Antibody Fragments as Probe in Biosensor Development

EpiScan: accurate high-throughput mapping of antibody-specific epitopes using sequence information

The identification of antibody-specific epitopes on virus proteins is crucial for vaccine development and drug design. Nonetheless, traditional wet-lab approaches for the identification of epitopes are both costly and labor-intensive, underscoring the need for the development of efficient and cost-effective computational tools. Here, EpiScan, an attention-based deep learning framework for predicting antibody-specific epitopes, is presented. EpiScan adopts a multi-input and single-output strategy by designing independent blocks for different parts of antibodies, including variable heavy chain (VH), variable light chain (VL), complementary determining regions (CDRs), and framework regions (FRs). The block predictions are weighted and integrated for the prediction of potential epitopes. Using multiple experimental data samples, we show that EpiScan, which only uses antibody sequence information, can accurately map epitopes on specific antigen structures. The antibody-specific epitopes on the receptor binding domain (RBD) of SARS coronavirus 2 (SARS-CoV-2) were located by EpiScan, and the potentially valuable vaccine epitope was identified. EpiScan can expedite the epitope mapping process for high-throughput antibody sequencing data, supporting vaccine design and drug development. Availability: For the convenience of related wet-experimental researchers, the source code and web server of EpiScan are publicly available at https://github.com/gzBiomedical/EpiScan .

Oriented immobilization of nanobodies using SpyCatcher/SpyTag significantly enhances the capacity of affinity chromatography

The use of nanobodies (Nbs) in affinity chromatography for biomacromolecule purification is gaining popularity. However, high-performance Nb-based affinity resins are not readily available, mainly due to the lack of suitable immobilization methods. In this study, we explored an autocatalytic coupling strategy based on the SpyCatcher/SpyTag chemistry to achieve oriented immobilization of Nb ligands. To facilitate this approach, a variant cSpyCatcher003 (cSC003) was coupled onto agarose microspheres, providing a specific attachment site for SpyTagged nanobody ligands. The cSC003 easily purified from Escherichia coli through a two-step procedure, exhibits exceptional alkali resistance and structural recovery capability, highlighting its robustness as a linker in the coupling strategy. To validate the effectiveness of cSC003-derivatized support, we employed VHSA, a nanobody against human serum albumin (HSA), as the model ligand. Notably, the immobilization of SpyTagged VHSA onto the cSC003-derivatized support was achieved with a coupling efficiency of 90 %, significantly higher than that of traditional thiol-based coupling method. This improvement directly correlated to the preservation of the native conformation of nanobodies during the coupling process. In addition, the Spy-immobilized resin demonstrated better performance in the binding capacity, with a 3-fold improvement in capture efficiency, underscoring the advantages of the Spy immobilization strategy for oriented immobilization of VHSA ligands. Moreover, online purification and immobilization of SpyTagged VHSA from crude bacterial lysate was achieved using the cSC003-derivatized support. The resulting resin exhibited high binding specificity towards HSA, yielding a purity above 95 % directly from human serum, and maintained good stability throughout multiple purification cycles. These findings highlight the potential of the Spy immobilization strategy for developing Nb-based affinity chromatographic materials, with significant implications for biopharmaceutical downstream processes.

Rapid and Convenient Single-Chain Variable Fragment-Employed Electrochemical C-Reactive Protein Detection System

Although IgG-free immunosensors are in high demand owing to ethical concerns, the development of convenient immunosensors that alternatively integrate recombinantly produced antibody fragments, such as single-chain variable fragments (scFvs), remains challenging. The low affinity of antibody fragments, unlike IgG, caused by monovalent binding to targets often leads to decreased sensitivity. We improved the affinity owing to the bivalent effect by fabricating a bivalent antibody-enzyme complex (AEC) composed of two scFvs and a single glucose dehydrogenase, and developed a rapid and convenient scFv-employed electrochemical detection system for the C-reactive protein (CRP), which is a homopentameric protein biomarker of systemic inflammation. The development of a point-of-care testing (POCT) system is highly desirable; however, no scFv-based CRP-POCT immunosensors have been developed. As expected, the bivalent AEC showed higher affinity than the single scFv and contributed to the high sensitivity of CRP detection. The electrochemical CRP detection using scFv-immobilized magnetic beads and the bivalent AEC as capture and detection antibodies, respectively, was achieved in 20 min without washing steps in human serum and the linear range was 1-10 nM with the limit of detection of 2.9 nM, which has potential to meet the criteria required for POCT application in rapidity, convenience, and hand-held detection devices without employing IgGs.

