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This lesson delves into the concept of protection and deprotection of a functional group fundamental to synthetic organic chemistry. These phenomena are explained in the context of aliphatic and aromatic alcohols.
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Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-O-thiophenylmethyl Modification and Characterization via Circular Dichroism
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Dim and Dmoc Protecting Groups for Oligodeoxynucleotide Synthesis.

Shiyue Fang1, Dhananjani Eriyagama1, Yinan Yuan2

  • 1Department of Chemistry, Michigan Technological University, Houghton, Michigan.

Current Protocols in Nucleic Acid Chemistry
|July 7, 2020
PubMed
Summary

This study introduces Dim-Dmoc phosphoramidites and a Dmoc linker for synthesizing sensitive oligodeoxynucleotides (ODNs). This novel method allows for mild deprotection and cleavage, preserving delicate functional groups during ODN synthesis.

Keywords:
base-labileoligodeoxynucleotideprotecting groupsensitivesolid phase synthesis

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Area of Science:

  • Organic Chemistry
  • Biochemistry
  • Molecular Biology

Background:

  • Traditional oligodeoxynucleotide (ODN) synthesis employs harsh deprotection conditions incompatible with sensitive functional groups.
  • Existing methods limit the incorporation of modified nucleobases and functionalized ODNs.

Purpose of the Study:

  • To develop a novel phosphoramidite chemistry for synthesizing ODNs with sensitive functional groups.
  • To establish mild deprotection and cleavage conditions compatible with various labile moieties.

Main Methods:

  • Preparation of nucleoside phosphoramidites utilizing 1,3-dithian-2-yl-methyl (Dim) and 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) protecting groups.
  • Solid-phase synthesis of ODNs using a Dmoc-cleavable linker and Dim-Dmoc phosphoramidites.
  • Mild deprotection and cleavage involving sodium periodate oxidation and subsequent aniline treatment.

Main Results:

  • Successful synthesis of sensitive ODNs using the Dim-Dmoc strategy under modified phosphoramidite chemistry conditions.
  • Demonstration of mild deprotection and cleavage preserving sensitive functional groups like esters, thioesters, and halides.
  • Compatibility of the method with various sensitive moieties that are degraded by conventional ODN synthesis techniques.

Conclusions:

  • The Dim-Dmoc ODN synthesis technology provides a robust platform for creating modified ODNs with sensitive functional groups.
  • This approach expands the scope of ODN synthesis, enabling the creation of novel nucleic acid-based therapeutics and research tools.
  • The developed protocol is expected to significantly advance the field of synthetic oligonucleotides.