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Updated: Jun 26, 2026

Using Modified Synthetic Oligonucleotides to Assay Nucleic Acid-Metabolizing Enzymes
05:33

Using Modified Synthetic Oligonucleotides to Assay Nucleic Acid-Metabolizing Enzymes

Published on: July 5, 2024

Furan-modified oligonucleotides for fast, high-yielding and site-selective DNA inter-strand cross-linking with

Kristof Stevens1, Annemieke Madder

  • 1Laboratory for Organic and Biomimetic Chemistry, Department of Organic Chemistry, Ghent University, Krijgslaan 281, S4, 9000 Gent, Belgium.

Nucleic Acids Research
|January 20, 2009
PubMed

Insights

Researchers developed a new method to synthesize stable, site-specific DNA inter-strand cross-links (ICLs). This breakthrough enables better study of DNA repair mechanisms and the development of targeted cancer therapies.

Area of Science:

  • Molecular Biology
  • Organic Chemistry
  • Genetics

Background:

  • Inter-strand cross-links (ICLs) are highly cytotoxic DNA lesions that impede essential cellular processes like replication and transcription.
  • Understanding ICL formation and repair is crucial for developing effective anticancer drugs and addressing drug resistance.
  • Stable, site-specific cross-linked DNA duplexes are essential tools for studying ICL repair mechanisms.

Purpose of the Study:

  • To develop a novel method for synthesizing stable, site-specifically cross-linked DNA duplexes.
  • To enable detailed investigation of inter-strand cross-link repair pathways.
  • To provide tools for studying the mechanism of action of ICL-inducing anticancer agents.

Main Methods:

  • Synthesis of DNA duplexes containing a site-specifically incorporated acyclic furan nucleoside.
  • In situ oxidation of the furan moiety to generate a reactive oxo-enal intermediate.
  • Instantaneous reaction of the intermediate with the complementary base on the non-modified strand to form a stable ICL.

Main Results:

  • Successful synthesis of site-specifically cross-linked DNA duplexes with high yields and short reaction times.
  • Demonstrated high selectivity for cross-linking to complementary Adenine (A) or Cytosine (C) bases, without off-target modifications.
  • The synthesized cross-linked duplexes are stable and can be stored for extended periods, facilitating structural and mechanistic studies.

Conclusions:

  • The developed method provides a reliable route to generate site-specific DNA inter-strand cross-links.
  • This technique facilitates the study of DNA damage and repair mechanisms, particularly ICLs.
  • The synthesized cross-linked DNA serves as a valuable tool for cancer research and drug development.

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