Dim and Dmoc Protecting Groups for Oligodeoxynucleotide Synthesis

Shiyue Fang; Dhananjani Eriyagama; Yahong Yuan; Shahien Shahsavari; Junmei Chen; Xi Lin; Bhaskar Halami

doi:10.1002/cpnc.111

journal article Jul 06, 2020

Dim and Dmoc Protecting Groups for Oligodeoxynucleotide Synthesis

Shiyue Fang

Dhananjani Eriyagama Yahong Yuan

Shahien Shahsavari Junmei Chen Xi Lin

Bhaskar Halami

Current Protocols in Nucleic Acid Chemistry Vol. 82 No. 1 · Wiley

View at Publisher Save 10.1002/cpnc.111

Abstract

AbstractThis protocol provides details for the preparation of nucleoside phosphoramidites with 1,3‐dithian‐2‐yl‐methyl (Dim) and 1,3‐dithian‐2‐yl‐methoxycarbonyl (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. © 2020 Wiley Periodicals LLC.Basic Protocol: Synthesis, deprotection, cleavage, and purification of sensitive oligodeoxynucleotidesSupport Protocol 1: Synthesis of Dim‐Dmoc nucleoside phosphoramiditesSupport Protocol 2: Preparation of CPG with a Dmoc linkerSupport Protocol 3: Synthesis of a phosphoramidite containing a sensitive alkyl ester group

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Details

Published: Jul 06, 2020
Vol/Issue: 82(1)
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Authors

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Shiyue Fang