Recent advances in the development and applications of luminescent bacteria-based biosensors

Luminescent bacteria-based biosensors are widely used for fast and sensitive monitoring of food safety, water quality, and other environmental pollutions. Recent advancements in biomedical engineering technology have led to improved portability, integration, and intelligence of these biotoxicity assays. Moreover, genetic engineering has played a significant role in the development of recombinant luminescent bacterial biosensors, enhancing both detection accuracy and sensitivity. This review provides an overview of recent advances in the development and applications of novel luminescent bacteria-based biosensors, and future perspectives and challenges in the cutting-edge research, market translation, and practical applications of luminescent bacterial biosensing are discussed.

Continuous Monitoring Biosensing Mediated by Single-Molecule Plasmon-Enhanced Fluorescence in Complex Matrices

Continuous detection of critical markers directly at the point of interest and in undiluted biological fluids represents the next fundamental step in biosensing. The goal of realizing such a platform is utterly challenging because it requires a reversible biosensor that enables the tracking of pico- to nanomolar molecular concentrations over long time spans in a compact device. Here we describe a sensing method based on plasmon-enhanced fluorescence capable of single-molecule detection of unlabeled analyte by employing biofunctionalized gold nanoparticles. The very strong plasmon-enhanced fluorescence signals allow for single-molecule sensing in unaltered biological media, while the use of low-affinity interactions ensures the continuous tracking of increasing and decreasing analyte concentrations with picomolar sensitivity. We demonstrate the use of a sandwich assay for a DNA cancer marker with a limit of detection of picomolar and a time response of 10 min. The enhanced single-molecule signals will allow for miniaturization into a small and cheap platform with multiplexing capability for application in point-of-care diagnostics, monitoring of industrial processes, and safe keeping of the environment.

Epitope imprinted polymeric materials: application in electrochemical detection of disease biomarkers

Epitope imprinting is a promising method for creating specialized recognition sites that resemble natural biorecognition elements. Epitope-imprinted materials have gained a lot of attention recently in a variety of fields, including bioanalysis, drug delivery, and clinical therapy. The vast applications of epitope imprinted polymers are due to the flexibility in choosing monomers, the simplicity in obtaining templates, specificity toward targets, and resistance to harsh environments along with being cost effective in nature. The "epitope imprinting technique," which uses only a tiny subunit of the target as the template during imprinting, offers a way around various drawbacks inherent to biomacromolecule systems i.e., traditional molecular imprinting techniques with regards to the large size of proteins, such as the size, complexity, accessibility, and conformational flexibility of the template. Electrochemical based sensors are proven to be promising tool for the quick, real-time monitoring of biomarkers. This review unravels epitope imprinting techniques, approaches, and strategies and highlights the applicability of these techniques for the electrochemical quantification of biomarkers for timely disease monitoring. In addition, some challenges are discussed along with future prospective developments.

An Overview of Biosensors for the Detection of Patulin Focusing on Aptamer-Based Strategies

Patulin is a low molecular weight mycotoxin and poses a global problem, especially threatening food safety. It is also resistant to processing temperatures and is commonly found in fruits and vegetables. Studies have shown that it has toxic effects on animals and humans and the severity of patulin toxicity depends on the amount ingested. Therefore, the consumption of contaminated products, especially in infants and children, is important. The maximum daily intake of PAT that can be tolerated is found to be 0.4 µg/kg body weight to prevent chronic effects and the maximum residue limits in food samples were given as 50 ng/g (∼320 nM). Conventional methods for the detection of PAT have many disadvantages such as the use of expensive equipment, the need for trained personnel, and complicated sample preparation steps. To this extent, various numbers of research have been conducted on selective and sensitive detection of patulin using biosensor platforms in various media. This review presents an overview of the current literature dealing with the studies to develop patulin-specific aptamer-based biosensors and adapts various immobilization methods to increase the sensor response using different nanomaterials. Furthermore, a comparison of biosensors with conventional methods is presented using analytical performance parameters and their practicality for the detection of patulin.

Engineering a thermostable biosensor based on biomimetic mineralization HRP@Fe-MOF for Alzheimer's disease

The development of disease detection by biosensors represents one of the key components of medical science. However, millions of people are still misdiagnosed each year due to the poor efficacy and thermal instability of biosensors. Using horseradish peroxidase (HRP) as a paradigm, we offer a rational design strategy to optimize the thermostability and activity of biosensors by biomimetic mineralization. To overcome the weak thermostability of the biosensor, the mineralization of Fe-MOF forms an armor on HRP that protects against high temperature. Additionally, the biomimetic mineralization HRP@Fe-MOF can double-catalyze the TMB/H₂O₂ chromogenic system for color development. The biosensor can also be recycled through simple heat treatment due to the thermally stable aptamer and biomimetic mineralization HRP@Fe-MOF. The optical biosensor based on this sensitive spectral transformation was successfully developed for the measurement of AβO with an outstanding linear range (0.0001-10 nM) and a low limit of detection (LOD) of 0.03 pM. This promising platform will open up new avenues for the detection of AβO in the early diagnosis of Alzheimer's disease (AD).

