Electrochemical and theoretical studies of the interaction between anticancer drug ponatinib and dsDNA

At a Glance

Metadata	Details
Publication Date	2024-01-27
Journal	Scientific Reports
Authors	Sylwia Smarzewska, Anna Ignaczak, Kamila Koszelska
Institutions	University of Łódź
Citations	9
Analysis	Full AI Review Included

Technical Documentation & Analysis: MPCVD Diamond for Advanced Electrochemistry

Executive Summary

This documentation analyzes the application of Boron-Doped Diamond (BDD) electrodes in the study of Ponatinib (PNT)—a third-generation tyrosine kinase inhibitor (TKI)—and its interaction mechanism with double-stranded DNA (dsDNA).

Material Validation: The research successfully validates the use of Boron-Doped Diamond Electrodes (BDDE) for highly sensitive Square Wave Voltammetry (SWV) analysis of complex drug-DNA interactions in physiological and acidic media.
Interaction Mechanism: Electrochemical and Density Functional Theory (DFT) calculations confirm that PNT interacts with dsDNA primarily through major groove binding, effectively excluding intercalation as the dominant mechanism.
Nucleobase Specificity: PNT shows a strong preference for binding to guanine (dGua) residues, although interaction with adenine (dAdo) also occurs at physiological pH (7.4).
Electrochemical Stability: The BDDE demonstrated stable, irreversible oxidation peaks for PNT across a wide pH range (1.7-9.0), confirming the material’s robustness and wide potential window for complex biological studies.
Process Control: The PNT oxidation process was determined to be adsorption-controlled (or mixed diffusion-adsorption controlled), highlighting the critical need for high-quality, polished BDD surfaces to ensure measurement repeatability.
6CCVD Value: 6CCVD specializes in providing the high-conductivity, custom-dimensioned, and ultra-polished BDD substrates necessary to replicate and advance this type of cutting-edge biosensing research.

Technical Specifications

Hard data extracted from the research paper detailing experimental and computational parameters.

Parameter	Value	Unit	Context
Working Electrode Material	Boron-Doped Diamond (BDD)	N/A	Used for SWV/CV analysis
Working Electrode Diameter	3	mm	Used in the conventional three-electrode cell
Physiological Buffer pH	7.4	N/A	Phosphate-Buffered Saline (PBS)
Acidic Buffer pH	4.7	N/A	Acetate Buffer
PNT Concentration (SWV)	5.0 x 10^-6	mol L^-1	Fixed concentration for interaction studies
dsDNA Concentration Range	10 - 80	mg L^-1	Used for concentration-dependent studies
SWV Amplitude	30	mV	Optimized measurement condition
SWV Frequency	25	Hz	Optimized measurement condition
SWV Step Potential	4	mV	Optimized measurement condition
PNT Oxidation Peak Potential (pH 7.4)	~1.15 and ~1.25	V	Two well-separated anodic peaks
Most Stable Complexation Energy (119D:MaG_ST)	-65.6	kcal mol^-1	DFT Calculation (M062X-GD3)
Preferred Binding Site	Major Groove (MaG)	N/A	Confirmed by DFT calculations

Key Methodologies

A concise outline of the experimental and theoretical procedures used to analyze the PNT-dsDNA interaction.

