DNA Electrochemical Biosensors for In Situ Probing of Pharmaceutical Drug Oxidative DNA Damage

Atomic force microscopy investigation of DNA denaturation on a highly oriented pyrolytic graphite surface

Understanding of DNA interaction with carbonaceous surfaces (including graphite, graphene and carbon nanotubes) is important for the development of DNA-based biosensors and other biotechnological devices. Though many issues related to DNA adsorption on graphitic surfaces have been studied, some important aspects of DNA interaction with graphite remain unclear. In this work, we use atomic force microscopy (AFM) equipped with super-sharp cantilevers to analyze the morphology and conformation of relatively long DNA molecule adsorbed on a highly oriented pyrolytic graphite (HOPG) surface. We have revealed the effect of DNA embedding into an organic monolayer of N,N'-(decane-1,10-diyl)-bis(tetraglycinamide) (GM), which may "freeze" DNA conformation on a HOPG surface during drying. The dependence of the mean squared point-to-point distance on the contour length suggests that DNA adsorbs on a bare HOPG by a "kinetic trapping" mechanism. For the first time, we have estimated the unfolded fraction of DNA upon contact with a HOPG surface (24 ± 5 %). The obtained results represent a novel experimental model for investigation of the conformation and morphology of DNA adsorbed on graphitic surfaces and provide with a new insight into DNA interaction with graphite.

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

In this study, electrochemical and theoretical studies were performed to explain the interaction mechanism between ponatinib (PNT), a third generation tyrosine kinase inhibitor, and dsDNA. The electrochemical part was conducted in phosphate-buffered saline (PBS) at physiological pH of 7.4 and in acetate buffer with a pH of 4.7, using square wave voltammetry. A boron-doped diamond electrode was used in a bulk-incubated solution. The theoretical part was investigated using computational methods, such as the semiempirical method PM7 and density functional theory (DFT). Significant differences in the electrochemical behavior of PNT in the presence of DNA confirmed the occurrence of interactions. The results obtained in the acetate buffer strongly suggested the preferential interaction of PNT with guanine residues. However, at physiological pH, it can be concluded that PNT interacts with dGua and dAdo in the dsDNA molecule. These results are consistent with outcomes from the theoretical studies, where quantum-chemical calculations showed that both electrochemically detectable nucleobases form hydrogen bonds with the drug. These bonds appeared to be stronger with guanine than with adenine. According to the computational studies, the dsDNA major groove is the energetically preferred site for the complexation of PNT.

Trends on Aerogel-Based Biosensors for Medical Applications: An Overview

Aerogels are unique solid-state materials composed of interconnected 3D solid networks and a large number of air-filled pores. This structure leads to extended structural characteristics as well as physicochemical properties of the nanoscale building blocks to macroscale, and integrated typical features of aerogels, such as high porosity, large surface area, and low density, with specific properties of the various constituents. Due to their combination of excellent properties, aerogels attract much interest in various applications, ranging from medicine to construction. In recent decades, their potential was exploited in many aerogels' materials, either organic, inorganic or hybrid. Considerable research efforts in recent years have been devoted to the development of aerogel-based biosensors and encouraging accomplishments have been achieved. In this work, recent (2018-2023) and ground-breaking advances in the preparation, classification, and physicochemical properties of aerogels and their sensing applications are presented. Different types of biosensors in which aerogels play a fundamental role are being explored and are collected in this manuscript. Moreover, the current challenges and some perspectives for the development of high-performance aerogel-based biosensors are summarized.

Electroanalysis in Pharmacogenomic Studies: Mechanisms of Drug Interaction with DNA

The review discusses electrochemical methods for analysis of drug interactions with DNA. The electroanalysis method is based on the registration of interaction-induced changes in the electrochemical oxidation potential of heterocyclic nitrogenous bases in the DNA molecule and in the maximum oxidation current amplitude. The mechanisms of DNA-drug interactions can be identified based on the shift in the electrooxidation potential of heterocyclic nitrogenous bases toward more negative (cathodic) or positive (anodic) values. Drug intercalation into DNA shifts the electrochemical oxidation potential to positive values, indicating thermodynamically unfavorable process that hinders oxidation of nitrogenous bases in DNA. The potential shift toward the negative values indicates electrostatic interactions, e.g., drug binding in the DNA minor groove, since this process does not interfere with the electrochemical oxidation of bases. The concentration-dependent decrease in the intensity of electrochemical oxidation of DNA bases allows to quantify the type of interaction and calculate the binding constants.

