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Dim and Dmoc Protecting Groups for Oligodeoxynucleotide Synthesis.
Curr Protoc Nucleic Acid Chem. 2020 Sep; 82(1):e111.CP

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.

Authors+Show Affiliations

Department of Chemistry, Michigan Technological University, Houghton, Michigan.Department of Chemistry, Michigan Technological University, Houghton, Michigan.College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan.Department of Chemistry, Michigan Technological University, Houghton, Michigan.Department of Chemistry, Michigan Technological University, Houghton, Michigan.Department of Chemistry, Michigan Technological University, Houghton, Michigan.Department of Chemistry, Michigan Technological University, Houghton, Michigan.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32628352

Citation

Fang, Shiyue, et al. "Dim and Dmoc Protecting Groups for Oligodeoxynucleotide Synthesis." Current Protocols in Nucleic Acid Chemistry, vol. 82, no. 1, 2020, pp. e111.
Fang S, Eriyagama D, Yuan Y, et al. Dim and Dmoc Protecting Groups for Oligodeoxynucleotide Synthesis. Curr Protoc Nucleic Acid Chem. 2020;82(1):e111.
Fang, S., Eriyagama, D., Yuan, Y., Shahsavari, S., Chen, J., Lin, X., & Halami, B. (2020). Dim and Dmoc Protecting Groups for Oligodeoxynucleotide Synthesis. Current Protocols in Nucleic Acid Chemistry, 82(1), e111. https://doi.org/10.1002/cpnc.111
Fang S, et al. Dim and Dmoc Protecting Groups for Oligodeoxynucleotide Synthesis. Curr Protoc Nucleic Acid Chem. 2020;82(1):e111. PubMed PMID: 32628352.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Dim and Dmoc Protecting Groups for Oligodeoxynucleotide Synthesis. AU - Fang,Shiyue, AU - Eriyagama,Dhananjani, AU - Yuan,Yinan, AU - Shahsavari,Shahien, AU - Chen,Jinsen, AU - Lin,Xi, AU - Halami,Bhaskar, PY - 2020/7/7/entrez PY - 2020/7/7/pubmed PY - 2020/7/7/medline KW - base-labile KW - oligodeoxynucleotide KW - protecting group KW - sensitive KW - solid phase synthesis SP - e111 EP - e111 JF - Current protocols in nucleic acid chemistry JO - Curr Protoc Nucleic Acid Chem VL - 82 IS - 1 N2 - 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. SN - 1934-9289 UR - https://www.unboundmedicine.com/medline/citation/32628352/Dim_and_Dmoc_Protecting_Groups_for_Oligodeoxynucleotide_Synthesis L2 - https://doi.org/10.1002/cpnc.111 DB - PRIME DP - Unbound Medicine ER -
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