Dim and Dmoc Protecting Groups for Oligodeoxynucleotide Synthesis

Abstract

This protocol provides details for the preparation of nucleoside phosphoramidites with 1,3-dithian-2-yl-methyl (Dim) and 1,3-dithian-2-ylmethoxycarbonyl (Dmoc) as protecting groups, and a linker with Dmoc as the cleavable function, then using them for solid phase synthesis of sensitive oligodeoxynucleotides (ODNs). Using these Dim-Dmoc phosphoramidites and Dmoc linker, ODN synthesis can be achieved under typical conditions using phosphoramidite chemistry with slight modifications, and ODN deprotection and cleavage can be achieved under mild conditions involving oxidation with sodium periodate at pH 4 followed by aniline at pH 8. Under the mild deprotection and cleavage conditions, many sensitive functional groups including but not limited to esters, thioesters, alkyl halides, N-aryl amides, and α-chloroamides-which cannot survive the basic and nucleophilic deprotection and cleavage conditions such as concentrated ammonium hydroxide and dilute potassium methoxide used in typical ODN synthesis technologies-can survive. Thus, it is expected that the Dim-Dmoc ODN synthesis technology will find applications in the synthesis of ODNs that contain a wide range of sensitive functional groups.

Oligonucleotide synthesis under mild deprotection conditions

“…The sensitive groups tested included alkyl ester, aryl ester, thioester, alkyl halide, α-halo amide and chloropurine. 7,9–11,13 It should be reasonable to believe that these groups should survive the conditions used here for the deprotection of aDim and aDmoc groups because the conditions are the same. In the current study, we decided to test if N 4 -acetyldeoxycytidine could survive the deprotection and cleavage conditions.…”

“…10 Later, we tested the used of Dim for phosphate protection and Dmoc for amino protection. 11 The ODNs synthesized can be represented by 1c (Scheme 1). Deprotection and cleavage were achieved in two steps by oxidation with sodium periodate followed by excess aniline.…”

Advances in the mechanisms and applications of inhibitory oligodeoxynucleotides against immune-mediated inflammatory diseases

“…The novel chemical modification can resist the degradation of nuclease and peptidase, improving the nuclease stability, target affinity and pharmacokinetic characteristics of inhibitory ODNs ( Araie et al, 2021 ). Chemical modifications carried out over the past decades have given inhibitory ODNs greater specificity and the ability to function more stably, reliably and safely ( Fang et al, 2020 ).…”

aDim-aDmoc Protection for ODN Synthesis Allows Deprotection under Non-nucleophilic and Nearly Neutral Conditions

“…[17] Later, we tested the used of Dim for phosphate protection and Dmoc for amino protection. [20][21] The ODNs synthesized can be represented by 1c (Scheme 1). Deprotection and cleavage were achieved in two steps by oxidation with sodium periodate followed by excess aniline.…”