Electrochemical and theoretical study on interaction between erlotinib and DNA

A comprehensive investigation of tyrosine kinase inhibitor erlotinib (ERL) electrochemical behavior and interaction with DNA was performed with the aim to clarify its redox mechanism and to determine the mode of binding. Irreversible oxidation and reduction processes of ERL on glassy carbon electrode were investigated using three voltammetric techniques CV, DPV, SWV in pH range between 2.0 and 9.0. Oxidation was established as an adsorption-controlled process, while the reduction manifested diffusion-adsorption mixed controlled process in acidic medium and adsorption became predominant in the neutral solutions. According to the determined number of transferred electrons and protons, oxidation and reduction mechanism of ERL are proposed. To follow the interaction between ERL and DNA, the multilayer ct-DNA electrochemical biosensor was incubated in ERL solutions concentrations ranged from 2 × 10-7 M to 5 × 10-5 M (pH 4.6) for 30 min. SWV measurements have shown the decrease in deoxyadenosine peak current as a consequence of ERL increased concentration and binding to ct-DNA. The calculated value of binding constant was K = 8.25 × 104 M-1. Molecular docking showed that ERL forms hydrophobic interactions when docked into minor groove, as well as when intercalated, and molecular dynamics analysis predicted the stability of obtained complexes. These results together with voltammetric studies imply that the intercalation could be more dominant way ERL binding to DNA compared to minor groove binding.

Advances in Electrochemical Biosensor Technologies for the Detection of Nucleic Acid Breast Cancer Biomarkers

Breast cancer is the second leading cause of cancer deaths in women worldwide; therefore, there is an increased need for the discovery, development, optimization, and quantification of diagnostic biomarkers that can improve the disease diagnosis, prognosis, and therapeutic outcome. Circulating cell-free nucleic acids biomarkers such as microRNAs (miRNAs) and breast cancer susceptibility gene 1 (BRCA1) allow the characterization of the genetic features and screening breast cancer patients. Electrochemical biosensors offer excellent platforms for the detection of breast cancer biomarkers due to their high sensitivity and selectivity, low cost, use of small analyte volumes, and easy miniaturization. In this context, this article provides an exhaustive review concerning the electrochemical methods of characterization and quantification of different miRNAs and BRCA1 breast cancer biomarkers using electrochemical DNA biosensors based on the detection of hybridization events between a DNA or peptide nucleic acid probe and the target nucleic acid sequence. The fabrication approaches, the biosensors architectures, the signal amplification strategies, the detection techniques, and the key performance parameters, such as the linearity range and the limit of detection, were discussed.

Advancements in Nanofiber-Based Electrochemical Biosensors for Diagnostic Applications

Biosensors are analytical tools that can be used as simple, real-time, and effective devices in clinical diagnosis, food analysis, and environmental monitoring. Nanoscale functional materials possess unique properties such as a large surface-to-volume ratio, making them useful for biomedical diagnostic purposes. Nanoengineering has resulted in the increased use of nanoscale functional materials in biosensors. Various types of nanostructures i.e., 0D, 1D, 2D, and 3D, have been intensively employed to enhance biosensor selectivity, limit of detection, sensitivity, and speed of response time to display results. In particular, carbon nanotubes and nanofibers have been extensively employed in electrochemical biosensors, which have become an interdisciplinary frontier between material science and viral disease detection. This review provides an overview of the current research activities in nanofiber-based electrochemical biosensors for diagnostic purposes. The clinical applications of these nanobiosensors are also highlighted, along with a discussion of the future directions for these materials in diagnostics. The aim of this review is to stimulate a broader interest in developing nanofiber-based electrochemical biosensors and improving their applications in disease diagnosis. In this review, we summarize some of the most recent advances achieved in point of care (PoC) electrochemical biosensor applications, focusing on new materials and modifiers enabling biorecognition that have led to improved sensitivity, specificity, stability, and response time.

