Selective functionalization at N<sup>2</sup>-position of guanine in oligonucleotides <i>via</i> reductive amination

Bhoge, Bapurao A.; Mala, Purnima; Kurian, Jo Sony; Srinivasan, Varadharajan; Saraogi, Ishu

doi:10.1039/d0cc05492e

Cited by 13 publications

(8 citation statements)

References 40 publications

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“…The position at N 2 was chosen because guanine can be naturally modified at N 2 , [25] and it has prevously been shown that N 2 modifications do not hinder enzymatic digestion. [26] The modifed G35 nucleoside was then linked to Lac azide or alternatively to Neu5Ac-Lac azide via copper promoted azide-alkyne cycloaddition, leading to their respective conjugates (Y5 RNA-Lac and Y5 RNA-Neu5Ac-Lac) (Scheme 1). Using a denaturing gel, a clear shift was observed after conjugation of the Lac and Neu5AcLac (Figure 1 Panel A).…”

Section: Conjugation Of Glycans To Synthetic Y5 Rna and Chemical Anal...mentioning

confidence: 99%

Identification of glycosylated nucleosides in small synthetic glyco‐RNAs

Michael,

Hamouda,

Stupak

et al. 2024

ChemBioChem

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Recently, the post‐transcriptional modification of RNA with N‐glycans was reported, changing the paradigm that RNAs are not commonly N‐glycosylated. Moreover, glycan modifications of RNA are investigated for therapeutic targeting purposes. But the glycoRNA field is in its infancy with many challenges to overcome. One question is how to accurately characterize glycosylated RNA constructs. Thus, we generated glycosylated forms of Y5 RNA mimics, a short non‐coding RNA. The simple glycans lactose and sialyllactose were attached to the RNA backbone using azide‐alkyne cycloadditions. Using nuclease digestion followed by LC‐MS, we confirmed the presence of the glycosylated nucleosides, and characterized the chemical linkage. Next, we probed if glycosylation would affect the cellular response to Y5 RNA. We treated human foreskin fibroblasts in culture with the generated compounds. Key transcripts in the innate immune response were quantified by RT‐qPCR. We found that under our experimental conditions, exposure of cells to the Y5 RNA did not trigger an interferon response, and glycosylation of this RNA did not have an impact. Thus, we have identified a successful approach to chemically characterize synthetic glyco‐RNAs, which will be critical for further studies to elucidate how the presence of complex glycans on RNA affects the cellular response.

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Section: Conjugation Of Glycans To Synthetic Y5 Rna and Chemical Anal...mentioning

confidence: 99%

Identification of glycosylated nucleosides in small synthetic glyco‐RNAs

Michael,

Hamouda,

Stupak

et al. 2024

ChemBioChem

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“…This mild reducing agent selectively reduces imines over unreacted aldehydes at pH 6. [20] NaBH 3 CN was used for a variety of chemical reductions especially for bioconjugation. [21] For the reaction in presence of a template strand, the complementary sequence to ODN1 contained a natural nucleobase opposite to the amino site (T C , T G , T A , T T : 5'-CGCTATY-TATCGC, where Y=C, G, A, T; Table 1).…”

Section: Chembiochemmentioning

confidence: 99%

Template‐Directed Incorporation of Functional Molecules into DNA

Kanlidere

2023

ChemBioChem

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We report a versatile method for the incorporation of functional molecules into oligonucleotides carrying reactive groups by using a template-directed postsynthetic approach in the solution phase. For this purpose, we prepared oligonucleotides carrying an amino group on the backbone by using an acylic threoninol scaffold. The resulting oligonucleotides could be used to introduce almost any molecule carrying aldehyde, which can be, among other things, a metal-binding ligand or a fluorophore. In our study, we incorporated aldehyde-bearing phenanthroline, a metal-binding ligand, into oligonucleotides by template-directed reversible conjugation. We observed that the use of an abasic sugar site instead of a natural nucleobase in the template strand increased the yield of conjugation and induced selective incorporation of the phenanthroline. This method could lead progress in the development of probes for the recognition of abasic regions in duplex DNA. Moreover, template-directed formation of metal ligand-oligonucleotide conjugates might have potential applications in hybrid biocatalysis for enantioselective transformations.

