Measuring Ultra-low Levels of Nucleotide Biomarkers Using Quartz Crystal Microbalance and SPR Microarray Imaging Methods: A Comparative Analysis

Label-free OIRD detection of protein microarrays on high dielectric constant substrate with enhanced intrinsic sensitivity

Oblique-incidence reflectivity difference (OIRD) is a dielectric constant-sensitive technique and exhibits intriguing applications in label-free and high-throughput detection of protein microarrays. With the outstanding advantage of being compatible with arbitrary substrates, however, the effect of the substrate, particularly its dielectric constant on the OIRD sensitivity has not been fully disclosed. In this paper, for the first time we investigated the dependence of OIRD sensitivity on the dielectric constant of the substrate under top-incident OIRD configuration by combining theoretical modeling and experimental evaluation. Optical modeling suggested that the higher dielectric constant substrate exhibits a higher intrinsic sensitivity. Experimentally, three substrates including glass, fluorine-doped tin oxide (FTO) and silicon (Si) with different dielectric constants were selected as microarray substrates and their detection performances were evaluated. In good agreement with the modeling, high dielectric constant Si-based microarray exhibited the highest sensitivity among three chips, reaching a detection limit of as low as 5 ng mL-1 with streptavidin as the model target. Quantification of captured targets on three chips with on-chip enzyme-linked immunosorbent assay (ELISA) further confirmed that the enhanced performance originates from the high dielectric constant enhanced intrinsic OIRD sensitivity. This work thus provides a new way to OIRD-based label-free microarrays with improved sensitivity.

Recent Advances in Biosensor Technology for Early-Stage Detection of Hepatocellular Carcinoma-Specific Biomarkers: An Overview

Hepatocellular carcinoma is currently the most common malignancy of the liver. It typically occurs due to a series of oncogenic mutations that lead to aberrant cell replication. Most commonly, hepatocellular carcinoma (HCC) occurs as a result of pre-occurring liver diseases, such as hepatitis and cirrhosis. Given its aggressive nature and poor prognosis, the early screening and diagnosis of HCC are crucial. However, due to its plethora of underlying risk factors and pathophysiologies, patient presentation often varies in the early stages, with many patients presenting with few, if any, specific symptoms in the early stages. Conventionally, screening and diagnosis are performed through radiological examination, with diagnosis confirmed by biopsy. Imaging modalities tend to be limited by their requirement of large, expensive equipment; time-consuming operation; and a lack of accurate diagnosis, whereas a biopsy's invasive nature makes it unappealing for repetitive use. Recently, biosensors have gained attention for their potential to detect numerous conditions rapidly, cheaply, accurately, and without complex equipment and training. Through their sensing platforms, they aim to detect various biomarkers, such as nucleic acids, proteins, and even whole cells extracted by a liquid biopsy. Numerous biosensors have been developed that may detect HCC in its early stages. We discuss the recent updates in biosensing technology, highlighting its competitive potential compared to conventional methodology and its prospects as a tool for screening and diagnosis.

Advances in Bioreceptor Layer Engineering in Nanomaterial-based Sensing of Pseudomonas Aeruginosa and its Metabolites

Pseudomonas aeruginosa is a pathogen that infects wounds and burns and causes severe infections in immunocompromised humans. The high virulence, the rise of antibiotic-resistant strains, and the easy transmissibility of P. aeruginosa necessitate its fast detection and control. The gold standard for detecting P. aeruginosa, the plate culture method, though reliable, takes several days to complete. Therefore, developing accurate, rapid, and easy-to-use diagnostic tools for P. aeruginosa is highly desirable. Nanomaterial-based biosensors are at the forefront of detecting P. aeruginosa and its secondary metabolites. This review summarises the biorecognition elements, biomarkers, immobilisation strategies, and current state-of-the-art biosensors for P. aeruginosa. The review highlights the underlying principles of bioreceptor layer engineering and the design of optical, electrochemical, mass-based, and thermal biosensors based on nanomaterials. The advantages and disadvantages of these biosensors and their future point-of-care applications are also discussed. This review outlines significant advancements in biosensors and sensors for detecting P. aeruginosa and its metabolites. Research efforts have identified biorecognition elements specific and selective towards P. aeruginosa. The stability, ease of preparation, cost-effectiveness, and integration of these biorecognition elements onto transducers are pivotal for their application in biosensors and sensors. At the same time, when developing sensors for clinically significant analytes such as P. aeruginosa, virulence factors need to be addressed, such as the sensor's sensitivity, reliability, and response time in samples obtained from patients. The point-of-care applicability of the developed sensor may be an added advantage since it enables onsite determination. In this context, optical methods developed for P. aeruginosa offer promising potential.