Rapid on-site nucleic acid testing: On-chip sample preparation, amplification, and detection, and their integration into all-in-one systems

As nucleic acid testing is playing a vital role in increasingly many research fields, the need for rapid on-site testing methods is also increasing. The test procedure often consists of three steps: Sample preparation, amplification, and detection. This review covers recent advances in on-chip methods for each of these three steps and explains the principles underlying related methods. The sample preparation process is further divided into cell lysis and nucleic acid purification, and methods for the integration of these two steps on a single chip are discussed. Under amplification, on-chip studies based on PCR and isothermal amplification are covered. Three isothermal amplification methods reported to have good resistance to PCR inhibitors are selected for discussion due to their potential for use in direct amplification. Chip designs and novel strategies employed to achieve rapid extraction/amplification with satisfactory efficiency are discussed. Four detection methods providing rapid responses (fluorescent, optical, and electrochemical detection methods, plus lateral flow assay) are evaluated for their potential in rapid on-site detection. In the final section, we discuss strategies to improve the speed of the entire procedure and to integrate all three steps onto a single chip; we also comment on recent advances, and on obstacles to reducing the cost of chip manufacture and achieving mass production. We conclude that future trends will focus on effective nucleic acid extraction via combined methods and direct amplification via isothermal methods.

Interaction between Benzo[a]anthracene 7,2-dione 7-oxime (BZA) and calf thymus dsDNA using electroanalytical genosensor

In the present study, the objective was to evaluate in situ interaction between Benzo[a]anthracene 7,2-dione 7-oxime (BZA) and calf thymus dsDNA (ct-dsDNA) using electroanalytical genosensor. Analytical techniques based on Ultraviolet/Visible (UV-Vis) spectroscopy and electroanalytical were used to investigate the interaction processes in solution and immobilized on carbon screen-printed electrodes modified with electrochemical mediator Meldola blue. In addition, was possible to evaluate the degree of damage caused to the genetic material by the analyte through of toxicity estimate (S%). The interaction evaluated by genosensor showed processes of intercalation, degradation, and breaks of the double strand of ct-dsDNA, suggesting that the interaction simulates highly toxic (values varying from 0.6 to 0.8 μA in 48 h of interaction), such as 8-oxoguanine (+0.48 V), which is a by-product of guanine oxidation. Furthermore, monitoring A (+1.10 V) after 1 h showed an S% value between 50 and 90%, indicative of high toxicity, and monitoring G (+0.85 V), which showed S>90%, indicated no toxicity after 10 min. Overall, the electroanalytical genosensor developed in a miniaturized system displayed good reproducibility and stability over time being a quick alternative for assesses the degree of toxicity between toxic xenobiotics and biologically electroactive molecules, such as DNA.

Electrochemical DNA Biosensor Based on Mercaptopropionic Acid-Capped ZnS Quantum Dots for Determination of the Gender of Arowana Fish

A new electrochemical DNA biosensor based on mercaptopropionic acid (MPA)-capped ZnS quantum dots (MPA-ZnS QDs) immobilization matrix for covalent binding with 20-base aminated oligonucleotide has been successfully developed. Prior to the modification, screen-printed carbon paste electrode (SPE) was self-assembled with multilayer gold nanoparticles (AuNPs) and cysteamine (Cys). The inclusion of MPA-ZnS QDs semiconducting material in modified electrodes has enhanced the electron transfer between the SPE transducer and DNA leading to improved bioanalytical assay of target biomolecules. Electrochemical studies performed by cyclic voltammetry (CV) and differential pulsed voltammetry (DPV) demonstrated that the MPA-ZnS QDs modified AuNPs electrode was able to produce a lower charge transfer resistance response and hence higher electrical current response. Under optimal conditions, the immobilized synthetic DNA probe exhibited high selectivity towards synthetic target DNA. Based on the DPV response of the reduction of anthraquinone monosulphonic acid (AQMS) redox probe, the MPA-ZnS QDs-based electrochemical DNA biosensor responded to target DNA concentration from 1 × 10⁻⁹ μM to 1 × 10⁻³ μM with a sensitivity 1.2884 ± 0.12 µA, linear correlation coefficient (R²) of 0.9848 and limit of detection (LOD) of 1 × 10⁻¹¹ μM target DNA. The DNA biosensor exhibited satisfactory reproducibility with an average relative standard deviation (RSD) of 7.4%. The proposed electrochemical transducer substrate has been employed to immobilize the aminated Arowana fish (Scleropages formosus) DNA probe. The DNA biosensor showed linearity to target DNA from 1 × 10⁻¹¹ to 1 × 10⁻⁶ µM (R² = 0.9785) with sensitivity 1.1251 ± 0.243 µA and LOD of 1 × 10⁻¹¹ µM. The biosensor has been successfully used to determine the gender of Arowana fish without incorporating toxic raw materials previously employed in the hazardous processing conditions of polypyrrole chemical conducting polymer, whereby the cleaning step becomes difficult with thicker films due to high levels of toxic residues from the decrease in polymerization efficacy as films grew.

