes for copper-free click chemistry. Unlike dibenzocyclooctyne (DBCO), BCN is reactive both to azides (strain-promoted azyde-alkyne cycloaddition, SPAAC) and tetrazines (inverse electron demand Diels-Alder reaction, IEDDA). Being an endo-stereoisomer, bicyclononine in endo-BCN CE-phosphoramidite provides not significantly different rate of cycloaddition compared to its exo-conformer.
BCN-labeled oligonucleotides may be used for the conjugation to azide- or tetrazine-containing solid surfaces, polymers, and large proteins.
Coupling time is standard, like for amidites of natural nucleosides. Exclude the dimethoxytrityl (DMT) removal step and use the Dmt-ON protocol after amidite coupling and oxidation.
Use standard conditions for deprotection and ammonia solution, or AMA mixture (ammonium hydroxide / 40% methylamine, 1:1).
