Detection of DNA hybridization using the TISPR-1 surface plasmon resonance biosensor

Current progress on COVID-19 related to biosensing technologies: New opportunity for detection and monitoring of viruses

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COVID-19 infection poses a serious risk to human life by causing acute lung damage.

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Various techniques used to identify and quantify COVID-19 infection.

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Major challenges for containing the spread of COVID-19 is the ability to identify asymptomatic cases.

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Currently available diagnostic methods, biosensing technology developed during COVID-19 infection.

The technologies used for coronavirus testing consist of a pre-existing device developed to examine different pathologies, such as bacterial infections, or cancer biomarkers. However, for the 2019 pandemic, researchers knew that their technology could be modified to detect a low viral load at an early stage. Today, countries around the world are working to control the new coronavirus disease (n-SARS-CoV-2). From this perspective, laboratories, universities, and companies around the world have embarked on a race to develop and produce much-needed test kits. This review has been developed to provide an overview of current trends and strategies in n-SARS-CoV-2 diagnostics based on traditional and new emerging assessment technologies, to continuous innovation. It focuses on recent trends in biosensors to build a fast, reliable, more sensitive, accessible, user-friendly system and easily adaptable technology n-SARS-CoV-2 detection and monitoring. On the whole, we have addressed and identified research evidence supporting the use of biosensors on the premise that screening people for n-SARS-CoV-2 is the best way to contain its spread.

Optoplasmonic characterisation of reversible disulfide interactions at single thiol sites in the attomolar regime

Probing individual chemical reactions is key to mapping reaction pathways. Trace analysis of sub-kDa reactants and products is obfuscated by labels, however, as reaction kinetics are inevitably perturbed. The thiol-disulfide exchange reaction is of specific interest as it has many applications in nanotechnology and in nature. Redox cycling of single thiols and disulfides has been unresolvable due to a number of technological limitations, such as an inability to discriminate the leaving group. Here, we demonstrate detection of single-molecule thiol-disulfide exchange using a label-free optoplasmonic sensor. We quantify repeated reactions between sub-kDa thiolated species in real time and at concentrations down to 100’s of attomolar. A unique sensing modality is featured in our measurements, enabling the observation of single disulfide reaction kinetics and pathways on a plasmonic nanoparticle surface. Our technique paves the way towards characterising molecules in terms of their charge, oxidation state, and chirality via optoplasmonics.

Visualising single-molecule reactions, to understand their mechanisms, is a challenging task. Here, the authors investigate disulfide exchange reactions with thiolates immobilised on a gold nanoparticle through a label-free optoplasmonic sensor, and detect individual disulfide interactions in solution

Nanomaterials and phase sensitive based signal enhancment in surface plasmon resonance

Measurement of small molecules in extremely dilute concentrations of analyte play an important role in different issues ranging from food industry to biological, pharmaceutical and therapeutical applications. Surface plasmon resonance (SPR) sensors can be a suitable choice for detection of small molecules based on interactions with biomolecules. However, sensitivity of the system for detection of these molecules is very low. Improving sensitivity has been a challenge for years. Therefore, different methods have been used to enhance SPR signals. The SPR signal enhancement using numerous nanomaterials has provided exciting results. Among various nanomaterials, metal nanoparticles (for instance gold, silver and magnetic nanoparticles), quantum dots, nanorads, and carbon-based nanostructures have got much attention due to ease in fabrication, appropriate size and shape. In addition to the advantages provided by using nanomaterials, signal enhancement provided by the appropriate use of phase information of the reflected light could be also important to improve SPR sensitivity. Phase-sensitive SPR sensors are able to detect infinitesimal changes in external properties of target while traditional type of SPR cannot demonstrate these changes. This article provides an overview on signal enhancment in SPR using nanomaterials and properties of light. We also discuss on recent progresses of the field, describing basic concepts concerning nanostructures as well as phase-sensitive sensors as platform for enhancement of signal in SPR.

Surface plasmon resonance: a versatile technique for biosensor applications

Surface plasmon resonance (SPR) is a label-free detection method which has emerged during the last two decades as a suitable and reliable platform in clinical analysis for biomolecular interactions. The technique makes it possible to measure interactions in real-time with high sensitivity and without the need of labels. This review article discusses a wide range of applications in optical-based sensors using either surface plasmon resonance (SPR) or surface plasmon resonance imaging (SPRI). Here we summarize the principles, provide examples, and illustrate the utility of SPR and SPRI through example applications from the biomedical, proteomics, genomics and bioengineering fields. In addition, SPR signal amplification strategies and surface functionalization are covered in the review.