Carbon nanomaterials and its applications in pharmaceuticals: A brief review

Nanotechnology for the past decade has made tremendous improvement and diverse applications in various sector. Among the nanomaterials synthesized, carbon allotropes are advantageous due to its easy functionalization, conductivity, surface area and electrical activity. Hence, they are termed as "Wonder materials". Allotropes such as carbon nanotubes, graphene, graphene oxide, fullerens, and carbon dots has paved its importance in the pharmaceuticals. They are coated in the biomedical devices, applied in the therapeutics and diagnosis. These are also used in the treatment of cancer and they possess anti-microbial and antiviral activity. Carbon nanomaterials possess several applications from biosensors to remediation of pollutants. Detection of hazardous compounds in food, pharmaceutical products, gene and drug delivery. They are also used in tissue regeneration and gene therapy. Application of carbon allotropes in the current scenario provides a wide scope in future with improvisations in building electrochemical biosensors. Its selectivity, sensitivity and cost-effectiveness prove it to be better alternative compared to other nanomaterials. The review focuses on the carbon allotropes used in pharmaceuticals, biosensors, pollutants detection and treatment were discussed in detail.

Designing Electrochemical Biosensing Platforms Using Layered Carbon-Stabilized Porous Silicon Nanostructures

Porous silicon (pSi) is an established porous material that offers ample opportunities for biosensor design thanks to its tunable structure, versatile surface chemistry, and large surface area. Nonetheless, its potential for electrochemical sensing is relatively unexplored. This study investigates layered carbon-stabilized pSi nanostructures with site-specific functionalities as an electrochemical biosensor. A double-layer nanostructure combining a top hydrophilic layer of thermally carbonized pSi (TCpSi) and a bottom hydrophobic layer of thermally hydrocarbonized pSi (THCpSi) is prepared. The modified layers are formed in a stepwise process, involving first an electrochemical anodization step to generate a porous layer with precisely defined pore morphological features, followed by deposition of a thin thermally carbonized coating on the pore walls via temperature-controlled acetylene decomposition. The second layer is then generated beneath the first by following the same two-step process, but the acetylene decomposition conditions are adjusted to deposit a thermally hydrocarbonized coating. The double-layer platform features excellent electrochemical properties such as fast electron-transfer kinetics, which underpin the performance of a TCpSi-THCpSi voltammetric DNA sensor. The biosensor targets a 28-nucleotide single-stranded DNA sequence with a detection limit of 0.4 pM, two orders of magnitude lower than the values reported to date by any other pSi-based electrochemical DNA sensor.

8-oxoguanine and 8-oxodeoxyguanosine Biomarkers of Oxidative DNA Damage: A Review on HPLC-ECD Determination

Reactive oxygen species (ROS) are continuously produced in living cells due to metabolic and biochemical reactions and due to exposure to physical, chemical and biological agents. Excessive ROS cause oxidative stress and lead to oxidative DNA damage. Within ROS-mediated DNA lesions, 8-oxoguanine (8-oxoG) and its nucleotide 8-oxo-2′-deoxyguanosine (8-oxodG)—the guanine and deoxyguanosine oxidation products, respectively, are regarded as the most significant biomarkers for oxidative DNA damage. The quantification of 8-oxoG and 8-oxodG in urine, blood, tissue and saliva is essential, being employed to determine the overall effects of oxidative stress and to assess the risk, diagnose, and evaluate the treatment of autoimmune, inflammatory, neurodegenerative and cardiovascular diseases, diabetes, cancer and other age-related diseases. High-performance liquid chromatography with electrochemical detection (HPLC–ECD) is largely employed for 8-oxoG and 8-oxodG determination in biological samples due to its high selectivity and sensitivity, down to the femtomolar range. This review seeks to provide an exhaustive analysis of the most recent reports on the HPLC–ECD determination of 8-oxoG and 8-oxodG in cellular DNA and body fluids, which is relevant for health research.

