Spherical Nucleic Acid Enhanced FO-SPR DNA Melting for Detection of Mutations in Legionella pneumophila

Solid-Phase PCR-Amplified DNAzyme Activity for Real-Time FO-SPR Detection of the MCR-2 Gene

The polymerase chain reaction (PCR) has been the gold standard molecular analysis technique for decades and has seen quite some evolution in terms of reaction components, methodology, and readout mechanisms. Nucleic acid enzymes (NAzymes) have been used to further exploit the applications of PCR, but so far the work was limited to the colorimetric G-quadruplex or fluorescent substrate cleaving NAzymes. In this study, a solid-phase, fiber optic surface plasmon resonance (FO-SPR) technique is presented as an alternative readout for PCR utilizing NAzymes. First, the surface cleavage activity of DNAzyme-extended amplicons (DNAzyme-amps) is established, followed by optimization of the PCR conditions, which are required for compatibility with the FO-SPR system. Next, by integrating the complement of a 10-23 DNAzyme into the primer pair, PCR-amplified DNAzyme-amps were generated, tested, and validated on qPCR for the detection of the antimicrobial resistance gene MCR-2. Once validated, this primer concept was developed as a one-step assay, driven by PCR-amplified DNAzymes, for FO-SPR-based sensitive and specific detection. Using gold nanoparticle labeled RNA-DNA hybrid strands as substrate for the DNAzyme, PCR-amplified DNAzyme-amps generated in the presence of MCR-2 gene were monitored in real-time, which resulted in an experimental limit of detection of 4 × 10⁵ copy numbers or 6.6 fM. In addition, the DNAzyme-based FO-PCR assay was able to discriminate between the MCR-1 and MCR-2 genes, to further prove the specificity of this assay. Henceforth, this DNAzyme-based fiber optic PCR assay provides a universally applicable, real-time system for the detection of virtually any target NA, in a specific and sensitive manner.

Advancements in SPR biosensing technology: An overview of recent trends in smart layers design, multiplexing concepts, continuous monitoring and in vivo sensing

Inspired by the rapid progress and existing limitations in surface plasmon resonance (SPR) biosensing technology, we have summarized the recent trends in the fields of both chip-SPR and fiber optic (FO)-SPR biosensors during the past five years, primarily regarding smart layers design, multiplexing, continuous monitoring and in vivo sensing. Versatile surface chemistries, biomaterials and nanomaterials have been utilized thus far to generate smart layers on SPR platforms and as such achieve oriented immobilization of bioreceptors, improved fouling resistance and sensitivity enhancement, collectively aiming to improve the biosensing performance. Furthermore, often driven by the desires for time- and cost-effective quantification of multiple targets in a single measurement, efforts have been made to implement multiplex bioassays on SPR platforms. While this aspect largely remains difficult to attain, numerous alternative strategies arose for obtaining parallel analysis of multiple analytes in one single device. Additionally, one of the upcoming challenges in this field will be to succeed in using SPR platforms for continuous measurements and in vivo sensing, and as such match up other biosensing platforms where these goals have been already conquered. Overall, this review will give insight into multiple possibilities that have become available over the years for boosting the performance of SPR biosensors. However, because combining them all into one optimal sensor is practically not feasible, the final application needs to be considered while designing an SPR biosensor, as this will determine the requirements of the bioassay and will thus help in selecting the essential elements from the recent progress made in SPR sensing.

Improvement of fiber optic based localized surface plasmon resonance sensor by optical fiber surface etching and Au capping

Fiber optic based localized surface plasmon resonance (FO-LSPR) sensor is one of the biosensors that detects specific biomolecules and can detect the onset of disease. In this paper, we propose two methods to improve the signal to noise ratio (SNR) of the sensor, which is one of the main characteristics of the FO-LSPR sensor. The first method is to increase the intensity of the sensor by increasing the size of gold nanoparticle (Au NP) formed on the optical fiber surface by Au capping method. The second method is to form a structure that reduces the reflection by increasing the roughness of the surface by etching the surface of the optical fiber using the Au NP formed on the surface of the optical fiber as a mask. Increasing the roughness of the optical fiber surface can reduce the background signal of the sensor. The two methods mentioned above can increase the SNR of the sensor. When the SNR of the sensor is increased, the efficiency of the sensor is improved.

