Oligonucleotide synthesis involving deprotection of amidine-type protecting groups for nucleobases under acidic conditions

Oligonucleotide Synthesis on Porous Glass Resins Containing Activators

For the advancement of nucleic acid-related research, high-efficiency, low-cost synthesis of high-purity oligonucleotides is necessary. Herein, we introduced hydroxybenzotriazole (HOBt) activators on controlled pore glass resins to improve the efficiency of chain elongation (the synthesis efficiency increased from 48% without an activator to 92% with an activator). In particular, the use of the resin containing 6-trifluoromethyl HOBt with a linker of lauric acid and succinic acid significantly improved the synthesis efficiency for both DNA and RNA syntheses.

Nucleobase Protection of Deoxyribo- and Ribonucleosides

Oligonucleotides carrying a variety of chemical modifications including conjugates are finding increasing applications in therapeutics, diagnostics, functional genomics, proteomics, and as research tools in chemical and molecular biology. The successful synthesis of oligonucleotides primarily depends on the use of appropriately protected nucleoside building blocks including the exocyclic amino groups of the nucleobases, the hydroxyl groups at the 2'-, 3'-, and 5'-positions of the sugar moieties, and the internucleotide phospho-linkage. This unit is a thoroughly revised update of the previously published version and describes the recent development of various protecting groups that facilitate reliable oligonucleotide synthesis. In addition, various protecting groups for the imide/lactam function of thymine/uracil and guanine, respectively, are described to prevent irreversible nucleobase modifications that may occur in the presence of reagents used in oligonucleotide synthesis. © 2017 by John Wiley & Sons, Inc.

FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA

N⁶-methyladenosine (m⁶A) is a prevalent internal modification in mRNA and non- coding RNA affecting various cellular pathways. Here we report the discovery of two additional modifications, N⁶-hydroxymethyladenosine (hm⁶A) and N⁶- formyladenosine (f⁶A), in mammalian mRNA. We show that Fe^II- and α-ketoglutarate (α-KG)-dependent fat mass and obesity associated (FTO) protein oxidizes m⁶A to generates hm⁶A as an intermediate modification and f⁶A as a further oxidized product. hm⁶A and f⁶A have half-life times of ~3 h in aqueous solution under physiological relevant conditions, and are present in isolated mRNA from human cells as well as mouse tissues. These previously unknown modifications derived from the prevalent m⁶A in mRNA, formed through oxidative RNA demethylation, may dynamically modulate RNA-protein interactions to affect gene expression regulation.

[Protection of 2'-hydroxyls in the chemical synthesis of oligoribonucleotides]

The review is devoted to the chemical synthesis of oligoribonucleotides and the protecting groups used. In particular the existent methods of blocking 2'-OH function in nucleotide monomers for the RNA synthesis are discussed in detail.

Utilization of natural sunlight and air in the aerobic oxidation of benzyl halides

A novel, efficient oxidation of α-aryl halogen derivatives to the corresponding α-aryl carbonyl compounds at room temperature has been disclosed. Natural sunlight and air are successfully utilized in this approach through the combination of photocatalysis and organocatalysis. A plausible mechanism was proposed on the basis of the mechanistic studies.