Kinetics and Mechanism of Plasmon-Driven Dehalogenation Reaction of Brominated Purine Nucleobases on Ag and Au

Plasmon-driven photocatalysis is an emerging and promising application of noble metal nanoparticles (NPs). An understanding of the fundamental aspects of plasmon interaction with molecules and factors controlling their reaction rate in a heterogeneous system is of high importance. Therefore, the dehalogenation kinetics of 8-bromoguanine (BrGua) and 8-bromoadenine (BrAde) on aggregated surfaces of silver (Ag) and gold (Au) NPs have been studied to understand the reaction kinetics and the underlying reaction mechanism prevalent in heterogeneous reaction systems induced by plasmons monitored by surface enhanced Raman scattering (SERS). We conclude that the time-average constant concentration of hot electrons and the time scale of dissociation of transient negative ions (TNI) are crucial in defining the reaction rate law based on a proposed kinetic model. An overall higher reaction rate of dehalogenation is observed on Ag compared with Au, which is explained by the favorable hot-hole scavenging by the reaction product and the byproduct. We therefore arrive at the conclusion that insufficient hole deactivation could retard the reaction rate significantly, marking itself as rate-determining step for the overall reaction. The wavelength dependency of the reaction rate normalized to absorbed optical power indicates the nonthermal nature of the plasmon-driven reaction. The study therefore lays a general approach toward understanding the kinetics and reaction mechanism of a plasmon-driven reaction in a heterogeneous system, and furthermore, it leads to a better understanding of the reactivity of brominated purine derivatives on Ag and Au, which could in the future be exploited, for example, in plasmon-assisted cancer therapy.

Biosensors promising bio-device for pandemic screening "COVID-19"

Undoubtedly, the coronavirus pandemic is one of the most influential events not only in medicine but also in the economic field in the world. Rapid transmission and high mortality rates, as well as prolonged and asymptomatic communal periods, are the most important reasons for the global panic due to coronavirus. Since coronavirus treatment and specific vaccines are not yet available, early detection of the virus is critical. A rapid and accurate diagnosis can play a crucial role in the treatment and control of the COVID 19 disease. Serological, ELISA, and molecular-based tests, including PCR and RT-PCR, are among the most important routine methods for detecting coronaviruses. False-positive/negative results, low sensitivity and specificity, and the need for advanced equipment are among the disadvantages and problems of routine methods. To eliminate the drawbacks of routine methods, new technologies are being developed. Biosensors are one of the most important ones. This paper is a summary of the up-to-date states of innovative bio-sensing tools for the ultrasensitive detection of coronaviruses (COVID 19) with encouraging uses for future challenges in disease diagnosis.

Biosensors in Parkinson's disease

Parkinson's disease (PD) is one of the most critical disorders of the elderly and strongly associated with increased disability, and reduced quality of life. PD is a progressive neurodegenerative disease affecting more than six million people worldwide. Evaluation of clinical manifestations, as well as movement disorders by a neurologist and some routine laboratory tests are the most important diagnostic methods for PD. However, routine and old methods have several disadvantages and limitations such as low sensitivity and selectivity, high cost, and need for advanced equipment. Biosensors technology opens up new diagnoses approach for PD with the use of a new platform that allows reliable, repeatable, and multidimensional identification to be made with minimal problem and discomfort for patients. For instance, biosensing systems can provide promising tools for PD treatment and monitoring. Amongst biosensor technology, electrochemical techniques have been at the frontline of this progress, thanks to the developments in material science, such as gold nanoparticles (AuNPs), quantum dots (QDs), and carbon nanotubes (CNTs). This paper evaluates the latest progress in electrochemical and optical biosensors for PD diagnosis.