Synthesis of sensitive oligodeoxynucleotides containing acylated cytosine, adenine, and guanine nucleobases

TL;DR

This paper describes a method to synthesize sensitive DNA-like molecules with modified nucleobases, which could help study their properties and therapeutic potential.

Contribution

A new synthetic method for creating DNA with acylated nucleobases that remain stable during deprotection.

Findings

The modified nucleotides 4acC, 6acA, 2acG, and 4mcC remained stable under non-nucleophilic deprotection conditions.

4acC, found in nature, was shown to enhance DNA duplex stability.

The method enables the synthesis of ODNs for studying modified nucleobases in therapeutic contexts like antisense and CRISPR.

Abstract

The synthesis of oligodeoxynucleotides (ODNs) containing the base-labile N6-acetyladenosine (6acA), N2-acetylguanosine (2acG), and N4-methyoxycarbonyldeoxycytidine (4mcC), as well as up to four N4-acetyldeoxycytidine (4acC) modifications is described. The 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) group was used as the linker for solid phase synthesis, and the methyl Dmoc (meDmoc) group was used for the protection of the exo-amino groups of nucleobases. Deprotection and cleavage were achieved under non-nucleophilic conditions, under which the highly sensitive 4acC, 6acA, 2acG, and 4mcC were found completely stable. Among the modified nucleotides, 4acC has been found in nature, and proven beneficial to DNA duplex stability. Although 6acA, 2acG and 4mcC have not been found in nature, a synthetic route to ODNs containing them is expected to facilitate projects aimed at studying their biophysical properties as well as potential for antisense, RNAi, CRISPR, and mRNA therapeutic applications.

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