Novel cyanine dye as competitive ligand for probing the drug–nucleic acid interactions

  • O. Zhytniakivska Department of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University, 4 Svobody Sq., Kharkiv, 61022, Ukraine
  • U. Tarabara Department of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University, 4 Svobody Sq., Kharkiv, 61022, Ukraine
  • A. Kurutos Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 9 Acad. G. Bonchev Blvd., Sofia, 1113, Bulgaria
  • A. Zabrudska Department of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University, 4 Svobody Sq., Kharkiv, 61022, Ukraine
  • K. Vus Department of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University, 4 Svobody Sq., Kharkiv, 61022, Ukraine
  • V. Trusova Department of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University, 4 Svobody Sq., Kharkiv, 61022, Ukraine
  • G. Gorbenko Department of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University, 4 Svobody Sq., Kharkiv, 61022, Ukraine
  • T. Deligeorgiev Faculty of Chemistry and Pharmacy, Sofia University “St. Kliment Ohridski” 1 J. Bourchier Blvd., Sofia, 1164, Bulgaria
Keywords: trimethine cyanine dye, europium coordination complexes, RNA, DNA, antitumor drug, association constant


Background: During the past decades, increasing attention has been given to elucidating the molecular details of interactions between the pharmacological agents and nucleic acids since the drug–DNA complexation may lead to impairment of DNA replication, strand breaking and mutations. A variety of techniques have been developed to characterize the drug-nucleic acid binding, among which the fluorescence dye displacement assay is one of the most informative approaches. Recently, it was demonstrated that cyanine dyes can be successfully employed for the high throughput screening of the interactions between nucleic acids and drugs. To the best of our knowledge, so far, the potential application of cyanine dyes for the drug-displacement studies remains insufficiently evaluated.

Objectives: The aim of the present study was to investigate the ability of a novel cyanine dye to serve as a competitor for the potential antitumor compounds, lanthanide complexes bearing europium (III) tris-β-diketonate (EC) for the DNA and RNA binding sites.

Materials and methods: Calf thymus DNA, yeast RNA, trimethine cyanine dye and lanthanide complexes bearing europium (III) tris-β-diketonate were used for sample preparation. The fluorescence data were acquired using Perkin-Elmer LS-55 spectrofluorimeter.

Results: Using the fluorescence spectroscopy technique we conducted the displacement reaction trimethine cyanine dye/europium coordination complexes in the presence of double stranded DNA and single-stranded RNA. An increase of the EC concentration in the systems AK3-5/DNA or AK3-5/RNA was followed by a gradual reduction in the AK3-5 fluorescence intensity, indicating that europium (III) tris-β-diketonate compounds can serve as competitors for the trimethine cyanine dye on the nucleic acids. Both the drug chemical structure and the type of nucleic acid proved to control the extent of EC-induced decrease of AK3-5 fluorescence in the presence of the DNA or RNA.

Conclusion: By recruiting the potential antitumor agents europium chelate complexes as the competitive ligands for the cyanine dye for the DNA and RNA binding sites, we found that a novel trimethine compound can be effectively used in the fluorescence drug displacement assays.


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How to Cite
Zhytniakivska, O., Tarabara, U., Kurutos, A., Zabrudska, A., Vus, K., Trusova, V., Gorbenko, G., & Deligeorgiev, T. (2020). Novel cyanine dye as competitive ligand for probing the drug–nucleic acid interactions. Biophysical Bulletin, (43), 111-120.
Molecular biophysics