Enhancing sensitivity and selectivity of long-period grating sensors using structure-switching aptamers bound to gold-doped macroporous silica coatings

A Fiber Bragg Grating Sensor Based on Cladding Mode Resonance for Label-Free Biosensing

A fiber-optic biosensing platform based on ultra-narrowband cladding mode resonances was developed on a high-reflectivity fiber Bragg grating (FBG) for targeting biomolecular detection. The multiple cladding modes with a high sensitivity to the refractive index (RI) were excited in the FBG by coupling between the forward-propagating guided core mode of the multimode fiber and the backward-propagating guided cladding mode of the FBG without any damage to the fiber structure or any change to the standard FBG manufacturing process. The full width at half maximum and the Q-factor of the typical cladding mode resonance operation of the proposed sensor are 80 pm and 19,270, respectively, which are better than those of most fiber-optic biosensors reported to date. In addition, the FBG sensor demonstrated a high sensitivity in protein detection and a high selectivity in serum sample assays. The sensitivity of this sensor was further increased simply by coating it with graphene oxide (GO) sheets on the sensing surface without using a signal amplification strategy. Furthermore, an ultra-low limit of detection (LOD) of 32 pM was obtained by the GO-coated FBG sensor for IgG detection. The proposed FBG sensor provides a competitive fiber-optic platform for biomolecular detection. It has a great potential for applications in label-free biosensing.

Recent progress in fluorescent aptasensors for the detection of aflatoxin B1 in food

Aflatoxin B1 pollution is one of the most critical issues of food safety and has been categorized as a group I carcinogen by the International Agency for Research on Cancer. Aflatoxin B1 exists in various foods and feedstuff products and can be produced and contaminate food products in all processes, including growth, harvest, storage, or processing. Therefore, it is of great value for detecting and on-site monitoring aflatoxin B1. Aptamers are short single-stranded DNA or RNA obtained from the nucleic acid molecular library through SELEX. With advantages of high specificity, large affinity, and easy modification, aptasensors have become popular in a wide range of promising applications. This review focuses on recent advances on fluorescent aptamer sensors for the detection of aflatoxin B1, including their design strategies, working mechanisms, and applications to on-site detection. Finally, the current challenges and prospects are discussed.

Development of an optical microfiber immunosensor for prostate specific antigen analysis using a high-order-diffraction long period grating

Fiber-optic biosensors are of great interest to many bio/chemical sensing applications. In this study, we demonstrate a high-order-diffraction long period grating (HOD-LPG) for the detection of prostate specific antigen (PSA). A HOD-LPG with a period number of less than ten and an elongated grating pitch could realize a temperature-insensitive and bending-independent biosensor. The bio-functionalized HOD-LPG was capable of detecting PSA in phosphate buffered saline with concentrations ranging from 5 to 500 ng/ml and exhibited excellent specificity. A limit of detection of 9.9 ng/ml was achieved, which is promising for analysis of the prostate specific antigen.

Functionalized etched tilted fiber Bragg grating aptasensor for label-free protein detection

An aptasensor based on etched tilted fiber Bragg grating (eTFBG) is developed on a single-mode optical fiber targeting biomolecule detection. TFBGs were chemically etched using hydrofluoric acid (HF) to partially remove the fiber cladding. The sensor response was coarsely interrogated, resulting on a sensitivity increase from 1.25 nm/RIU (refractive index unit) at the beginning of the process, up to 23.38 nm/RIU at the end of the etching, for a RI range from 1.3418 to 1.4419 RIU. The proposed aptasensor showed improved RI sensitivity as compared to the unetched TFBG, without requiring metal depositions on the fiber surface or polarization control during the measurements. The proposed sensor was tested for the detection of thrombin-aptamer interactions based on silane-coupling surface chemistry, with thrombin concentrations ranging from 2.5 to 40 nM. Functionalized eTFBGs provided a competitive platform for biochemical interaction measurements, showing sensitivity values ranging from 2.3 to 3.3 p.m./nM for the particular case of thrombin detection.

Label-free cocaine aptasensor based on a long-period fiber grating

In this Letter, we combined a promising bioreceptor, a cocaine aptamer MN6, with an ultrasensitive optical platform long-period fiber grating (LPFG) to create a new cocaine biosensor. The cocaine induces a conformational rearrangement of the aptamer which changes the refractive index around the LPFG producing a measurable shift of the transmission spectrum. We were able to track subtle interaction between the receptor and cocaine molecules over a concentration range of 25 to 100 μM. The presented biosensor does not require labeling or signal enhancement, resulting in a simple user-friendly device.

