Immobilization of DNA at Glassy Ccarbon Electrodes: A Critical Study of Adsorbed Layer

Surface immobilization strategies for the development of electrochemical nucleic acid sensors

Following the recent pandemic and with the emergence of cell-free nucleic acids in liquid biopsies as promising biomarkers for a broad range of pathologies, there is an increasing demand for a new generation of nucleic acid tests, with a particular focus on cost-effective, highly sensitive and specific biosensors. Easily miniaturized electrochemical sensors show the greatest promise and most typically rely on the chemical functionalization of conductive materials or electrodes with sequence-specific hybridization probes made of standard oligonucleotides (DNA or RNA) or synthetic analogues (e.g. Peptide Nucleic Acids or PNAs). The robustness of such sensors is mostly influenced by the ability to control the density and orientation of the probe at the surface of the electrode, making the chemistry used for this immobilization a key parameter. This exhaustive review will cover the various strategies to immobilize nucleic acid probes onto different solid electrode materials. Both physical and chemical immobilization techniques will be presented. Their applicability to specific electrode materials and surfaces will also be discussed as well as strategies for passivation of the electrode surface as a way of preventing electrode fouling and reducing nonspecific binding.

Electrochemical DNA sensors for drug determination

In this review, recent achievements in the development of the DNA biosensors developed for the drug determination have been presented with particular emphasis to the main principles of their assembling and signal measurement approaches. The design of the DNA sensors is considered with characterization of auxiliary components and their necessity for the biosensor operation. Carbon nanomaterials, metals and their complexes as well as electropolymerized polymers are briefly described in the assembly of DNA sensors. The performance of the DNA sensors is summarized within 2017-2022 for various drugs and factors influencing the sensitivity and selectivity of the response are discussed. Special attention is paid to the mechanism of the signal generation and possible drawbacks in the analysis of real samples.

Multi-walled carbon nanotube-based nanobiosensor for the detection of cadmium in water

Industrial and agricultural processes have led to the prevalence of cadmium in the ecosystem. A successive build-up of cadmium in food and drinking water can result in inadvertent consumption of hazardous concentrations. Such environmental contamination of cadmium can pose a substantial threat to human and animal life. In humans, it is known to cause hypertension, cardiovascular diseases, DNA lesions, inhibition of DNA repair protein or disturb the functioning of lung, liver, prostate and kidney. The development of a reliable method for Cd (II) ions detection would reduce the exposure and complement existing conventional methods. In this study, a DNA based electrochemical method is employed for the detection of Cd (II) ions using ethyl green (EG) and multi-walled carbon nanotube (MWCNT). Glassy carbon electrode (GCE)/MWCNT forms the working electrode for differential pulse voltammetry (DPV) analysis for the detection of Cd (II) ions. The dsDNA is immobilized onto the working electrode. The indicator dye EG, preferably binds to ssDNA and its reduction peak current is noticeably less in the presence of dsDNA. The Cd (II) ions after interacting with dsDNA, unwinds the dsDNA to ssDNA, upon which the EG molecules bind to ssDNAs, giving a higher reduction peak current. The difference in the reduction peak currents in the presence and absence of Cd (II) ions is proportional to its concentration. The linear detection range achieved in this method is 2 nM-10.0 nM with a sensitivity of around 5 nA nM^-1 and the limit of detection is 2 nM, which is less than the permissible limit of WHO for human exposure. This study considerably broadens the possible application of multi-walled carbon nanotube modified electrodes as biosensors and holds prospects for the detection of other heavy metals in environmental samples.

Plasmid DNA adsorption on silica: kinetics and conformational changes in monovalent and divalent salts

A quartz crystal microbalance with dissipation (QCM-D) is used to determine the adsorption rate of a supercoiled plasmid DNA onto a quartz surface and the structure of the resulting adsorbed DNA layer. To better understand the DNA adsorption mechanisms and the adsorbed layer physicochemical properties, the QCM-D data are complemented by dynamic light scattering measurements of diffusion coefficients of the DNA molecules as a function of solution ionic composition. The data from simultaneous monitoring of variations in frequency and dissipation energy with the QCM-D suggest that the adsorbed DNA layer is more rigid in the presence of divalent (calcium) cations compared to monovalent (sodium) cations. Adsorption rates are significantly higher in the presence of calcium, attaining a transport-limited rate at about 1 mM Ca2+. Results further suggest that in low ionic strength solutions containing 1 mM Ca2+ and in moderately high ionic strength solutions containing 300 mM NaCl, plasmid DNA adsorption to negatively charged mineral surfaces is irreversible.

Hydrogen bonding versus ion pairing in polyelectrolyte multilayers with homopolynucleotides

Homopolynucleotides--poly(adenylic acid), poly(A), and poly(uridylic acid), poly(U)--were assembled, layer-by-layer, into thin films with poly(ethylenimine), PEI. Various combinations and sequences of polynucleotide and PEI were used to highlight contributions of electrostatic versus hydrogen bonding as driving forces for multilayer build-up. Assembly of alternating poly(A) and poly(U) failed to yield growing films, due to excessively strong interactions between these complimentary strands. The surface morphology of multilayers depended on the deposition order and whether films had been annealed by salt. Films assembled from preformed A/U duplexes (having high persistence lengths) were very smooth. Individual adsorption steps, followed by optical waveguide light-mode spectroscopy, showed that only complementary polynucleotides adsorb by H-bonding to the surface of a growing multilayer. In contrast to behavior usually observed for polyelectrolyte multilayer build-up, the films decreased in thickness with increasing salt concentration.

Adsorption of plasmid DNA to a natural organic matter-coated silica surface: kinetics, conformation, and reversibility

A quartz crystal microbalance with dissipation (QCM-D) has been used to determine the adsorption rate of ampicillin-resistant linear and supercoiled plasmid DNA onto a silica surface coated with natural organic matter (NOM). The structure of the resulting adsorbed DNA layer was determined by analyzing the viscoelastic properties of the adsorbed DNA layers as they formed and were then exposed to solutions of different ionic composition. The QCM-D data were complemented by dynamic light scattering measurements of diffusion coefficients of the DNA molecules as a function of solution ionic composition. The obtained results suggest that electrostatic interactions control the adsorption and structural changes of the adsorbed plasmid DNA on the NOM-coated silica surface. The adsorption of DNA molecules to the NOM layer took place at moderately high monovalent (sodium) electrolyte concentrations. A sharp decrease in solution ionic strength did not result in the release of the adsorbed DNA, indicating that DNA adsorption on the NOM-coated silica surface is irreversible under the studied solution conditions. However, the decrease in electrolyte concentration influenced the structure of the adsorbed layer, causing the adsorbed DNA to adopt a less compact conformation. The linear and supercoiled DNA had similar adsorption rates, but the linear DNA formed a thicker and less compact adsorbed layer than the supercoiled DNA.