Surface modification of plasmonic nanostructured materials with thiolated oligonucleotides in 10 seconds using selective microwave heating

This study demonstrates the proof-of-principle of rapid surface modification of plasmonic nanostructured materials with oligonucleotides using low power microwave heating. Due to their interesting optical and electronic properties, silver nanoparticle films (SNFs, 2 nm thick) deposited onto glass slides were used as the model plasmonic nanostructured materials. Rapid surface modification of SNFs with oligonucleotides was carried out using two strategies (1) Strategy 1: for ss-oligonucleotides, surface hybridization and (2) Strategy 2: for ds-oligonucleotides, solution hybridization), where the samples were exposed to 10, 15, 30 and 60 seconds microwave heating. To assess the efficacy of our new rapid surface modification technique, identical experiments carried out without the microwave heating (i.e., conventional method), which requires 24 hours for the completion of the identical steps. It was found that SNFs can be modified with ss- and ds-oligonucleotides in 10 seconds, which typically requires several hours of incubation time for the chemisorption of thiol groups on to the planar metal surface using conventional techniques.

Options available for labelling nucleic acid samples in DNA microarray-based detection methods

DNA microarrays are considered by many researchers to be the platform of choice for the high-throughput analysis of nucleic acids. Since the past two decades, they have been used constantly as powerful tools in differential gene expression, SNP genotyping, DNA sequencing, gene discovery, disease diagnostic and pathways reconstruction. Several methods have been developed to enable samples of limited amounts of RNA to be quantified. Here we evaluate classical and up-to-date assays made available for labelling those samples. This review also sheds light on the recently developed strategies that ensure high sensitivity such as sample and signal amplification, quantum dot, surface plasmom resonance, nanoparticles and cationinc polythiophenes.

Concentration-enhanced rapid detection of human chorionic gonadotropin (hCG) on a Au surface using a nanofluidic preconcentrator

Here, we report a new method of concentration-enhanced binding kinetics for a rapid immunoassay screening test on a gold surface in a poly(dimethylsiloxane) (PDMS) microfluidic chip format. The use of alkylthiolate self-assembled monolayers on gold surfaces of a PDMS-glass microchip resulted in accelerated binding kinetics of Human chorionic gonadotropin (hCG) at an electrokinetic trapping zone. We used a PBS solution (buffer concentration ~ 150 mM), not a dibasic buffer system (~10 mM), for the dynamic preconcentrating operation and the preconcentration of cy3 labeled streptavidin onto biotinylated Au surface revealed that the binding kinetics of the protein were linearly proportional to the concentration profile of the preconcentration plug. We showed rapid detection of hCG in the clinical range with a shorten assay time of 10 min. Also, we demonstrated that the amount of sample needed were detection was decreased from ~4 mL to ~25 μL in the standard serum tests. The enhanced binding kinetics between hcG Ag-Ab via preconcentration showed good feasibility for use in a rapid immunoassay screening test.

Surface plasmon resonance (SPR) sensors: approaching their limits?

We report on a unified theoretical model of the resolution of SPR sensors which makes it possible to predict the ultimate performance of all major configurations of SPR sensors. The theory indicates that the performance of SPR sensors is independent of the method of excitation of surface plasmons (prism or grating coupling) or the method of modulation (amplitude, angular or wavelength) and depends dominantly on the noise properties of the light source and detector. Results of the theoretical analysis are compared with the performance reported for several SPR sensors to illustrate that the best state-of-art SPR sensors are approaching their theoretical limits. Possibilities for further advances in the performance of SPR sensor technology are discussed.

Hybrid differential interrogation method for sensitive surface plasmon resonance measurement enabled by electro-optically tunable SPR sensors

A novel detection method enabled by electro-optically tunable waveguide-coupled surface plasmon resonance sensors is demonstrated. Both the WCSPR response of sensor and the interrogation light are varied simultaneously in this hybrid scheme. Modulation and demodulation of the sensor's response are achieved by applying a high-frequency AC electrical signal and electrically filtering the detected signal. Scanning the incident angle at a lower speed yields an angular dependent response. Theoretical analyses and experimental results show that the angular-dependent signal is closely related to the derivative of the SPR reflectivity with a sharp, linear jump near the minimum of the SPR peak. Thus, simple linear-fitting and zero-finding algorithms can be used to locate the SPR angle, and sophisticated data processing algorithms and electronic hardware can be avoided.