Real-Time FO-SPR Monitoring of Solid-Phase DNAzyme Cleavage Activity for Cutting-Edge Biosensing

DNA nanotechnology has a great potential in biosensor design including nanostructuring of the biosensor surface through DNA origami, target recognition by means of aptamers, and DNA-based signal amplification strategies. In this paper, we use DNA nanotechnology to describe for the first time the concept of real-time solid-phase monitoring of DNAzyme cleavage activity for the detection of specific single-stranded DNA (ssDNA) with a fiber optic surface plasmon resonance (FO-SPR) biosensor. Hereto, we first developed a robust ligation strategy for the functionalization of the FO-SPR biosensing surface with ssDNA-tethered gold nanoparticles, serving as the substrate for the DNAzyme. Next, we established a relation between the SPR signal change, due to the cleavage activity of the 10-23 DNAzyme, and the concentration of the DNAzyme, showing faster cleavage kinetics for higher DNAzyme concentrations. Finally, we implemented this generic concept for biosensing of ssDNA target in solution. Hereto, we designed a DNAzyme-inhibitor complex, consisting of an internal loop structure complementary to the ssDNA target, that releases active DNAzyme molecules in a controlled way as a function of the target concentration. We demonstrated reproducible target detection with a theoretical limit of detection of 1.4 nM, proving that the presented ligation strategy is key to a universal DNAzyme-based FO-SPR biosensing concept with promising applications in the medical and agrofood sector.

Three-Dimensional DNA Origami as Programmable Anchoring Points for Bioreceptors in Fiber Optic Surface Plasmon Resonance Biosensing

Many challenges in biosensing originate from the fact that the all-important nanoarchitecture of the biosensor surface, including precise density and orientation of bioreceptors, is not entirely comprehended. Here, we introduced a three-dimensional DNA origami as a bioreceptor carrier to functionalize the fiber optic surface plasmon resonance (FO-SPR) sensor with nanoscale precision. Starting from a 24-helix bundle, two distinct DNA origami structures were designed to position thrombin-specific aptamers with different densities and distances (27 and 113 nm) from the FO-SPR surface. The origami-based biosensors not only proved to be capable of reproducible, label-free thrombin detection but revealed also valuable innovative features: (1) a significantly better performance in the absence of backfilling, known as essential in the biosensing field, suggesting improved bioreceptor orientation and accessibility, and (2) a wider linear range compared to previously reported thrombin biosensors. We envisage that our method will be beneficial for both scientists and clinicians looking for new surface (bio)chemistry and improved diagnostics.

Identification and Quantification of Celery Allergens Using Fiber Optic Surface Plasmon Resonance PCR

Abstract: Accurate identification and quantification of allergens is key in healthcare, biotechnology and food quality and safety. Celery (Apium graveolens) is one of the most important elicitors of food allergic reactions in Europe. Currently, the golden standards to identify, quantify and discriminate celery in a biological sample are immunoassays and two-step molecular detection assays in which quantitative PCR (qPCR) is followed by a high-resolution melting analysis (HRM). In order to provide a DNA-based, rapid and simple detection method suitable for one-step quantification, a fiber optic PCR melting assay (FO-PCR-MA) was developed to determine different concentrations of celery DNA (1 pM-0.1 fM). The presented method is based on the hybridization and melting of DNA-coated gold nanoparticles to the FO sensor surface in the presence of the target gene (mannitol dehydrogenase, Mtd). The concept was not only able to reveal the presence of celery DNA, but also allowed for the cycle-to-cycle quantification of the target sequence through melting analysis. Furthermore, the developed bioassay was benchmarked against qPCR followed by HRM, showing excellent agreement (R² = 0.96). In conclusion, this innovative and sensitive diagnostic test could further improve food quality control and thus have a large impact on allergen induced healthcare problems.

