Development of the electrochemical, spectroscopic and molecular docking approaches toward the investigation of interaction between DNA and anti-leukemic drug azacytidine

Rafia Nimal; Didem Nur Unal; Cem Erkmen; Burcin Bozal-Palabiyik; Muhammad Siddiq; Gokcen Eren; Afzal Shah; Bengi Uslu

doi:10.1016/j.bioelechem.2022.108135

Development of the electrochemical, spectroscopic and molecular docking approaches toward the investigation of interaction between DNA and anti-leukemic drug azacytidine

Bioelectrochemistry. 2022 Aug:146:108135. doi: 10.1016/j.bioelechem.2022.108135. Epub 2022 Apr 18.

Authors

Rafia Nimal¹, Didem Nur Unal², Cem Erkmen², Burcin Bozal-Palabiyik², Muhammad Siddiq³, Gokcen Eren⁴, Afzal Shah³, Bengi Uslu⁵

Affiliations

¹ Quaid-i-Azam University, Department of Chemistry, 45320 Islamabad, Pakistan; Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560 Ankara, Turkey.
² Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560 Ankara, Turkey.
³ Quaid-i-Azam University, Department of Chemistry, 45320 Islamabad, Pakistan.
⁴ Gazi University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 06330 Etiler-Ankara, Turkey.
⁵ Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560 Ankara, Turkey. Electronic address: buslu@pharmacy.ankara.edu.tr.

PMID: 35468353
DOI: 10.1016/j.bioelechem.2022.108135

Abstract

This study examines the interaction between pyrimidine nucleoside analogue azacytidine, an anti-leukemic drug, and DNA by employing electrochemical, UV-vis spectroscopy, fluorescence spectroscopy and molecular docking techniques. In the electrochemical technique, azacytidine and dsDNA interaction was investigated in two different ways: (1) in solution and (2) with a biosensor using differential pulse voltammetry (DPV) at a glassy carbon electrode. The interaction between azacytidine and dsDNA at increasing interaction times was investigated in line with the changes in adenine and guanine oxidation signals. In addition, interaction studies of polyguanine-azacytidine and polyadenine-azacytidine were performed with DPV. The binding constant values were calculated as 2.420 × 10⁴ M^-1 and 3.266 × 10⁴ M^-1 at 25 °C using UV and fluorescence spectroscopy, respectively. In conclusion, based on electrochemical and spectroscopic methods as well as molecular docking studies, it was predicted that azacytidine can bind to dsDNA via groove binding.

Keywords: Azacytidine; Binding; DNA; Interaction; Spectroscopy; Voltammetry.

MeSH terms

Azacitidine*
Biosensing Techniques* / methods
DNA / chemistry
Electrochemical Techniques / methods
Electrodes
Molecular Docking Simulation
Spectrum Analysis

Substances

DNA
Azacitidine