Surface plasmon resonance spectro-imaging sensor for biomolecular surface interaction characterization

Surface plasmon resonance (SPR) techniques have become, over the last ten years, powerful tools to study biomolecular surface interaction kinetics in real-time without any use of labels. The highest resolution is currently obtained using spectroscopic SPR systems through the measurement of the complete surface plasmon resonance curve in angular or spectral configuration. But, these systems are limited to a few independent channels (<10). In order to expand their capability to an array format, SPR sensors have also been developed in an imaging mode, allowing parallel monitoring of hundreds of sensing spots onto a camera. However, such sensors rely on the intensity variation measurement at a single position of the resonance spectrum, hence resulting in smaller resolution. We present in this work a SPR spectro-imaging system which aims at keeping the advantage of a mono-channel SPR sensor based on the full resonance curve measurement while introducing an additional spatial dimension (linear multi-spot array). The system is based on the illumination of a biochip through a vertical slit (y-dimension) by a white light source. The reflected light spectrum obtained through a diffracting grating is then imaged on the x-dimension of the camera. The complete spectral resonance curve of a full column of sensing spots can be monitored in parallel and in real-time. We demonstrate that data processing is key to reduce the noise and to improve the resolution. We report on the detection of signals with resolution comparable to the one obtained with a classical SPR mono-channel spectroscopic sensor (3.5 x 10(-7) Refractive Index Unit), gaining an order of magnitude compared to SPR imaging sensors. Eventually, we show that short base DNA-DNA hybridizations with concentrations as low as 100 pM can be detected and discriminated in a few tens of minutes following injection by the SPR spectro-imaging system.

DNA–DNA interaction on dendron-functionalized sol–gel silica films followed with surface plasmon fluorescence spectroscopy

Since we observed that dendron-assembled surface provided high single nucleotide polymorphism discrimination efficiency for DNA microarrays, and that the binding yield for streptavidin increased when biotin was immobilized on top of it, the nanoscale-controlled surface is examined for surface plasmon field-enhanced fluorescence spectroscopy (or SPFS). Firstly, a silica film was coated onto a gold substrate using the sol-gel technique, followed by the covalent immobilization of a layer of second-generation dendrons with a DNA catcher strand at their apex. The thickness of the inorganic interlayer (d=33 nm) was effectively suppressing fluorescence quenching. Thus, the kinetics and affinity characteristics of DNA hybridization could be investigated very sensitively by SPFS. The kinetic rate constants found for DNA hybridization on the dendron-modified surface were larger than those reported for a streptavidin-modified surface by one order of magnitude, except for dissociation rate constant for a single mismatched case. In addition, we observed that the DNA on the cone-shaped linker maintained its capability to capture DNA target strands even after extended storage at ambient conditions.

The role of biosensors in the detection of emerging infectious diseases

Global biosecurity threats such as the spread of emerging infectious diseases (i.e., avian influenza, SARS, Hendra, Nipah, etc.) and bioterrorism have generated significant interest in recent years. There is considerable effort directed towards understanding and negating the proliferation of infectious diseases. Biosensors are an attractive tool which have the potential to detect the outbreak of a virus and/or disease. Although there is a host of technologies available, either commercially or in the scientific literature, the development of biosensors for the detection of emerging infectious diseases (EIDs) is still in its infancy. There is no doubt that the glucose biosensor, the gene chip, the protein chip, etc. have all played and are still playing a significant role in monitoring various biomolecules. Can biosensors play an important role for the detection of emerging infectious diseases? What does the future hold and which biosensor technology platform is suitable for the real-time detection of infectious diseases? These and many other questions will be addressed in this review. The purpose of this review is to present an overview of biosensors particularly in relation to EIDs. It provides a synopsis of the various types of biosensor technologies that have been used to detect EIDs, and describes some of the technologies behind them in terms of transduction and bioreceptor principles.