Quantum Dot-Based Lateral Flow Immunoassay as Point-of-Care Testing for Infectious Diseases: A Narrative Review of Its Principle and Performance

Infectious diseases are the world’s greatest killers, accounting for millions of deaths worldwide annually, especially in low-income countries. As the risk of emerging infectious diseases is increasing, it is critical to rapidly diagnose infections in the early stages and prevent further transmission. However, current detection strategies are time-consuming and have exhibited low sensitivity. Numerous studies revealed the advantages of point-of-care testing, such as those which are rapid, user-friendly and have high sensitivity and specificity, and can be performed at a patient’s bedside. The Lateral Flow Immunoassay (LFIA) is the most popular diagnostic assay that fulfills the POCT standards. However, conventional AuNPs-LFIAs are moderately sensitive, meaning that rapid detection remains a challenge. Here, we review quantum dot (QDs)-based LFIA for highly sensitive rapid diagnosis of infectious diseases. We briefly describe the principles of LFIA, strategies for applying QDs to enhance sensitivity, and the published performance of the QD-LFIA tested against several infectious diseases.

Fabrication of Fragment Antibody–Enzyme Complex as a Sensing Element for Immunosensing

Antibody–enzyme complexes (AECs) are ideal molecular recognition elements for immunosensing applications. One molecule possesses both a binding ability to specific targets and catalytic activity to gain signals, particularly oxidoreductases, which can be integrated into rapid and sensitive electrochemical measurements. The development of AECs using fragment antibodies rather than intact antibodies, such as immunoglobulin G (IgG), has attracted attention for overcoming the ethical and cost issues associated with the production of intact antibodies. Conventionally, chemical conjugation has been used to fabricate AECs; however, controlling stoichiometric conjugation using this method is difficult. To prepare homogeneous AECs, methods based on direct fusion and enzymatic conjugation have been developed, and more convenient methods using Catcher/Tag systems as coupling modules have been reported. In this review, we summarize the methods for fabricating AECs using fragment antibodies developed for sensing applications and discuss the advantages and disadvantages of each method.

Covalently grafting first-generation PAMAM dendrimers onto MXenes with self-adsorbed AuNPs for use as a functional nanoplatform for highly sensitive electrochemical biosensing of cTnT

2D MXene-Ti₃C₂T_χ has demonstrated promising application prospects in various fields; however, it fails to function properly in biosensor setups due to restacking and anodic oxidation problems. To expand beyond these existing limitations, an effective strategy to for modifying the MXene by covalently grafting first-generation poly(amidoamine) dendrimers onto an MXene in situ (MXene@PAMAM) was reported herein. When used as a conjugated template, the MXene not only preserved the high conductivity but also conferred a specific 2D architecture and large specific surface areas for anchoring PAMAM. The PAMAM, an efficient spacer and stabilizer, simultaneously suppressed the substantial restacking and oxidation of the MXene, which endowed this hybrid with improved electrochemical performance compared to that of the bare MXene in terms of favorable conductivity and stability under anodic potential. Moreover, the massive amino terminals of PAMAM offer abundant active sites for adsorbing Au nanoparticles (AuNPs). The resulting 3D hierarchical nanoarchitecture, AuNPs/MXene@PAMAM, had advanced structural merits that led to its superior electrochemical performance in biosensing. As a proof of concept, this MXene@PAMAM-based nanobiosensing platform was applied to develop an immunosensor for detecting human cardiac troponin T (cTnT). A fast, sensitive, and highly selective response toward the target in the presence of a [Fe(CN)₆]^3-/4- redox marker was realized, ensuring a wide detection of 0.1-1000 ng/mL with an LOD of 0.069 ng/mL. The sensor's signal only decreased by 4.38% after 3 weeks, demonstrating that it exhibited satisfactory stability and better results than previously reported MXene-based biosensors. This work has potential applicability in the bioanalysis of cTnT and other biomarkers and paves a new path for fabricating high-performance MXenes for biomedical applications and electrochemical engineering.