Highly sensitive aptasensor based on interferometric reflectance spectroscopy for the determination of amyloid β as an Alzheimer's disease biomarkers using nanoporous anodic alumina

It is well known that Alzheimer's disease is one of the global challenges for the 21st century. Therefore, it is urgent to develop a reliable biosensor for the detection of this disease. Here in, we have developed for the first time, an aptasensor based on interferometric reflectance spectroscopy (IRS) for the determination of amyloid β (Aβ) oligomers that is an Alzheimer's disease biomarker. For this purpose, the nanoporous anodic alumina (NAA) was first fabricated. After that, the pore walls of the NAA were modified with (3-aminopropyl) trimethoxysilane (NAA-NH₂). The amino-terminal aptamers probe were then attached to the pore walls of the NAA-NH₂ by using glutaraldehyde (GA) as the cross-linking agent. Subsequently, methylene blue (MB) was immobilized into the aptamer as the photo-probe, generating the MB/G-quadruplex complex. Since MB has a high absorption coefficient, the intensity of the reflected white light to the charge-coupled device (CCD) detector decreased. In the presence of the Aβ oligomers that have high affinity to the immobilized aptamer, the MB/quadruplex complex broke and MB washed away from the aptasensor. Therefore, the intensity of the reflected white light to the CCD detector increased. The increased signal intensity of the aptasensor has a logarithmic relationship with the concentration of Aβ oligomers. The proposed aptasensor exhibited a good response to the concentration of Aβ oligomers in the range of 0.5-50.0 μg × mL^-1. The experimental detection limit was of 0.02 μg × mL^-1 (at 3σ/S). The proposed optical aptasensor exhibited good selectivity, linear range, and stability.

Duplexed aptamers: history, design, theory, and application to biosensing

Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.

C4-HSL aptamers for blocking qurom sensing and inhibiting biofilm formation in Pseudomonas aeruginosa and its structure prediction and analysis

This study aimed to screen DNA aptamers against the signal molecule C4-HSL of the rhl system for the inhibition of biofilm formation of Pseudomonas aeruginosa using an improved systematic evolution of ligand by exponential enrichment (SELEX) method based on a structure-switching fluorescent activating bead. The aptamers against the C4-HSL with a high affinity and specifity were successfully obtained and evaluated in real-time by this method. Results of biofilm inhibition experiments in vitro showed that the biofilm formation of P. aeruginosa was efficiently reduced to about 1/3 by the aptamers compared with that of the groups without the aptamers. Independent secondary structure simulation and computer-aided tertiary structure prediction (3dRNA) showed that the aptamers contained a highly conserved Y-shaped structural unit. Therefore, this study benefits the search for new methods for the detection and treatment of P. aeruginosa biofilm formation.

Towards a Uniform Metrological Assessment of Grating-Based Optical Fiber Sensors: From Refractometers to Biosensors

A metrological assessment of grating-based optical fiber sensors is proposed with the aim of providing an objective evaluation of the performance of this sensor category. Attention was focused on the most common parameters, used to describe the performance of both optical refractometers and biosensors, which encompassed sensitivity, with a distinction between volume or bulk sensitivity and surface sensitivity, resolution, response time, limit of detection, specificity (or selectivity), reusability (or regenerability) and some other parameters of generic interest, such as measurement uncertainty, accuracy, precision, stability, drift, repeatability and reproducibility. Clearly, the concepts discussed here can also be applied to any resonance-based sensor, thus providing the basis for an easier and direct performance comparison of a great number of sensors published in the literature up to now. In addition, common mistakes present in the literature made for the evaluation of sensor performance are highlighted, and lastly a uniform performance assessment is discussed and provided. Finally, some design strategies will be proposed to develop a grating-based optical fiber sensing scheme with improved performance.

Sol-Gel-Based Titania-Silica Thin Film Overlay for Long Period Fiber Grating-Based Biosensors

An evanescent wave optical fiber biosensor based on titania-silica-coated long period grating (LPG) is presented. The chemical overlay, which increases the refractive index (RI) sensitivity of the sensor, consists of a sol-gel-based titania-silica thin film, deposited along the sensing portion of the fiber by means of the dip-coating technique. Changing both the sol viscosity and the withdrawal speed during the dip-coating made it possible to adjust the thickness of the film overlay, which is a crucial parameter for the sensor performance. After the functionalization of the fiber surface using a methacrylic acid/methacrylate copolymer, an antibody/antigen (IgG/anti-IgG) assay was carried out to assess the performance of sol-gel based titania-silica-coated LPGs as biosensors. The analyte concentration was determined from the wavelength shift at the end of the binding process and from the initial binding rate. This is the first time that a sol-gel based titania-silica-coated LPG is proposed as an effective and feasible label-free biosensor. The specificity of the sensor was validated by performing the same model assay after spiking anti-IgG into human serum. With this structured LPG, detection limits of the order of tens of micrograms per liter (10(-11) M) are attained.

