Automated Synthesis and Purification of Guanidine-Backbone Oligonucleotides

Kacper Skakuj, Katherine E. Bujold, Chad A. Mirkin*

*Corresponding author for this work

Research output: Contribution to journalArticle

Abstract

This protocol describes a method based on iodine and a base as mild coupling reagents to synthetize deoxyribonucleic guanidines (DNGs)—oligodeoxynucleotide analogues with a guanidine backbone. DNGs display unique properties, such as high cellular uptake with low toxicity and increased stability against nuclease degradation, but have been impeded in their development by the requirement for toxic and iterative manual synthesis protocols. The novel synthesis method reported here eliminates the need for the toxic mercuric chloride and pungent thiophenol that were critical to previous DNG synthesis methods and translates their synthesis to a MerMadeTM 12 automated oligonucleotide synthesizer. This method can be used to synthesize DNG strands up to 20 bases in length, along with 5′-DNG-DNA-3′ chimeras, at 1- to 5-μmol scales in a fully automated manner. We also present detailed and accessible instructions to adapt the MerMadeTM 12 oligonucleotide synthesizer to enable the parallel synthesis of DNG and DNA/RNA oligonucleotides. Because DNG linkages alter the overall charge of the oligonucleotides, we also describe purification strategies to generate oligonucleotides with varying lengths and numbers of DNGs, based on extraction or preparative-scale gel electrophoresis, along with methods to characterize the final products. Overall, this article provides an overview of the synthesis, purification, and handling of DNGs and mixed-charge DNG-DNA oligonucleotides.

Original languageEnglish (US)
Article numbere110
JournalCurrent Protocols in Nucleic Acid Chemistry
Volume81
Issue number1
DOIs
StatePublished - Jun 1 2020

Keywords

  • automated oligonucleotide synthesis
  • deoxynucleic guanidines (DNG)
  • oligonucleotide backbone modifications
  • positively charged oligonucleotides

ASJC Scopus subject areas

  • Biochemistry
  • Organic Chemistry

Fingerprint Dive into the research topics of 'Automated Synthesis and Purification of Guanidine-Backbone Oligonucleotides'. Together they form a unique fingerprint.

  • Cite this