SPRi-Based Biosensing Platforms for Detection of Specific DNA Sequences Using Thiolate and Dithiocarbamate Assemblies

A Careful Insight into DDI-Type Receptor Layers on the Way to Improvement of Click-Biology-Based Immunosensors

Protein-based microarrays are important tools for high-throughput medical diagnostics, offering versatile platforms for multiplex immunodetection. However, challenges arise in protein microarrays due to the heterogeneous nature of proteins and, thus, differences in their immobilization conditions. This article advocates DNA-directed immobilization (DDI) as a solution, emphasizing its rapid and cost-effective fabrication of biosensing platforms. Thiolated single-stranded DNA and its analogues, such as ZNA® and PNA probes, were used to immobilize model proteins (anti-CRP antibodies and SARS-CoV nucleoprotein). The study explores factors influencing DDI-based immunosensor performance, including the purity of protein-DNA conjugates and the stability of their duplexes with DNA and analogues. It also provides insight into backfilling agent type and probe surface density. The research reveals that single-component monolayers lack protection against protein adsorption, while mixing the probes with long-chain ligands may hinder DNA-protein conjugate anchoring. Conventional DNA probes offer slightly higher surface density, while ZNA® probes exhibit better binding efficiency. Despite no enhanced stability in different ionic strength media, the cost-effectiveness of DNA probes led to their preference. The findings contribute to advancing microarray technology, paving the way for new generations of DDI-based multiplex platforms for rapid and robust diagnostics.

A New Approach to the Quantification of Fibroblast Growth Factor 23-An Array Surface Plasmon Resonance Imaging Biosensor

A new biosensor based on the "surface plasmon resonance imaging (SPRi)" detection technique for the quantification of "fibroblast growth factor 23 (FGF23)" has been developed. FGF23 is mainly produced in bone tissues as a phosphaturic hormone that forms a trimeric complex with "fibroblast growth factor receptor 1 (FGFR1)" and αKlotho upon secretion. FGF23 stimulates phosphate excretion and inhibits the formation of active vitamin D in the kidneys. FGF23 has been shown to play a role in bone carcinogenesis and metastasis. The newly developed method, based on the array SPRi biosensor, was validated-the precision, accuracy, and selectivity were acceptable, and yielded less than ±10% recovery. The rectilinear response of the biosensor ranges from 1 to 75 pg/mL. The limit of detection was 0.033 pg/mL, and the limit of quantification was 0.107 pg/mL. The biosensor was used to determine FGF23 concentrations in the blood plasma of healthy subjects and patients with "clear cell" renal cell carcinoma (ccRCC). The obtained results were compared with those measured through an "enzyme-linked immunosorbent assay (ELISA)". The determined Pearson correlation coefficients were 0.994 and 0.989, demonstrating that the newly developed biosensor can be used as a competitive method for the ELISA.

Au-X (X=Pt/Ru)-decorated magnetic nanocubes as bifunctional nanozyme labels in colorimetric, magnetically-enhanced, one-step sandwich CRP immunoassay

Scientific interest in the investigation and application of multifunctional nanomaterials in medical diagnostics has been increasing. The employment of magnetocatalytic immunoconjugates as both analyte-capturing agents and enzyme-like catalytic labels may enable rapid preconcentration and determination of relevant antigens. In this work, we synthesized and comprehensively characterized two types of noble metal-decorated magnetic nanocubes (MDMCs) which were subsequently applied in the one-step, sandwich nanozyme-linked immunosorbent assay (NLISA). Magnetic cores allow for rapid separation from complex samples of biological origin. The catalytically active shell composed of Au-decorated Pt or Ru can effectively mimic the activity of horseradish peroxididase, retaining at the same time the ability to form stable bioconstructs through self-assembly of thiolated ligands. As a result, hybrid multifunctional nanoparticles were synthesized and used to detect C-reactive protein (CRP) in serum samples. We have also paid considerable attention to the mechanistic studies of the formation of sandwich immunocomplexes with nanoparticle labels by means of immunoenzymatic methods and surface plasmon resonance. Analytical parameters of the Pt-MDMCs-labeled NLISA (detection limit LOD = 0.336 ng mL-1, recovery = 98.0%, linear response window covering two logarithmic units) turned out to be superior to the classical, one-step ELISA based on a horseradish peroxidase. In addition, our method offers further possibility of sensitivity adjustment by changing the parameters of magnetic preconcentration, together with good long-term stability of MDMCs conjugates and their good resistance to common interferences. We believe that the proposed simple synthetic protocol will guide a new approach to applying metal-decorated magnetic nanozymes as versatile and multifunctional labels for application in subsequent pre-analytical analyte concentration and immunoassays towards clinical applications.

Strategies for Surface Design in Surface Plasmon Resonance (SPR) Sensing

Surface plasmon resonance (SPR) comprises several surface-sensitive techniques that enable the trace and ultra-trace detection of various analytes through affinity pairing. Although enabling label-free, sensitive detection and real-time monitoring, several issues remain to be addressed, such as poor stability, non-specific adsorption and the loss of operational activity of biomolecules. In this review, the progress over sensor modification, immobilization techniques and novel 2D nanomaterials, gold nanostructures and magnetic nanoparticles for signal amplification is discussed. The advantages and disadvantages of each design strategy will be provided together with some of the recent achievements.