Development of a POCT type insulin sensor employing anti-insulin single chain variable fragment based on faradaic electrochemical impedance spectroscopy under single frequency measurement

To improve glycemic control managed through insulin administration, recent studies have focused on developing hand-held point-of-care testing (POCT) electrochemical biosensors for insulin measurement. Amongst them, anti-insulin IgG-based sensors show promise in detecting insulin with high specificity and sensitivity. However, fabrication of electrochemical sensors with IgG antibodies can prove challenging because of their larger molecular size. To overcome these limitations, this study focuses on utilizing the anti-insulin single chain variable fragment (scFv) as a biosensing molecule with single-frequency faradaic electrochemical impedance spectroscopy (EIS). By comparing two different immobilization methods, covalent conjugation via succinimidyl ester and non-covalent poly-histidine chelation, we demonstrated effective modification of the electrode surface with anti-insulin scFv, while retaining its specific recognition toward insulin. Sensor performance was confirmed via the concentration-dependent faradaic electrochemical impedance change using potassium ferricyanide as a redox probe. The optimal frequency for measurement was determined to be the peak slope of the calculated impedance correlation with respect to frequency. Based on the identified optimized frequency, we performed single-frequency measurement of insulin within a concentration range of 10 pM-100 nM. This study can aid in developing a future point-of-care sensor which rapidly and sensitively measures insulin across a dynamic range of physiological concentrations, with label-free detection.

A comprehensive comparison between camelid nanobodies and single chain variable fragments

By the emergence of recombinant DNA technology, many antibody fragments have been developed devoid of undesired properties of natural immunoglobulins. Among them, camelid heavy-chain variable domains (VHHs) and single-chain variable fragments (scFvs) are the most favored ones. While scFv is used widely in various applications, camelid antibodies (VHHs) can serve as an alternative because of their superior chemical and physical properties such as higher solubility, stability, smaller size, and lower production cost. Here, these two counterparts are compared in structure and properties to identify which one is more suitable for each of their various therapeutic, diagnosis, and research applications.

Antibody-Free Rapid Detection of SARS-CoV-2 Proteins Using Corona Phase Molecular Recognition to Accelerate Development Time

To develop better analytical approaches for future global pandemics, it is widely recognized that sensing materials are necessary that enable molecular recognition and sensor assay development on a much faster scale than currently possible. Previously developed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) point-of-care devices are based on the specific molecular recognition using subunit protein antibodies and protein receptors that selectively capture the viral proteins. However, these necessarily involve complex and lengthy development and processing times and are notoriously prone to a loss of biological activity upon sensor immobilization and device interfacing, potentially limiting their use in applications at scale. Here, we report a synthetic strategy for nanoparticle corona interfaces that enables the molecular recognition of SARS-CoV-2 proteins without any antibody and receptor design. Our nanosensor constructs consist of poly(ethylene glycol) (PEG)─phospholipid heteropolymers adsorbed onto near-infrared (nIR) fluorescent single-walled carbon nanotubes (SWCNTs) that recognize the nucleocapsid (N) and spike (S) protein of SARS-CoV-2 using unique three-dimensional (3D) nanosensor interfaces. This results in rapid and label-free nIR fluorescence detection. This antibody-free nanosensor shows up to 50% sensor responses within 5 min of viral protein injections with limit of detection (LOD) values of 48 fM and 350 pM for N and S proteins, respectively. Finally, we demonstrate instrumentation based on a fiber-optic platform that interfaces the advantages of antibody-free molecular recognition and biofluid compatibility in human saliva conditions.

Advances in point-of-care testing for cardiovascular diseases

Point-of-care testing (POCT) is a specific format of diagnostic testing that is conducted without accompanying infrastructure or sophisticated instrumentation. Traditionally, such rapid sample-to-answer assays provide inferior analytical performances to their laboratory counterparts when measuring cardiac biomarkers. Hence, their potentially broad applicability is somewhat bound by their inability to detect clinically relevant concentrations of cardiac troponin (cTn) in the early stages of myocardial injury. However, the continuous refinement of biorecognition elements, the optimization of detection techniques, and the fabrication of tailored fluid handling systems to manage the sensing process has stimulated the production of commercial assays that can support accelerated diagnostic pathways. This review will present the latest commercial POC assays and examine their impact on clinical decision-making. The individual elements that constitute POC assays will be explored, with an emphasis on aspects that contribute to economically feasible and highly sensitive assays. Furthermore, the prospect of POCT imparting a greater influence on early interventions for medium to high-risk individuals and the potential to re-shape the paradigm of cardiovascular risk assessments will be discussed.