Simultaneous Detection of Exosomal microRNAs Isolated from Cancer Cells Using Surface Acoustic Wave Sensor Array with High Sensitivity and Reproducibility

We present a surface acoustic wave (SAW) sensor array for microRNA (miRNA) detection that utilizes photocatalytic silver staining on titanium dioxide (TiO2) nanoparticles as a signal enhancement technique for high sensitivity with an internal reference sensor for high reproducibility. A sandwich hybridization was performed on working sensors of the SAW sensor array that could simultaneously capture and detect three miRNAs (miRNA-21, miRNA-106b, and miRNA-155) known to be upregulated in cancer. Sensor responses due to signal amplification varied depending on the concentration of synthetic miRNAs. It was confirmed that normalization (a ratio of working sensor response to reference sensor response) screened out background interferences by manipulating data and minimized non-uniformity in the photocatalytic silver staining step by suppressing disturbances to both working sensor signal and reference sensor signal. Finally, we were able to successfully detect target miRNAs in cancer cell-derived exosomal miRNAs with performance comparable to the detection of synthetic miRNAs.

Photonic Crystal Surface Mode Real-Time Imaging of RAD51 DNA Repair Protein Interaction with the ssDNA Substrate

Photonic crystals (PCs) are promising tools for label-free sensing in drug discovery screening, diagnostics, and analysis of ligand-receptor interactions. Imaging of PC surface modes has emerged as a novel approach to the detection of multiple binding events at the sensor surface. PC surface modification and decoration with recognition units yield an interface providing the highly sensitive detection of cancer biomarkers, antibodies, and oligonucleotides. The RAD51 protein plays a central role in DNA repair via the homologous recombination pathway. This recombinase is essential for the genome stability and its overexpression is often correlated with aggressive cancer. RAD51 is therefore a potential target in the therapeutic strategy for cancer. Here, we report the designing of a PC-based array sensor for real-time monitoring of oligonucleotide-RAD51 recruitment by means of surface mode imaging and validation of the concept of this approach. Our data demonstrate that the designed biosensor ensures the highly sensitive multiplexed analysis of association-dissociation events and detection of the biomarker of DNA damage using a microfluidic PC array. The obtained results highlight the potential of the developed technique for testing the functionality of candidate drugs, discovering new molecular targets and drug entities. This paves the way to further adaption and bioanalytical use of the biosensor for high-content screening to identify new DNA repair inhibitor drugs targeting the RAD51 nucleoprotein filament or to discover new molecular targets.

Kinetics and interaction studies of anti-tetraspanin antibodies and ICAM-1 with extracellular vesicle subpopulations using continuous flow quartz crystal microbalance biosensor