Highly sensitive optical fibre long period grating biosensor anchored with silica core gold shell nanoparticles

An optical fibre long period grating (LPG), modified with a coating of silica core gold shell (SiO2:Au) nanoparticles (NPs) deposited using the layer-by-layer method, was employed for the development of a biosensor. The SiO2:Au NPs were electrostatically assembled onto the LPG with the aid of a poly(allylamine hydrochloride) (PAH) polycation layer. The LPG sensor operates at the phase matching turning point to provide the highest sensitivity. The SiO2:Au NPs were modified with biotin, which was used as a ligand for streptavidin (SV) detection. The sensing mechanism is based on the measurement of the refractive index change induced by the binding of the SV to the biotin. The effect on sensitivity of increasing the surface area by virtue of the SiO2:Au nanoparticles' diameter and film thickness was studied. The lowest measured concentration of SV was 2.5nM, achieved using an LPG modified with a 3 layer (PAH/SiO2:Au) thin film composed of SiO2 NPs of 300nm diameter with a binding constant of k=1.7(pM)(-1), sensitivity of 6.9nm/ng/mm(2) and limit of detection of 19pg/mm(2).

Identification of the target binding site of ethanolamine-binding aptamers and its exploitation for ethanolamine detection

Aptamers are promising recognition elements for sensitive and specific detection of small molecules. We have previously selected ssDNA aptamers for ethanolamine, one of the smallest aptamer targets so far. The work presented here focuses on the determination of the binding region within the aptamer structure and its exploitation for the development of an aptamer-based assay for detection of ethanolamine. Sequence analysis of the aptamers resulted in the identification of a G-rich consensus sequence, which was able to fold in a typical two- or three-layered G-quartet structure. Experiments with stepwise truncated variants of the aptamers revealed that the consensus sequence is responsible and sufficient for binding to the target. On the basis of the knowledge of the aptamers binding site, we developed an aptamer-based microarray assay relying on competition between ethanolamine and an oligonucleotide complementary to the consensus sequence. Competitive binding of ethanolamine and fluorescently labeled complementary oligonucleotides resulted in fluorescence intensities dependent on ethanolamine concentration with a limit of detection of 10 pM. This method enables detection of small molecules without any labeling of analytes. The competitive assay could potentially be transferred to other aptamers and thus provides a promising system for aptamer-based detection of diverse small molecules.

Fabricating Nanoporous Silica Structure on D-Fibres through Room Temperature Self-Assembly

The room temperature deposition of self-assembling silica nanoparticles onto D-shaped optical fibres (“D-fibre”), drawn from milled preforms fabricated by modified chemical vapour deposition (MCVD), is studied. Vertical dip-and-withdraw produces tapered layers, with one end thicker (surface coverage >0.85) than the other, whilst horizontal dip-and-withdraw produces much more uniform layers over the core region. The propagation of induced fracturing over the core region during drying is overcome using a simple protrusion of the inner cladding. Thick coatings are discernible through thin film interference colouring, but thinner coatings require scanning electron microscopy (SEM) imaging. Here, we show that fluorescence imaging, using Rhodamine B, in this example, can provide some qualitative and speedy assessment of coverage.

Nucleic acid aptamers as high affinity ligands in biotechnology and biosensorics

Aptamers are small nucleic acid molecules capable of binding to a wide range of target molecules with high affinity and specificity. They have been developed and widely used not only as research tools, but also as biosensors, specific antagonists, and diagnostic markers and as protein purification platform for many pharmaceutical and clinical applications. Here, in this paper we will explore biochemical aspects of aptamer-target interactions and show why aptamers rival antibodies in target recognition and purification procedures. This review will focus on strategies of using aptamers as affinity ligands for molecules of therapeutic and pharmaceutical interest including applications in chromatography and capillary electrophoresis for protein and small molecule purification. Moreover, we will also discuss aptamers whose binding parameters can be controlled on demand for diagnostic approaches and used as sensitive receptors in biosensorics. Aptamers have opened up exciting fields in basic and applied research of pharmaceutical and biotechnological interest.

Photonic crystal fiber for layer-by-layer assembly and measurements of polyelectrolyte thin films

The cladding air channels of an endlessly single-mode photonic crystal fiber (PCF) and the high-index sensitivity of its long-period gratings (LPG) inscribed by CO(2) laser have been exploited to deposit poly(vinyl pyrrolidone) (PVPON)/poly(methacrylic acid) (PMAA) polyelectrolyte thin films via layer-by-layer assembly (LbL) and to measure the deposition process. We show that LbL can be controllably carried out within the axially aligned air channels. PCF-LPG is highly sensitive to the LbL process as reflected by ~1.625 nm shift in the resonance wavelength per polyelectrolyte layer incorporated. PCF-LPG is also very robust for in situ monitoring of the release of PVPON from cross-linked polyelectrolytes, which results in the formation of pH-responsive PMAA hydrogel. PCF-LPG containing the hydrogel exhibits well-behaved response to changes in solution pH over 2 to 7.5. We demonstrate that PCF-LPG is 2 orders of magnitude more sensitive than its traditional all-solid counterpart through parallel investigation.

Au(III)-assisted core-shell iron oxide@poly(o-phenylenediamine) nanostructures for ultrasensitive electrochemical aptasensors based on DNase I-catalyzed target recycling

A redox-active Au(III)-assisted core-shell iron oxide@poly(o-phenylenediamine) nanostructure was designed as a sensing platform for ultrasensitive electrochemical detection of small molecules (ATP, used as a model here) by coupling with DNase I-catalyzed target recycling.