Surface plasmon resonance-based sensors to identify cis-regulatory elements

In eukaryotes, transcription is regulated by multiprotein complexes binding to specific regions of genomic DNA, called cis-regulatory elements. Comprehensive identification of these elements is an important goal of functional genomics. Hence, it is of practical interest to develop a high-throughput assay to identify cis-regulatory elements. Toward that goal, we demonstrate that a surface plasmon resonance-based assay can identify whether a specific region of DNA binds to proteins present in raw nuclear lysate. Specifically, we immobilized a 16-basepair double-stranded DNA region of the SQSTM1 promoter to the Texas Instruments Spreeta, a surface plasmon resonance sensor. As a control, in a separate experiment, we immobilized a similar piece of DNA that differed by only a single base pair. We observed a significant difference in surface plasmon resonance signal when these two probes were exposed to raw nuclear lysate from NIH/3T3 cells. Using a luciferase-reporter vector transfected into live NIH/3T3 cells, we measured a significant difference in transcriptional activity between the two pieces of DNA. We conclude that a surface plasmon resonance-based sensor is capable of identifying physiologically significant cis-regulatory elements.

Formation and removal of alkylthiolate self-assembled monolayers on gold in aqueous solutions

We report the development of novel reagents and approaches for generating recyclable biosensors. The use of aqueous media for the formation of protein binding alkylthiolate monolayers on Au surfaces results in accelerated alkylthiolate monolayer formation and improvement in monolayer integrity as visualized by fluorescence microscopy and CV techniques. We have also developed an electrocleaning protocol that is compatible with microfluidics devices, and this technique serves as an on-chip method for cleaning Au substrates both before and after monolayer formation. The techniques for the formation and dissociation of biotinylated SAMs from aqueous solvents reported here may be applied towards the development of Au-based sensor devices and microfluidics chips in the future. A potential use of these devices includes the specific capture and triggered release of target cells, proteins, or small molecules from liquid samples.

Investigating oligonucleotide hybridization at subnanomolar level by surface plasmon resonance biosensor method

We have optimized surface plasmon resonance (SPR) biosensor technology for a rapid, direct, and low-consumption label-free multianalyte screening of synthetic oligonucleotides (ONs) with modified internucleotide linkages potentially applicable in antisense therapy. Monitoring of the ONs hybridization is based on the formation of complex between the natural oligonucleotide probe immobilized on the sensor surface and the ON in solution in contact with the sensor surface. An immobilization chemistry utilizing the streptavidin-biotin interaction was employed to obtain desired ligand density and high hybridization efficiency. It was demonstrated that the sensor is capable of detecting complementary 23-mer ONs in concentrations as low as 0.1 nM with high specificity and reproducibility.

Direct immobilisation of DNA probes for the development of affinity biosensors

An immobilisation procedure based on the direct coupling of thiolated probes (Probe-C6-SH) to bare gold sensor surfaces has been compared with a reference immobilisation method, based on the coupling of biotinylated probes onto a streptavidin-coated dextran-modified surface. The instrumentations used were a quartz crystal microbalance (QCM) and the optical instruments Biacore X and Spreeta based on surface plasmon resonance (SPR). The performances of the DNA-based sensors resulting from direct coupling of thiolated DNA probes onto electrodes of quartz crystals or gold SPR-chips have been studied in terms of the main analytical parameters, i.e. selectivity, sensitivity, reproducibility, etc. In particular, the two immobilisation approaches have been applied to the analysis of oligonucleotides, DNA amplified by polymerase chain reaction (PCR) and genomic DNA enzymatically digested.

A surface plasmon resonance probe with a novel integrated reference sensor surface

A surface plasmon resonance (SPR) sensor probe with integrated reference surface is described. In order to fabricate the integrated reference surface, two dielectric layers with different thickness were deposited on the single gold SPR sensor surface via plasma polymerization of hexamethyldisiloxane. The working sensor surface was a 34 nm dielectric layer with immobilized bovine serum albumin (BSA) antigen and an adjacent thin 1 nm dielectric layer without BSA provided reference surface. A specific immunoreaction of anti-BSA antibody was detected after immersion of the SPR probe into sample solution. Simultaneous observation of reference and working surface response enabled determination of the immunoreaction without the need for the baseline measurement. Moreover, compensation of nonspecific adsorption could be confirmed using anti-human serum albumin antibody.