Continuous flow quartz crystal microbalance (QCM) was utilized to study binding kinetics between EV subpopulations (exomere- and exosome-sized EVs) and four affinity ligands: monoclonal antibodies against tetraspanins (anti-CD9, anti-CD63, and anti-CD81) and recombinant intercellular adhesion molecule-1 (ICAM-1) or CD54 protein). High purity CD9⁺, CD63⁺, and CD81⁺ EV subpopulations of <50 nm exomeres and 50-80 nm exosomes were isolated and fractionated using our recently developed on-line coupled immunoaffinity chromatography - asymmetric flow field-flow fractionation system. Adaptive Interaction Distribution Algorithm (AIDA), specifically designed for the analysis of complex biological interactions, was used with a four-step procedure for reliable estimation of the degree of heterogeneity in rate constant distributions. Interactions between exomere-sized EVs and anti-tetraspanin antibodies demonstrated two interaction sites with comparable binding kinetics and estimated dissociation constants K_d ranging from nM to fM. Exomeres exhibited slightly higher affinity compared to exosomes. The highest affinity with anti-tetraspanin antibodies was achieved with CD63⁺ EVs. The interaction of EV subpopulations with ICAM-1 involved in cell internalization of EVs was also investigated. EV - ICAM-1 interaction was also of high affinity (nM to pM range) with overall lower affinity compared to the interactions of anti-tetraspanin antibodies and EVs. Our findings proved that QCM is a valuable label-free tool for kinetic studies with limited sample concentration, and that advanced algorithms, such as AIDA, are crucial for proper determination of kinetic heterogeneity. To the best of our knowledge, this is the first kinetic study on the interaction between plasma-derived EV subpopulations and anti-tetraspanin antibodies and ICAM-1.

Photoelectrochemical detection of microRNAs based on target-triggered self-assembly of energy band position-matched CdS QDs and C3N4 nanosheets

An ultrasensitive photochemical biosensor based on the target miRNA-triggered catalytic hairpin assembly (CHA) reaction between Au nanoparticles (AuNPs)/C₃N₄ nanosheets and CdS quantum dots (QDs) was developed for the determination of miRNAs. Firstly, AuNPs/C₃N₄ nanosheets were immobilized onto a working glassy carbon electrode. Then, the hairpin probe 1 (H1) was loaded through Au-S bonding. Afterward, the unbound sites were blocked with 6-mercaptohexanol to avoid nonspecific adsorption. In the presence of the target miRNA, the CHA reaction between the H1 and hairpin probe 2-CdS QDs (H2-CdS QDs) could be triggered. As a result, the AuNPs/C₃N₄ nanosheet and CdS QDs were linked by the double helix structure H1-H2. Unlike the other CHA reactions, H2 used in this work is longer than H1 so that the AuNPs/C₃N₄ nanosheets could touch the CdS QDs. Given the matched energy band positions between the C₃N₄ nanosheet and CdS QDs, a strong photocurrent could be obtained after the CHA reaction was triggered by the target miRNA. In addition, p-type C₃N₄ nanosheets and n-type CdS QDs presented reduction photocurrents and oxidation photocurrents, respectively. Therefore, the photocurrents were vectors in this design that can eliminate the interference of nonspecific adsorption and avoid the generation of false-positive signals. Under the optimal conditions, the limit of detection was 92 aM. The constructed photoelectrochemical biosensor showed good reproducibility and selectivity in the analysis of serum samples, which indicates its great prospects in disease diagnostics and bioanalysis.

Sensitive detection of microRNA using QCM biosensors: sandwich hybridization and signal amplification by TiO2 nanoparticles

MicroRNA-21 (miR-21) is known to act as an important biomarker for cancer, in that its up-regulation is closely related to several types of malignant tumor. Sensitive and accurate detection of miR-21 using a biosensor is highly challenging. In this study, sensitive and selective detection technology for miR-21 molecules using a quartz crystal microbalance (QCM) biosensor was developed. Sandwich hybridization between miR-21 and specially designed probes and a subsequent TiO2 photocatalytic silver enhancement reaction were the driving forces for sensitive detection with high selectivity for miR-21. Using this strategic approach under optimal conditions, the novel QCM biosensor can detect miR-21 with a LOD of 0.87 pM over the entire linear range from 0.1 pM to 10 μM, with a correlation coefficient of 0.988. In addition, the developed QCM biosensor was very effective in the quantification of miR-21 in serum samples, so the proposed miRNA detection method offers great potential for the diagnosis of early disease, such as cancer and vascular diseases, and could be an excellent alternative for biological research and clinical diagnosis.