Nanoscale patterning of gold-coated optical fibers for improved plasmonic sensing

Merging surface plasmon resonance (SPR) to fiber optic (FO) technology has brought remarkable achievements in the field by offering attractive advantages over the conventional prism-based SPR platforms, such as simplicity, cost-effectiveness and miniaturization. However, the performance of the existing FO-SPR instruments mainly depends on the device surface condition and in particular on the structural aspect of the thin gold (Au) plasmonic film deposited on the FO substrate. In this work, a simple cost-effective colloidal lithography technique (CLT) was adapted and applied for the first time to the micrometer-sized FO substrate, to design end reflection-type FO-SPR sensors with periodic arrays of Au triangularly-shaped nanostructures on the Au mirror FO tip distal end. The nanopatterned FO-SPR sensor tips were afterwards subjected to refractometric measurements in a sucrose dilution series and subsequently compared with their non-patterned counterparts. It was observed that the spectral dips of the nanopatterned FO-SPR sensor tips were shifted towards longer wavelengths after CLT patterning. Moreover, the sensor sensitivity was improved with up to 25% compared to the conventional non-patterned FO-SPR devices. The obtained results represent important steps in the development of a new generation of FO-SPR sensors with improved performance, which can ultimately be used in various applications, ranging from food analysis and environmental monitoring, to health control and medical diagnosis.

Real-time PCR melting analysis with fiber optic SPR enables multiplex DNA identification of bacteria

A fiber optic surface plasmon resonance (FO-SPR) technology was developed that enables simultaneous quantification and identification of multiple DNA targets on the same platform. The bioassay was based on the hybridization/melting of DNA-coated Au nanoparticles on the FO-SPR sensor when targets are present. The multiplex concept was successfully demonstrated on two related bacteria and for detection of multiple mutations in sequences. In conclusion, FO-SPR technology shows a great potential as a next generation in vitro diagnostics tool.

An electricity-fluorescence double-checking biosensor based on graphene for detection of binding kinetics of DNA hybridization

In this paper, an electricity-fluorescence double-checking biosensor based on graphene materials has been presented for detection of DNA hybridization kinetics.

Competitive inhibition assay for the detection of progesterone in dairy milk using a fiber optic SPR biosensor

Analytical methods that are often used for the quantification of progesterone in bovine milk include immunoassays and chromatographic techniques. Depending on the selected method, the main disadvantages are the cost, time-to-result, labor intensity and usability as an automated at-line device. This paper reports for the first time on a robust and practical method to quantify small molecules, such as progesterone, in complex biological samples using an automated fiber optic surface plasmon resonance (FO-SPR) biosensor. A FO-SPR competitive inhibition assay was developed to determine biologically relevant concentrations of progesterone in bovine milk (1-10 ng/mL), after optimizing the immobilization of progesterone-bovine serum albumin (P4-BSA) conjugate, the specific detection with anti-progesterone antibody and the signal amplification with goat anti-mouse gold nanoparticles (GAM-Au NPs). The progesterone was detected in a bovine milk sample with minimal sample preparation, namely ½ dilution of the sample. Furthermore, the developed bioassay was benchmarked against a commercially available ELISA, showing excellent agreement (R² = 0.95). Therefore, it is concluded that the automated FO-SPR platform can combine the advantages of the different existing methods for quantification of progesterone: sensitivity, accuracy, cost, time-to-result and ease-of-use.

A nanoparticle-based thermo-dynamic aptasensor for small molecule detection

Small molecules (MW < 1000 Da) represent a large class of biomarkers of interest. Recently, a new class of biosensors has been emerging thanks to the recognition properties of aptamers, short DNA or RNA single strands, selected against such small molecular targets. Among them, an adenosine-specific aptamer has been largely described and used due to its remarkable affinity to this small target (K_D = 6 μM). In this paper, we achieved the proof-of-principle of an aptasensor based on the thermodynamic follow-up of adenosine binding with engineered split-aptamer sequences. The detection is carried out by surface plasmon resonance imaging of split-aptamer micro-arrays, while signal amplification is ensured by gold nanoparticles (AuNPs). This original approach based on DNA sequence engineering and AuNP conjugation enabled us to reach limits of detection (LOD) 200 times lower than the K_D measured in solution with the native aptamer (LOD = 30 nM).