Substrate Materials for Biomolecular Immobilization within Electrochemical Biosensors

Electrochemical biosensors have potential applications for agriculture, food safety, environmental monitoring, sports medicine, biomedicine, and other fields. One of the primary challenges in this field is the immobilization of biomolecular probes atop a solid substrate material with adequate stability, storage lifetime, and reproducibility. This review summarizes the current state of the art for covalent bonding of biomolecules onto solid substrate materials. Early research focused on the use of Au electrodes, with immobilization of biomolecules through ω-functionalized Au-thiol self-assembled monolayers (SAMs), but stability is usually inadequate due to the weak Au-S bond strength. Other noble substrates such as C, Pt, and Si have also been studied. While their nobility has the advantage of ensuring biocompatibility, it also has the disadvantage of making them relatively unreactive towards covalent bond formation. With the exception of Sn-doped In2O3 (indium tin oxide, ITO), most metal oxides are not electrically conductive enough for use within electrochemical biosensors. Recent research has focused on transition metal dichalcogenides (TMDs) such as MoS2 and on electrically conductive polymers such as polyaniline, polypyrrole, and polythiophene. In addition, the deposition of functionalized thin films from aryldiazonium cations has attracted significant attention as a substrate-independent method for biofunctionalization.

Conformational Changes of Immobilized Polythymine due to External Stressors Studied with Temperature-Controlled Electrochemical Microdevices

Conformational changes of single-stranded DNA (ssDNA) play an important role in a DNA strand's ability to bind to target ligands. A variety of factors can influence conformation, including temperature, ionic strength, pH, buffer cation valency, strand length, and sequence. To better understand the effects of these factors on immobilized DNA structures, we employ temperature-controlled electrochemical microsensors to study the effects of salt concentration and temperature variation on the conformation and motion of polythymine (polyT) strands of varying lengths (10, 20, 50 nucleotides). PolyT strands were tethered to a gold working electrode at the proximal end through a thiol linker via covalent bonding between the Au electrode and sulfur link, which can tend to decompose between a temperature range of 60 and 90 °C. The strands were also modified with an electrochemically active methylene blue (MB) moiety at the distal end. Electron transfer (eT) was measured by square wave voltammetry (SWV) and used to infer information pertaining to the average distance between the MB and the working electrode. We observe changes in DNA flexibility due to varying ionic strength, while the effects of increased DNA thermal motion are tracked for elevated temperatures. This work elucidates the behavior of ssDNA in the presence of a phosphate-buffered saline at NaCl concentrations ranging from 20 to 1000 mmol/L through a temperature range of 10-50 °C in 1° increments, well below the decomposition temperature range. The results lay the groundwork for studies on more complex DNA strands in conjunction with different chemical and physical conditions.

Large Scale Fabrication of Ordered Gold Nanoparticle-Epoxy Surface Nanocomposites and Their Application as Label-Free Plasmonic DNA Biosensors

A robust and scalable technology to fabricate ordered gold nanoparticle arrangements on epoxy substrates is presented. The nanoparticles are synthesized by solid-state dewetting on nanobowled aluminum templates, which are prepared by the selective chemical etching of porous anodic alumina (PAA) grown on an aluminum sheet with controlled anodic oxidation. This flexible fabrication technology provides proper control over the nanoparticle size, shape, and interparticle distance over a large surface area (several cm²), which enables the fine-tuning and optimization of their plasmonic absorption spectra for LSPR and SERS applications between 535 and 625 nm. The nanoparticles are transferred to the surface of epoxy substrates, which are subsequently selectively etched. The resulting nanomushrooms arrangements consist of ordered epoxy nanopillars with flat, disk-shaped nanoparticles on top, and their bulk refractive index sensitivity is between 83 and 108 nm RIU^-1. Label-free DNA detection is successfully demonstrated with the sensors by using a 20 base pair long specific DNA sequence from the parasite Giardia lamblia. A red-shift of 6.6 nm in the LSPR absorbance spectrum was detected after the 2 h hybridization with 1 μM target DNA, and the achievable LOD was around 5 nM. The reported plasmonic sensor is one of the first surface AuNP/polymer nanocomposites ever reported for the successful label-free detection of DNA.

Functionalizing gold with single strand DNA: novel insight into optical properties via combined spectroscopic ellipsometry and nanolithography measurements

We have studied the self-assembly of 22-base oligonucleotides bound by a short alkyl thiol linker (C6-ssDNA) on flat Au films. The self-assembled monolayer (SAM) was modified by addition of a spacer (mercaptohexanol, MCH). Molecular depositions were monitored in situ by spectroscopic ellipsometry (SE). SAMs were characterized in a liquid environment by coupling SE (difference spectra method) with Atomic Force Microscope (AFM) measurements. We exploited the biofilm thickness obtained by AFM nanolithography and imaging to solve the refractive index/thickness correlation in optical measurements on ultrathin molecular layers. The combined SE/AFM analysis provided reliable estimates of the thickness and the refractive index of the biofilm in the NIR region (650-1300 nm) and revealed new aspects of DNA molecular organization: exposure to MCH leads to an increase of both film thickness and refractive index, which points to a reorganization of C6-ssDNA film. We show that the contribution of the thiol/Au interface has to be included in the optical model to obtain a more reliable determination of the refractive index of the biofilm in a liquid. The careful, correlative characterization of the mixed C6-ssDNA/MCH SAM represents a key step towards the optimization of a robust detection scheme based on helix-helix hybridization.