Thiol-mediated degradation of DNA adsorbed on a colloidal gold surface

When [³²P]-labeled DNA is adsorbed on colloidal gold from a 130mmol dm^-3 solution of KH₂PO₄, it can subsequently be eluted with cold DNA without undergoing detectable degradation. Similarly, DNA can be incubated in solution in the presence or absence of colloidal gold with high concentrations of β-mercaptoethanol or hexane-1-thiol without significant degradation. However, when adsorbed DNA is eluted from gold with solutions of one of the thiols, it is recovered as a mixture of mononucleotides and short oligomers. The extent of degradation increases with increasing concentration of the thiol and with increasing elution temperature. Our results emphasize that in designing protocols involving DNA adsorbed on gold surfaces, it is important to avoid allowing the DNA to come into contact with even moderate concentrations of thiols.

Instrumentation for the genome project

Much of the recent rapid progress in large-scale genomic sequencing has been driven by the dramatic improvements both in the area of biological protocols and in the availability of improved laboratory instrumentation and automation platforms. We discuss recent developments in the area of bioinstrumentation that are contributing to the current revolution in genetic analysis. Examples of systems for laboratory automation are described together with specific single-purpose instruments. Emphasis is placed on those tools that are contributing significantly to the scale-up of genomic mapping and sequencing efforts. In addition, we present a selection of more advanced measurement techniques and instrumentation developments that are likely to contribute significantly to future advances in sequencing and genome analysis.

Surface plasmon resonance: towards an understanding of the mechanisms of biological molecular recognition

With the introduction of new instruments and improved sensor chip chemistries, surface plasmon resonance (SPR) is finding new applications for molecular interaction studies. Easy access to high-quality kinetic and thermodynamic data for macromolecular binding events is providing insights into the fundamental mechanisms of molecular recognition. Progress is being made to allow larger-scale interaction studies. In addition, combining SPR with other analytical methods is enabling SPR-based analysis of interaction proteomics.

Use of optical biosensors for the study of mechanistically concerted surface adsorption processes

The advent of commercial optical biosensors, such as the BIAcore from Pharmacia and IAsys from Affinity Sensors, has made available to the biochemist a powerful means to examine and characterize the interaction of biological macromolecules with a binding surface. By analysis of the kinetic and equilibrium aspects of the observed experimental adsorption isotherms, rate and affinity constants can be determined. This Review focuses on pertinent aspects of the technology and its use for the performance and quantitative characterization of some various types of mechanistically concerted adsorption behavior.

Survey of the 1999 surface plasmon resonance biosensor literature

The application of surface plasmon resonance biosensors in life sciences and pharmaceutical research continues to increase. This review provides a comprehensive list of the commercial 1999 SPR biosensor literature and highlights emerging applications that are of general interest to users of the technology. Given the variability in the quality of published biosensor data, we present some general guidelines to help increase confidence in the results reported from biosensor analyses.

Rotating rod renewable microcolumns for automated, solid-phase DNA hybridization studies

The development of a new temperature-controlled renewable microcolumn flow cell for solid-phase nucleic acid hybridization in an automated sequential injection system is described. The flow cell included a stepper motor-driven rotating rod with the working end cut to a 45 degrees angle. In one position, the end of the rod prevented passage of microbeads while allowing fluid flow; rotation of the rod by 180 degrees releases the beads. This system was used to rapidly test many hybridization and elution protocols to examine the temperature and solution conditions required for sequence-specific nucleic acid hybridization. Target nucleic acids labeled with a near-infrared fluorescent dye were detected immediately postcolumn during all column perfusion and elution steps using a flow-through fluorescence detector. Temperature control of the column and the presence of Triton X-100 surfactant were critical for specific hybridization. Perfusion of the column with complementary oligonucleotide (200 microL, 10 nM) resulted in hybridization with 8% of the DNA binding sites on the microbeads with a solution residence time of less than 1 s and a total sample perfusion time of 40 s. The use of the renewable column system for detection of an unlabeled PCR product in a sandwich assay was also demonstrated.

Implementing surface plasmon resonance biosensors in drug discovery

Recent improvements in instrument hardware, experimental design and data processing have made it possible to use surface plasmon resonance (SPR) biosensor technology in the discovery and development of small-molecule drugs. The key features of SPR biosensors (i.e. real-time binding analysis and lack of labeling requirements) make this technology suitable for a wide range of applications. Current instruments have a throughput of approximately 100-400 assays per day, providing a complement to secondary screening. The ability to collect kinetic data on compounds binding to therapeutic targets yields new information for lead optimization. Small-molecule analysis and emerging applications in the areas of ADME (adsorption, distribution, metabolism and excretion) and proteomics have SPR biosensors poised to play a significant role in the pharmaceutical industry.