High resolution fiber optic surface plasmon resonance sensors with single-sided gold coatings

The surface plasmon resonance (SPR) performance of gold coated tilted fiber Bragg gratings (TFBG) at near infrared wavelengths is evaluated as a function of the angle between the tilt plane orientation and the direction of single- and double-sided, nominally 50 nm-thick gold metal depositions. Scanning electron microscope images show that the coating are highly non-uniform around the fiber circumference, varying between near zero and 50 nm. In spite of these variations, the experimental results show that the spectral signature of the TFBG-SPR sensors is similar to that of simulations based on perfectly uniform coatings, provided that the depositions are suitably oriented along the tilt plane direction. Furthermore, it is shown that even a (properly oriented) single-sided coating (over only half of the fiber circumference) is sufficient to provide a theoretically perfect SPR response with a bandwidth under 5 nm, and 90% attenuation. Finally, using a pair of adjacent TFBG resonances within the SPR response envelope, a power detection scheme is used to demonstrate a limit of detection of 3 × 10^-6 refractive index units.

SPR and SPR Imaging: Recent Trends in Developing Nanodevices for Detection and Real-Time Monitoring of Biomolecular Events

In this paper we review the underlying principles of the surface plasmon resonance (SPR) technique, particularly emphasizing its advantages along with its limitations regarding the ability to discriminate between the specific binding response and the interfering effects from biological samples. While SPR sensors were developed almost three decades, SPR detection is not yet able to reduce the time-consuming steps of the analysis, and is hardly amenable for miniaturized, portable platforms required in point-of-care (POC) testing. Recent advances in near-field optics have emerged, resulting in the development of SPR imaging (SPRi) as a powerful optical, label-free monitoring tool for multiplexed detection and monitoring of biomolecular events. The microarrays design of the SPRi chips incorporating various metallic nanostructures make these optofluidic devices more suitable for diagnosis and near-patient testing than the traditional SPR sensors. The latest developments indicate SPRi detection as being the most promising surface plasmon-based technique fulfilling the demands for implementation in lab-on-a-chip (LOC) technologies.

Fiber optic-SPR platform for fast and sensitive infliximab detection in serum of inflammatory bowel disease patients

Infliximab (IFX) is a therapeutic monoclonal antibody used for treating patients with inflammatory bowel disease (IBD). In order to improve therapeutic outcomes it is recommended to monitor IFX trough concentrations. Although ELISA is currently widely used for this purpose, this method is not suitable for single patient testing. In this paper we describe the development of a fast bioassay for determining IFX concentration in serum using an in-house developed fiber-optic surface plasmon resonance (FO-SPR) biosensor. Studies were first conducted to optimize covalent immobilization of the IFX-specific antibody on the sensor surface as well as to select an optimal blocking buffer for restraining the non-specific binding. In order to reach clinically relevant sensitivity for detecting IFX in patients' serum, the SPR signal was amplified by employing gold nanoparticles functionalized with another set of IFX specific antibodies. Using the optimized sandwich bioassay, calibration curves were made with series of IFX concentrations spiked in buffer and 100-fold diluted serum, reaching the limit of detection of 0.3 and 2.2ng/ml, respectively. The established bioassay was finally validated using five IFX treated IBD patients samples. Results from the FO-SPR platform were compared with an in-house developed, clinically validated ELISA resulting in excellent Pearson and intraclass correlation coefficient of 0.998 and 0.983, respectively. Furthermore, the assay time of the FO-SPR platform was significantly reduced compared to ELISA, demonstrating the potential of this platform to be used as a point-of-care diagnostic tool for improving therapeutic outcomes of IBD patients.

Review of plasmonic fiber optic biochemical sensors: improving the limit of detection

This paper presents a brief overview of the technologies used to implement surface plasmon resonance (SPR) effects into fiber-optic sensors for chemical and biochemical applications and a survey of results reported over the last ten years. The performance indicators that are relevant for such systems, such as refractometric sensitivity, operating wavelength, and figure of merit (FOM), are discussed and listed in table form. A list of experimental results with reported limits of detection (LOD) for proteins, toxins, viruses, DNA, bacteria, glucose, and various chemicals is also provided for the same time period. Configurations discussed include fiber-optic analogues of the Kretschmann-Raether prism SPR platforms, made from geometry-modified multimode and single-mode optical fibers (unclad, side-polished, tapered, and U-shaped), long period fiber gratings (LPFG), tilted fiber Bragg gratings (TFBG), and specialty fibers (plastic or polymer, microstructured, and photonic crystal fibers). Configurations involving the excitation of surface plasmon polaritons (SPP) on continuous thin metal layers as well as those involving localized SPR (LSPR) phenomena in nanoparticle metal coatings of gold, silver, and other metals at visible and near-infrared wavelengths are described and compared quantitatively.