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“…The overall method involves protection at the N 9 position of the guanine, alkylation at the N 2 position, and then deprotection to afford the corresponding N 2 ‐alkylguanine. The most reliable method for the synthesis of N 2 ‐ alkyl guanosine involves the condensation between the exocyclic amine of guanosine and the aldehyde, followed by sodium cyanoborohydride reduction (Sako et al., 1999; Bhoge et al., 2020). In addition to the use of sodium cyanoborohydride, sodium borohydride was used as a reducing agent for the reaction between guanosine and the aldehyde to afford the corresponding N 2 ‐ alkyl guanosine (Kemal & Reese, 1980).…”

Section: Commentarymentioning

confidence: 99%

Protocols for Efficient Chemical Synthesis of N²‐Modified Guanosine Phosphate Derivatives: Versatile Probes for mRNA Labeling

Senthilvelan,

Shanmugasundaram,

Kore

2023

Current Protocols

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A facile, reliable, and efficient method for the synthesis of N2‐modified guanosine nucleotides such as N2‐[benzyl‐N‐(propyl)carbamate]‐guanosine‐5′‐O‐monophosphate, N2‐[benzyl‐N‐(propyl)carbamate]‐guanosine‐5′‐O‐diphosphate, N2‐[benzyl‐N‐(propyl)carbamate]‐guanosine‐5′‐O‐triphosphate, and N2‐[benzyl‐N‐(propyl)carbamate]‐N7‐methyl‐guanosine‐5′‐O‐diphosphate, starting from the corresponding nucleotide is described. The general process entails condensation between the exocyclic amine of guanosine nucleotide and 3‐[(benzyloxycarbonyl)amino]propionaldehyde in aqueous methanol, followed by reduction using sodium cyanoborohydride to furnish the corresponding N2‐modified guanosine nucleotide in moderate yield with high purity (>99.5%). © 2023 Wiley Periodicals LLC.Basic Protocol: Synthesis of N2‐modified guanosine derivatives

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Selective functionalization at N²-position of guanine in oligonucleotides via reductive amination

Abstract: Chemo- and site-specific modifications in oligonucleotides have wide applicability as mechanistic probes in chemical biology. However, methods that label specific sites in nucleic acids are scarce, especially for labeling DNA/RNA...

Cited by 13 publications

References 40 publications

Identification of glycosylated nucleosides in small synthetic glyco‐RNAs

Identification of glycosylated nucleosides in small synthetic glyco‐RNAs

Template‐Directed Incorporation of Functional Molecules into DNA

Protocols for Efficient Chemical Synthesis of N²‐Modified Guanosine Phosphate Derivatives: Versatile Probes for mRNA Labeling

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Selective functionalization at N2-position of guanine in oligonucleotides via reductive amination

Abstract: Chemo- and site-specific modifications in oligonucleotides have wide applicability as mechanistic probes in chemical biology. However, methods that label specific sites in nucleic acids are scarce, especially for labeling DNA/RNA...

Cited by 13 publications

References 40 publications

Identification of glycosylated nucleosides in small synthetic glyco‐RNAs

Identification of glycosylated nucleosides in small synthetic glyco‐RNAs

Template‐Directed Incorporation of Functional Molecules into DNA

Protocols for Efficient Chemical Synthesis of N2‐Modified Guanosine Phosphate Derivatives: Versatile Probes for mRNA Labeling

Contact Info

Product

Resources

About

Selective functionalization at N²-position of guanine in oligonucleotides via reductive amination

Protocols for Efficient Chemical Synthesis of N²‐Modified Guanosine Phosphate Derivatives: Versatile Probes for mRNA Labeling