Electrochemical Setup:
- A conventional three-electrode system was employed using a µAutolab Type III potentiostat.
- The working electrode was a 3 mm diameter Boron-Doped Diamond Electrode (BDDE).
- A Platinum wire served as the auxiliary electrode, and Ag/AgCl was the reference electrode.
Electrode Surface Preparation:
- Prior to each voltammetric measurement, the BDDE surface was mechanically polished using alumina slurry on a polishing cloth.
- The electrode was subsequently rinsed with distilled and deionized water to ensure surface renewal and minimize adsorption effects.
Voltammetric Analysis:
- Cyclic Voltammetry (CV) was used for general characterization and redox mechanism evaluation (confirming irreversible oxidation).
- Square Wave Voltammetry (SWV) was used for high-sensitivity interaction studies, performed under fixed conditions (30 mV amplitude, 25 Hz frequency, 4 mV step potential).
- Interaction studies were conducted using two approaches: fixed concentration with varying incubation times, and varying dsDNA concentration ratios.
Computational Chemistry (Hierarchical Approach):
- Step 1 (Molecular Mechanics): Systematic rotation of two PNT conformers (PNT_LE, PNT_ST) within four dsDNA binding sites (External Binding, Major Groove, Minor Groove, Intercalation) using the Amber99 force field.
- Step 2 (Semiempirical): Optimization of selected structures using the PM7 method in water (COSMO) to determine complexation enthalpies (H_compl).
- Step 3 (DFT): Partial re-optimization (PNT relaxed, dsDNA frozen) using the high-accuracy M062X-GD3 functional with the 6-31G(d,p) basis set and Polarizable Continuum Model (PCM) for final complexation energy (E_compl) calculation.

6CCVD Solutions & Capabilities

As an expert material scientist and technical sales engineer for 6CCVD, we recognize that the success of this advanced electrochemical study hinges on the quality and consistency of the Boron-Doped Diamond (BDD) electrode. 6CCVD is uniquely positioned to supply the necessary high-specification MPCVD diamond materials to replicate and extend this research into next-generation biosensors.

Applicable Materials

To achieve the stable, repeatable, and low-background measurements demonstrated in this paper, researchers require highly conductive BDD material.

Heavy Boron-Doped Polycrystalline Diamond (BDD-PCD): This is the ideal material for electrochemical sensing applications requiring a wide potential window and chemical inertness, such as the analysis of PNT in complex buffers (PBS, Acetate). Our BDD-PCD offers high doping uniformity necessary for consistent electrode performance.
Optical Grade Single Crystal Diamond (SCD): For high-precision research requiring the ultimate in material purity and surface quality (e.g., combined electrochemistry and optical spectroscopy), we offer SCD plates up to 500 µm thick.

Customization Potential

The study utilized a specific 3 mm diameter BDDE. 6CCVD excels in providing custom dimensions and integration solutions for specialized electrochemical setups.

Research Requirement	6CCVD Customization Capability
Custom Electrode Dimensions	We provide BDD plates and wafers up to 125 mm (PCD) that can be precision laser-cut, diced, or machined to any required geometry, including the 3 mm diameter discs used in this study.
Surface Finish Requirements	The study relies on repeated polishing. 6CCVD offers ultra-low roughness polishing (Ra < 5 nm for PCD/BDD, Ra < 1 nm for SCD), ensuring minimal surface defects and maximizing the repeatability of adsorption-controlled processes.
Electrode Integration & Contacts	For seamless integration into electrode stands (like the mtm-anko M164), 6CCVD offers internal metalization services (Au, Pt, Ti, W, Cu) to create robust, low-resistance electrical contacts on the BDD substrate.
Substrate Thickness	We offer custom BDD substrates ranging from 0.1 µm films up to 10 mm thick substrates, allowing researchers to select the optimal mechanical stability for their specific cell design.

Engineering Support

The analysis of PNT-dsDNA interaction is a complex project requiring expertise in both electrochemistry and material science.

Material Optimization: 6CCVD’s in-house PhD engineering team can assist researchers in selecting the optimal boron doping concentration and surface termination (e.g., hydrogen or oxygen termination) for similar Tyrosine Kinase Inhibitor (TKI) analysis or drug-DNA interaction projects, ensuring maximum sensitivity and stability.
Replication and Extension: We provide technical consultation to help researchers replicate the high-performance BDDE results achieved in this paper and extend the methodology to other anticancer drug candidates or novel biosensor designs.

For custom specifications or material consultation, visit 6ccvd.com or contact our engineering team directly.

Tech Support

Original Source

DOI: https://doi.org/10.1038/s41598-024-52609-z