Smart design of fiber optic surfaces for improved plasmonic biosensing

Although the phenomenon of surface plasmon resonance (SPR) is known for more than a century now, traditional prism-based SPR platforms have hardly escaped the research laboratories despite being recognized for the sensitive and specific performance. Significant efforts have been made over the last years to overcome their existing limitations by coupling the SPR phenomenon to the fiber optic (FO) technology. While this platform has been promoted as cost-effective and simpler alternative capable of handling label-free bioassays, quantification and real-time monitoring of biomolecular interactions, examples of its applicability in sensing and biosensing remain to date very limited. The FO-SPR system is still in development and requires further advancements for reaching the stability and sensitivity of the benchmark SPR systems. Among existing strategies for device improvement, those based on modifying the FO tips using nanomaterials are mostly studied. These small-scale objects provide a wide range of possibilities for alternating the architecture of the FO sensitive zone, enabling also unique effects such as localized SPR (LSPR). This mini-review summarizes the latest innovations in the fabrication procedures which use nanoparticles or other nanomaterials, aiming at FO-SPR technology performance improvements, as well as addition of new device features and functionalities.

Current and emerging Legionella diagnostics for laboratory and outbreak investigations

Legionnaires' disease (LD) is an often severe and potentially fatal form of bacterial pneumonia caused by an extensive list of Legionella species. These ubiquitous freshwater and soil inhabitants cause human respiratory disease when amplified in man-made water or cooling systems and their aerosols expose a susceptible population. Treatment of sporadic cases and rapid control of LD outbreaks benefit from swift diagnosis in concert with discriminatory bacterial typing for immediate epidemiological responses. Traditional culture and serology were instrumental in describing disease incidence early in its history; currently, diagnosis of LD relies almost solely on the urinary antigen test, which captures only the dominant species and serogroup, Legionella pneumophila serogroup 1 (Lp1). This has created a diagnostic "blind spot" for LD caused by non-Lp1 strains. This review focuses on historic, current, and emerging technologies that hold promise for increasing LD diagnostic efficiency and detection rates as part of a coherent testing regimen. The importance of cooperation between epidemiologists and laboratorians for a rapid outbreak response is also illustrated in field investigations conducted by the CDC with state and local authorities. Finally, challenges facing health care professionals, building managers, and the public health community in combating LD are highlighted, and potential solutions are discussed.

Heat-transfer-based detection of SNPs in the PAH gene of PKU patients

Conventional neonatal diagnosis of phenylketonuria is based on the presence of abnormal levels of phenylalanine in the blood. However, for carrier detection and prenatal diagnosis, direct detection of disease-correlated mutations is needed. To speed up and simplify mutation screening in genes, new technologies are developed. In this study, a heat-transfer method is evaluated as a mutation-detection technology in entire exons of the phenylalanine hydroxylase (PAH) gene. This method is based on the change in heat-transfer resistance (R_th) upon thermal denaturation of dsDNA (double-stranded DNA) on nanocrystalline diamond. First, ssDNA (single-stranded DNA) fragments that span the size range of the PAH exons were successfully immobilized on nanocrystalline diamond. Next, it was studied whether an R_th change could be observed during the thermal denaturation of these DNA fragments after hybridization to their complementary counterpart. A clear R_th shift during the denaturation of exon 5, exon 9, and exon 12 dsDNA was observed, corresponding to lengths of up to 123 bp. Finally, R_th was shown to detect prevalent single-nucleotide polymorphisms, c.473G>A (R158Q), c.932T>C (p.L311P), and c.1222C>T (R408W), correlated with phenylketonuria, displaying an effect related to the different melting temperatures of homoduplexes and heteroduplexes.