Lateral field excited quartz crystal microbalances for biosensing applications

The most common bulk acoustic wave device used in biosensing applications is the quartz crystal microbalance (QCM), in which a resonant pure shear acoustic wave is excited via electrodes on both major faces of a thin AT-cut quartz plate. For biosensing, the QCM is used to detect the capture of a target by a target-capture film. The sensitivity of the QCM is typically based solely on the detection of mechanical property changes, as electrical property change detection is limited by the electrode on its sensing surface. A modification of the QCM called the lateral field excited (LFE) QCM (LFE-QCM) has been developed with a bare sensing surface as both electrodes are now on a single face of the quartz plate. Compared to the QCM, the LFE-QCM exhibits significantly higher sensitivity to both electrical and mechanical property changes. This paper presents theoretical and experimental aspects of LFE-QCMs. In particular, the presence and strength of the usual and newfound LFE-QCM modes depend on the electrical properties of the film and/or sensing environment. This work also presents examples of experimental setups for measuring the response of an LFE-QCM, followed by results of LFE-QCMs used to detect liquid electrical and mechanical properties, chemical targets, and biological targets. Finally, details are given about the attachment of various target-capture films to the LFE-QCM surface to capture biomarkers associated with diseases such as cancer.

QCM sensing of miR-21 by formation of microRNA-DNA hybrid duplexes and intercalation on surface-functionalized pyrene

MicroRNAs (miRNAs) are small non-coding RNA molecules that serve as important biomarkers for a variety of diseases such as cancer and vascular disease. However, sensitive and accurate detection of miR-21 is very challenging in that up-regulation of miR-21 is highly associated with several types of malignant tumors. Here, quartz crystal microbalance (QCM) biosensors were developed for sensitive and specific detection of miR-21 through formation of miR-21-DNA hybrid duplexes and non-specific intercalation of surface-modified pyrene molecules. High selectivity for miR-21 over other miRNAs came from the specific hybridization between miR-21 and gold nanoparticle (AuNP)-conjugated complementary oligonucleotides of miR-21. High sensitivity was obtained through formation of intercalated complexes on the surface with subsequent gold staining signal amplification. Under optimum condition using this strategic approach, our novel QCM biosensors could detect miR-21 concentration as low as 3.6 pM in the entire linear range from 2.5 pM to 2.5 μM with a correlation coefficient of 0.989. In addition, these sensors did not work at all for other miRNAs based on their high selectivity. miR-21 in human brain total RNA and total RNA extracted from A549 cell line could also be successfully detected. Therefore, miRNA detection technology using QCM biosensors and their detection mechanisms have potential as alternatives in biological studies and clinical diagnosis.

Plasmonic nucleotide hybridization chip for attomolar detection: localized gold and tagged core/shell nanomaterials

We report a large amplification of surface plasmon signals for a double hybridization microarray chip assembly that bridges localized gold and detection probe-carrying-core/shell Fe₃O₄@Au nanoparticles for detection of as low as 80 aM miRNA-155 marker in solution. The plasmonic wavelength match of the gold shell with surface localized gold nanoparticles and the additional scattering band of the core/shell material in resonance with the incident 800 nm light source are the underlying factors for the observed remarkable analyte signal at ultra-low (10^-18 order) concentrations.

A new amplification strategy for a quartz crystal microbalance miRNA sensor based on selective interactions between a metal–organic framework and miRNA

UiO-66 is used as an effective amplifier in a QCM miRNA sensor to detect Let-7a.

The cooperative interaction of triplex forming oligonucleotides on DNA-triplex formation at electrode surface: Molecular dynamics studies and experimental evidences

