Shiyue Fang, Dhananjani Eriyagama, Yinan Yuan, Shahien Shahsavari, Jinsen Chen, Xi Lin, Bhaskar Halami
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Abstract
This 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 oligodeoxynucleotides
Support Protocol 1 : Synthesis of Dim-Dmoc nucleoside phosphoramidites
Support Protocol 2 : Preparation of CPG with a Dmoc linker
Support Protocol 3 : Synthesis of a phosphoramidite containing a sensitive alkyl ester group
低聚脱氧核苷酸合成中的Dim和Dmoc保护基团
该方案详细介绍了以1,3-二硫代-2-基甲基(Dim)和1,3-二硫代-2-基甲氧羰基(Dmoc)为保护基团的核苷磷酰胺的制备,以及以Dmoc为可切割功能的连接体,然后将它们用于固相合成敏感的寡脱氧核苷酸(odn)。使用这些Dim-Dmoc磷酰胺和Dmoc连接剂,可以在典型的磷酰胺化学条件下进行轻微修饰合成ODN,并且可以在温和的条件下进行ODN的脱保护和裂解,即在pH为4的高酸钠氧化,然后在pH为8的苯胺氧化。在温和的脱保护和裂解条件下,许多敏感官能团(包括但不限于酯类、硫酯类、烷基卤化物、n -芳基酰胺和α-氯酰胺)可以在典型ODN合成技术中不能在碱性和亲核脱保护和裂解条件下存活,如浓氢氧化铵和稀甲氧基钾。因此,Dim-Dmoc ODN合成技术有望在含有广泛敏感官能团的ODN合成中得到应用。©2020 Wiley期刊有限责任公司基本方案:合成,去保护,裂解和纯化敏感的寡脱氧核苷酸支持方案1:合成Dim-Dmoc核苷磷酸酯支持方案2:用Dmoc连接剂制备CPG支持方案3:合成含有敏感烷基酯基团的磷酸酰胺
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