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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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Sensitive Oligodeoxynucleotide Synthesis Using Dim and Dmoc as Protecting Groups.

Shahien Shahsavari1, Dhananjani N A M Eriyagama1, Jinsen Chen1

  • 1Department of Chemistry , Michigan Technological University , 1400 Townsend Drive , Houghton , Michigan 49931 , United States.

The Journal of Organic Chemistry
|September 20, 2019
PubMed
Summary
This summary is machine-generated.

New Dim-Dmoc protecting groups enable mild deprotection during oligodeoxynucleotide (ODN) synthesis. This novel method allows for the creation of ODNs with sensitive functionalities, overcoming limitations of traditional synthesis techniques.

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Area of Science:

  • Chemical Synthesis
  • Oligonucleotide Chemistry
  • Organic Chemistry

Background:

  • Traditional oligodeoxynucleotide (ODN) synthesis relies on protecting groups like 2-cyanoethyl for phosphates and acyl for amines.
  • Deprotection in traditional ODN synthesis requires harsh conditions using strong bases and nucleophiles.
  • These conditions are incompatible with sensitive functional groups, limiting the scope of synthesizable ODNs.

Purpose of the Study:

  • To develop novel protecting groups for solid-phase ODN synthesis that allow for mild deprotection conditions.
  • To enable the synthesis of oligodeoxynucleotides (ODNs) containing sensitive functional groups.
  • To introduce Dim and Dmoc protecting groups based on the 1,3-dithian-2-yl-methyl function.

Main Methods:

  • Solid-phase synthesis of oligodeoxynucleotides (ODNs) utilizing Dim and Dmoc protecting groups.
  • Mild oxidative deprotection conditions were employed, avoiding strong bases and nucleophiles.
  • Purification via reversed-phase high-performance liquid chromatography (RP HPLC).
  • Characterization using MALDI-TOF MS and enzyme digestion assays.

Main Results:

  • Successful synthesis of seven 20-mer ODNs, including four with sensitive ester and alkyl chloride groups.
  • Demonstration of mild oxidative deprotection using the Dim-Dmoc strategy.
  • Obtained high-purity ODNs confirmed by analytical techniques.
  • Validation of the compatibility of the new method with sensitive functionalities.

Conclusions:

  • The Dim-Dmoc protection strategy offers a mild and effective alternative for ODN synthesis.
  • This technology significantly expands the possibilities for synthesizing modified oligonucleotides.
  • The developed method is suitable for producing high-purity ODNs with sensitive functional groups for various applications.