Synthesis and Purification of N3 -Methylcytidine (m3 C) Modified RNA Oligonucleotides

Johnsi Mathivanan; Jinxi Du; Song Mao; Ya Ying Zheng; Jia Sheng

doi:10.1002/cpz1.307

Synthesis and Purification of N³ -Methylcytidine (m³ C) Modified RNA Oligonucleotides

Curr Protoc. 2021 Nov;1(11):e307. doi: 10.1002/cpz1.307.

Authors

Johnsi Mathivanan¹, Jinxi Du¹, Song Mao¹, Ya Ying Zheng¹, Jia Sheng¹

Affiliation

¹ Department of Chemistry and the RNA Institute, University at Albany, State University of New York, Albany, New York.

PMID: 34792865
DOI: 10.1002/cpz1.307

Abstract

This protocol describes a step-by-step chemical synthesis approach to prepare N³ -methylcytidine (m³ C) and its phosphoramidite. The method for synthesizing m³ C starts from commercially available cytidine, and proceeds via N³ -methylation in the presence of MeI, which generates the N³ -methylcytidine (m³ C) nucleoside, followed by the installation of several protecting groups at sites that include the 5'-hydroxyl group (4,4'-dimethoxytrityl protection), the 4-amino group (benzoyl protection), and the 2'-hydroxyl group (tert-butyldimethylsilyl, TBDMS, protection). Standard phosphoramidite chemistry is applied to prepare the final m³ C phosphoramidite for solid-phase synthesis of a series of RNA oligonucleotides. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of N³ -methylcytidine (m³ C) and its phosphoramidite Basic Protocol 2: Automated synthesis of m³ C modified RNA oligonucleotides.

Keywords: N3-methylcytidine; RNA modification; phosphoramidite; solid-phase synthesis.

MeSH terms

Cytidine
Nucleosides
Oligonucleotides*
RNA*
Solid-Phase Synthesis Techniques

Substances

Nucleosides
Oligonucleotides
Cytidine
RNA