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Updated: Dec 13, 2025

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC Crosslinking of Small Molecules to Isolate Chromatin
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Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC Crosslinking of Small Molecules to Isolate Chromatin

Published on: January 20, 2016

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Discrimination between G/C Binding Sites by Olivomycin A Is Determined by Kinetics of the Drug-DNA Interaction

Artemy D Beniaminov1, Galina V Chashchina1, Mikhail A Livshits1

  • 1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia.

International Journal of Molecular Sciences
|July 30, 2020
PubMed

Insights

Olivomycin A (OA) binds G/C-rich DNA, but its sequence preference was unclear. Kinetic analysis revealed differing dissociation rates, explaining its DNA interaction mechanism and aiding new drug screening.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Drug Discovery

Background:

  • Olivomycin A (OA) is a cytotoxic drug that targets G/C-rich DNA sequences.
  • Its mechanism involves binding to the minor groove, interfering with DNA replication and transcription.

Purpose of the Study:

  • To investigate the sequence specificity of Olivomycin A binding to G/C-rich DNA.
  • To resolve discrepancies between equilibrium binding studies and electrophoretic mobility gel shift assays (EMSA).

Main Methods:

  • Electrophoretic mobility gel shift assay (EMSA) to screen G/C tetranucleotide sites.
  • Solution binding studies using fluorescence, circular dichroism, and isothermal titration calorimetry.
  • Kinetic analysis of drug-DNA interactions, focusing on dissociation rates.
  • In vitro transcription assays to assess functional relevance.

Main Results:

  • EMSA suggested sequence preference for OA binding at G/C sites with central GC or GG dinucleotides, but not CG.
  • Equilibrium binding studies showed similar affinities for all G/C sites, contradicting EMSA findings.
  • Kinetic analysis revealed significant differences in dissociation rates of OA from various G/C sites, resolving the discrepancy.
  • Differential kinetics correlated with functional outcomes in in vitro transcription.

Conclusions:

  • The kinetics of Olivomycin A-DNA interaction, specifically dissociation rates, are crucial for its mechanism of action.
  • Kinetic analysis provides a vital approach for screening and understanding new drug candidates targeting DNA.
Keywords:
DNA bindingOlivomycin Akineticssequence specificity

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