Electrochemical approach for the analysis of DNA degradation in native DNA and apoptotic cells

Lyubov E Agafonova; Dmitry D Zhdanov; Yulia A Gladilina; Anastasia N Shishparenok; Victoria V Shumyantseva

doi:10.1016/j.heliyon.2024.e25602

Electrochemical approach for the analysis of DNA degradation in native DNA and apoptotic cells

Heliyon. 2024 Feb 5;10(3):e25602. doi: 10.1016/j.heliyon.2024.e25602. eCollection 2024 Feb 15.

Authors

Lyubov E Agafonova¹, Dmitry D Zhdanov^{1

2}, Yulia A Gladilina¹, Anastasia N Shishparenok¹, Victoria V Shumyantseva^{1

3}

Affiliations

¹ Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121, Moscow, Russia.
² Department of Biochemistry, Рeoples' Friendship University of Russia Named After Patrice Lumumba (RUDN University), Miklukho-Maklaya St. 6, 117198, Moscow, Russia.
³ Department of Biochemistry, Pirogov Russian National Research Medical University, Ostrovitianova St. 1, 117997, Moscow, Russia.

Abstract

The aim of this work was to develop an electrochemical approach for the analysis of DNA degradation and fragmentation in apoptotic cells. DNA damage is considered one of the major causes of human diseases. We analyzed the cleavage processes of the circular plasmid pTagGFP2-N and calf thymus DNA, which were exposed to restriction endonucleases (the restriction endonucleases BstMC I and AluB I and the nonspecific endonuclease I). Genomic DNA from the leukemia K562 cell line was used as a marker of the early and late (mature) stages of apoptosis. Registration of direct electrochemical oxidation of nucleobases of DNA molecules subjected to restriction endonuclease or apoptosis processes was proposed for the detection of these biochemical events. Label-free differential pulse voltammetry (DPV) has been used to measure endonuclease activities and DNA damage using carbon nanotube-modified electrodes. The present DPV technique provides a promising platform for high-throughput screening of DNA hydrolases and for registering the efficiency of apoptotic processes. DPV comparative analysis of the circular plasmid pTagGFP2-N in its native supercoiled state and plasmids restricted to 4 and 23 parts revealed significant differences in their electrochemical behavior. Electrochemical analysis was fully confirmed by means of traditional methods of DNA analysis and registration of apoptotic process, such as gel electrophoresis and flow cytometry.

Keywords: Apoptosis; Bioelectrochemistry; Carbon nanotubes; DNA fragmentation; Modified electrodes; Plasmid DNA.