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The Influence of Single-Stranded or Double-Stranded DNA Tags on Ligand Binding Affinity in DNA-Encoded Libraries.

Philipp Bittner1, Andreas Gloger2, Julian A Harrison1

  • 1Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland.

Analytical Chemistry
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Summary
This summary is machine-generated.

DNA-encoded libraries are crucial for drug discovery. This study reveals that DNA tag structure significantly impacts compound binding affinity, with single-stranded DNA tags showing a synergistic binding effect.

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Area of Science:

  • Biochemistry
  • Drug Discovery
  • Molecular Biology

Background:

  • DNA-encoded libraries (DELs) are a powerful tool in drug discovery.
  • Various DNA tag formats (single-stranded, double-stranded) and linker chemistries exist.
  • Previous work noted binding affinity differences between DNA tag formats, but the molecular basis was unclear.

Purpose of the Study:

  • To investigate the impact of DNA tags on protein-ligand binding performance in DELs.
  • To elucidate the molecular basis for observed differences in binding affinities.
  • To assess the influence of DNA tag structure on binding dynamics.

Main Methods:

  • Utilized native ion mobility mass spectrometry.
  • Incorporated gas- and solution-phase activation techniques.
  • Systematically analyzed protein-ligand interactions with different DNA tags.

Main Results:

  • Binding affinity of DNA-coupled compounds is strongly influenced by the DNA tag setup.
  • Differences in binding affinities correlated with thermal stability of On-DNA protein-ligand complexes.
  • A synergistic binding effect was exclusively observed for ligands coupled to single-stranded DNA across various systems.

Conclusions:

  • The DNA tag format critically affects binding affinity in DELs.
  • Mass spectrometry can elucidate how DNA tags impact binding dynamics.
  • Understanding these effects is essential for optimizing screening and hit validation in DEL technology.