An extensive study on cooperative interaction of Triplex Forming Oligonucleotides (TFOs) with a double strand DNA, to form a triplex-DNA structure at electrode surface, is here reported. The cooperative effect on triplex structure formation was assumed by the higher binding enthalpy value, calculated for the interaction between the duplex DNA structure and the TFO1 and TFO2 probes (-67.3 KJ/mol), respect the sum of the single duplex-TFO1 and duplex-TFO2 interactions (-47.0 kJ/mol). The formation of triplex-DNA structure was proven by kinetic modelling study performed using the Luzar and Chandler model. The results indicate that after 500 ns from interaction, H-bonds between the base pairs in the double strand DNA are weaken while new H-bonds between the TFOs and duplex DNA are formed. Molecular dynamic (MD) simulations indicate that the TFOs sequence distance (138 bps) and the amount of TA*T triplet units are the keystones for the effectiveness of the cooperative effect, reaching for the selected target a minimum of energy value of -19452.6 kJ/mol. The MD data were experimentally corroborated by electrochemical measurements, detecting a HBV-clone genome at TFOs modified electrode surface. The interaction was electrochemical transduced by an intercalative Osmium based compound. The Langmuir isotherm model reports for the forming triplex DNA an association constant value of about 2.9 × 10¹⁶M^-1, this high value could be attributed to the synergic contribution of the TFOs cooperative effect and to the rigid circular duplex structure. Finally, AFM and SEM investigations suggest the formation of a triplex-DNA structure at electrode surface, consisting in circles of about 1.5 um in diameter with asymmetric stranded thickness. This finding data paving the way to future development of advanced miniaturized DNA computing and biosensors.

Applications of Gold Nanoparticles in Non-Optical Biosensors

Due to their unique properties, such as good biocompatibility, excellent conductivity, effective catalysis, high density, and high surface-to-volume ratio, gold nanoparticles (AuNPs) are widely used in the field of bioassay. Mainly, AuNPs used in optical biosensors have been described in some reviews. In this review, we highlight recent advances in AuNP-based non-optical bioassays, including piezoelectric biosensor, electrochemical biosensor, and inductively coupled plasma mass spectrometry (ICP-MS) bio-detection. Some representative examples are presented to illustrate the effect of AuNPs in non-optical bioassay and the mechanisms of AuNPs in improving detection performances are described. Finally, the review summarizes the future prospects of AuNPs in non-optical biosensors.

A facile DNA strand displacement reaction sensing strategy of electrochemical biosensor based on N-carboxymethyl chitosan/molybdenum carbide nanocomposite for microRNA-21 detection

Herein, we report a facile enzyme-free microRNA (miRNA) target-triggered strand displacement reaction (SDR) amplification strategy with ferrocene (Fc) as a signal molecule to fabricate a two-dimensional electroactive molybdenum carbide (Mo₂C)-based biosensor. In the presence of miRNA-21, SDR was initiated and many hairpin DNA1 (HDNA1) and hairpin DNA2 (HDNA2) duplexes, which could be captured by probe DNA leading the Fc-modified HDNA2 close to the electrode surface, were produced continuously. MiRNA-21 could be detected by monitoring the redox signal of Fc. The prepared N-carboxymethyl chitosan/Mo₂C nanocomposite featured excellent conductivity, great dispersion, and multiple functional groups (amine groups). When the nanocomposite was introduced to a miRNA biosensor electrode interface to ensure its strong connection to the DNA probe, the developed miRNA-21 biosensor demonstrated a reliable linear range of 1.0 fM to 1.0 nM with a detection limit of 0.34 fM and showed good selectivity, reproducibility, and stability. The biosensor was employed to detect miRNA-21 in human serum samples, and it showed great potential in the early clinical diagnosis of various genetic diseases.

Spectral Imaging Analysis for Ultrasensitive Biomolecular Detection Using Gold-Capped Nanowire Arrays

A spectral integration combined with a threshold method for the analysis of spectral scanning surface plasmon resonance (SPR) images can significantly increase signal recognition at low concentration of antibody solution. The 12-well SPR sensing plates consisted of gold-capped nanowire arrays with 500-nm period, 80-nm linewidth and 50-nm gold thickness which were used for generating multiple SPR images. A threshold method is introduced to eliminate background noises in spectral scanning images. Combining spectral integration and the threshold method, the detection limit of antibody concentration was 1.23 ng/mL. Using multiple-well SPR sensing plates and the proposed analytical method, multiple kinetic responses with spectral and spatial information on different sensing areas can be sensitively measured.