The potential of N(Me)-alkoxyamine glycosylation as a DNA-templated ligation has been studied. On a hairpin stem-template model, a notable rate enhancement and an increased equilibrium yield are observed compared to the corresponding reaction without a DNA catalyst. The N-glycosidic connection is dynamic at pH 5, whereas it becomes irreversible at pH 7. The N(Me)-alkoxyamine glycosylation may hence be an attractive pH controlled reaction for the assembly of DNA-based dynamic products.

DNA-templated formation and N,O-transacetalization of Nmethoxyoxazolidines have been studied. Compared to the reaction without a DNA-catalyst, the hybridization-driven Nmethoxyoxazolidine formation shows a marked rate acceleration, whereas the rate of corresponding N,O-transacetalization is limited by the rate of decay to aldehyde intermediates. In both cases, the equilibrium yield increases markedly on the DNA template. Different hairpin architectures have been studied to evaluate the role and limits of the template effect. Furthermore, an attention has been paid to stereochemical integrity (R/S) of the N-methoxyoxazolidine linkage. The Nmethoxyoxazolidine formation represents a dynamic pH-responsive DNA-templated ligation that occurs readily in slightly acidic conditions (pH 5).

A detailed protocol for preparation 3′‐glycoconjugated oligonucleotides is described based on one‐pot immobilization of 4,4′‐dimethoxytrityl‐protected carbohydrates to a solid support followed by on‐support peracetylation and automated oligonucleotide assembly. Compared to an appropriate building block approach and post‐synthetic manipulation of oligonucleotides, this protocol may simplify the synthesis scheme and increase overall yield of the conjugates. Furthermore, the immobilization to a solid support typically increases the stability of reactants, enabling prolonged storage, and makes subsequent processing convenient. Automated assembly on these carbohydrate‐modified supports using conventional phosphoramidite chemistry produces 3′‐glycoconjugated oligonucleotides in relatively high yield and purity. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 1‐O‐tert‐butyldimethylsilyl‐6‐O‐(4,4′‐dimethoxytrityl)‐β‐D‐glucose Basic Protocol 2: Synthesis of 6‐O‐dimethoxytrityl‐2,3,1′,3′,4′,6′‐hexa‐O‐benzoylsucrose Basic Protocol 3: Synthesis of 6″‐O‐dimethoxytrityl‐N‐trifluoroacetyl‐protected aminoglycosides Basic Protocol 4: Synthesis of 3‐O‐dimethoxytrityl‐propyl β‐D‐galactopyranoside Basic Protocol 5: Synthesis of trivalent N‐acetyl galactosamine cluster Basic Protocol 6: Synthesis of carbohydrate monosuccinates and their immobilization to a solid support Basic Protocol 7: Oligonucleotide synthesis using immobilized carbohydrates