DNA-Templated N(Me)-Alkoxyamine Glycosylation

Abstract

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.

Conjugation of Oligonucleotides to Peptide Aldehydes via a pH-Responsive N-Methoxyoxazolidine Linker

“…It has been applied to the synthesis of various carbohydrate conjugates, − due to its orthogonality and good isosteric similarity to native glycan structures. However, the equilibrium constant of this reaction is relatively small (in aqueous solution <100 L mol –1 , pH <6). , Upon application of this same alkoxyamine-promoted acid-catalyzed O,N-acetalization to form a five-membered oxaozolidine ring, − the equilibrium constant may increase with the same favorable pH profile of the reaction. To verify this hypothesis, the reaction with small molecular models was first studied.…”

Immobilized Carbohydrates for Preparation of 3′‐Glycoconjugated Oligonucleotides

“…In fact, this is the approach pharma companies would prefer, as chemically fine‐tuned libraries of the same active oligonucleotide sequence can be readily synthesized. In the current protocol (originally described in Kiviniemi & Virta, 2011; Österlund et al., 2018), six different carbohydrates are immobilized to a solid support and used for automated oligonucleotide assembly to produce 3′‐glycoconjugated oligonucleotides. A random immobilization of carbohydrates (as polyols) to a solid support via a succinyl linker may be applied.…”

“…Therefore, the building block approach may be inefficient in some cases, and even pointless if the conjugation site is in the 3′ terminus of the oligonucleotide sequence. This protocol, based on previously published work (Kiviniemi & Virta, 2011; Österlund, Korhonen, & Virta, 2018), describes an alternative approach for preparation 3′‐glycoconjugated oligonucleotides using one‐pot immobilization of 4,4′‐dimethoxytrityl‐protected carbohydrates as polyols on a solid support, followed by on‐support peracetylation and automated assembly of oligonucleotides on the carbohydrate‐modified solid supports. Detailed procedures for preparation of supports modified by galactose, glucose, sucrose, ribostamycin, neomycin B (mono‐, di‐, tri‐, and tetrasaccharides; the latter two are aminoglycosides) and one trivalent N ‐acetylgalactosamine, cluster are described (see Basic Protocols 1‐6), followed by preparation of the corresponding oligonucleotides (see Basic Protocol 7).…”

DNA‐Templated Formation and N,O‐Transacetalization of N‐Methoxyoxazolidines

“…The former reaction is irreversibly reduced to stable alkylamine products, whereas the boronic acid ligation is pH‐responsive, occurring in slightly basic conditions. We have evaluated the potential of N‐ (methyl)oxyamine glycosylation (i. e. neoglycosylation) as a dynamic DNA‐templated ligation [8] . This reaction occurs between sugar hemiacetals and N ‐alkyl alkoxyamines, it is bioorthogonal, reversible in slightly acidic conditions, can be halted by a mild pH change (pH>7), and a notable rate enhancement may be observed on a DNA‐template.…”

“…We have evaluated the potential of N-(methyl)oxyamine glycosylation (i. e. neoglycosylation) as a dynamic DNA-templated ligation. [8] This reaction occurs between sugar hemiacetals and N-alkyl alkoxyamines, it is bioorthogonal, reversible in slightly acidic conditions, can be halted by a mild pH change (pH > 7), and a notable rate enhancement may be observed on a DNAtemplate. Motivated by the same acid catalyzed N,O-acetalization, we recently introduced N-methoxyoxazolidine formation as a credible biorthogonal conjugation chemistry for oligonucleotides.…”