Chemical methods for the modification of RNA

• Published in: Methods (San Diego, Calif.) Calif.), 2019-05, Vol.161, p.64-82
• Main Authors: Flamme, Marie, McKenzie, Luke K, Sarac, Ivo, Hollenstein, Marcel
• Format: Article
• Language: English
• Subjects: Chemical Sciences; Modified nucleotides; Mutant T7 RNA polymerases; Organic chemistry; Phosphoramidites; Phosphorothioates; RNA aptamers; RNA solid-phase synthesis; SELEX; Sugar-base modifications
• ISSN: 1046-2023; 1095-9130
• DOI: 10.1016/j.ymeth.2019.03.018

•Description of main methods for chemical modification of RNA.•Chemical modification by solid-phase synthesis using phosphoramidites.•Description of existing methods for the synthesis of modified ribonucleotides.•Overview of transcription with modified nucleoside triphosphates.•Utility of these methods for aptamer selections and study of natural RNA modifications. RNA is often considered as being the vector for the transmission of genetic information from DNA to the protein synthesis machinery. However, besides translation RNA participates in a broad variety of fundamental biological roles such as gene expression and regulation, protein synthesis, and even catalysis of chemical reactions. This variety of function combined with intricate three-dimensional structures and the discovery of over 100 chemical modifications in natural RNAs require chemical methods for the modification of RNAs in order to investigate their mechanism, location, and exact biological roles. In addition, numerous RNA-based tools such as ribozymes, aptamers, or therapeutic oligonucleotides require the presence of additional chemical functionalities to strengthen the nucleosidic backbone against degradation or enhance the desired catalytic or binding properties. Herein, the two main methods for the chemical modification of RNA are presented: solid-phase synthesis using phosphoramidite precursors and the enzymatic polymerization of nucleoside triphosphates. The different synthetic and biochemical steps required for each method are carefully described and recent examples of practical applications based on these two methods are discussed.