Label-Free Immunoassay Using Droplet-Based Brewster's Angle Straddle Interferometry

We report the detection of antigen capture by immobilized antibodies using a simple, label-free version of monochromatic reflective interferometry. The technique is implemented on silicon with its native oxide and relies on choosing an incident angle between the Brewster angles for the air/oxide and oxide/silicon interfaces. We demonstrate sensitivity to anti-human and anti-rabbit immunoglobulin (anti-IgG) concentrations less than 100 nM using only 10 nL droplets of the analyte. We have introduced a protocol using a model sugar to reduce nonspecific binding and have been able to detect anti-IgG even in the presence of 100-fold larger concentrations of bovine serum albumin. The limit of detection is not yet associated with the optical method but is imposed by nonspecific binding. Evaluated in terms of pg/mm², our sensors are comparable in sensitivity to surface plasmon resonance (SPR) but are advantaged with respect to SPR in the tolerance of the optical components and alignment, the low material usage, and the ability to exploit multiplex detection without modification. The simplicity and convenience of the method are promising for eventual application to portable diagnostic applications.

Solubility, Stability, and Avidity of Recombinant Antibody Fragments Expressed in Microorganisms

Solubility of recombinant proteins (i.e., the extent of soluble versus insoluble expression in heterogeneous hosts) is the first checkpoint criterion for determining recombinant protein quality. However, even soluble proteins often fail to represent functional activity because of the involvement of non-functional, misfolded, soluble aggregates, which compromise recombinant protein quality. Therefore, screening of solubility and folding competence is crucial for improving the quality of recombinant proteins, especially for therapeutic applications. The issue is often highlighted especially in bacterial recombinant hosts, since bacterial cytoplasm does not provide an optimal environment for the folding of target proteins of mammalian origin. Antibody fragments, such as single-chain variable fragment (scFv), single-chain antibody (scAb), and fragment antigen binding (Fab), have been utilized for numerous applications such as diagnostics, research reagents, or therapeutics. Antibody fragments can be efficiently expressed in microorganisms so that they offer several advantages for diagnostic applications such as low cost and high yield. However, scFv and scAb fragments have generally lower stability to thermal stress than full-length antibodies, necessitating a judicious combination of designer antibodies, and bacterial hosts harnessed with robust chaperone function. In this review, we discuss efforts on not only the production of antibodies or antibody fragments in microorganisms but also scFv stabilization via (i) directed evolution of variants with increased stability using display systems, (ii) stabilization of the interface between variable regions of heavy (V_H) and light (V_L) chains through the introduction of a non-native covalent bond between the two chains, (iii) rational engineering of V_H-V_L pair, based on the structure, and (iv) computational approaches. We also review recent advances in stability design, increase in avidity by multimerization, and maintaining the functional competence of chimeric proteins prompted by various types of chaperones.

The application of antibody-aptamer hybrid biosensors in clinical diagnostics and environmental analysis

The growing number of various diseases and the increase of environmental contamination are the causes for the development of novel methods for their detection. The possibility of the application of affinity-based biosensors for such purposes seems particularly promising as they provide high selectivity and low detection limits. Recently, the usage of hybrid antibody-aptamer sandwich constructs was shown to be more advantageous in terms of working parameters in comparison to aptamer-based and immune-based biosensors. This review is focused on the usage of hybrid antibody-aptamer receptor layers for the determination of clinically and environmentally important target molecules. In this work, antibodies and aptamer molecules are characterized and the methods of their immobilization as well as analytical signal generation are shown. This is followed by the critical presentation of examples of hybrid sandwich biosensors that have been elaborated in the past 12 years.

Bio-assay of the non-amidated progastrin-derived peptide (G17-Gly) using the tailor-made recombinant antibody fragment and phage display method: a biomedical analysis

In this research, four novel and sensitive immunosensors for electrochemical determination of G17-Gly were designed based on signal amplification and tailor-made recombinant antibody technology. Anti-G17-Gly antibody fragments (i.e. scFv and VL specific to the N- and C-terminal of G17-Gly) were immobilized onto a polymeric nanocomposite comprising poly cetyl trimethyl ammonium bromide (P(CTAB)) as the conductive matrix, chitosan (CS) as a biocompatible agent and gold nanoparticles (AuNPs) as the signal amplification element. The high surface area provided by AuNPs and the small size of scFv/VL establish the basis for immobilizing a high amount of the anti-G17-Gly on the surface of the electrode for detecting G17-Gly in human plasma samples. Under optimal conditions, the designed immunosensors provide an excellent analytical capability for detecting and determining G17-Gly in human plasma samples with a linear range from 0.5 mM to 0.05 pM and a LLOQ of 0.05 pM. The sensitivity order of the immunosensors was Ag/2-mercaptoethanol/phage displaying scFv/P(CTAB-CS)-AuNP/GE, Ag/2-mercaptoethanol/phage displaying VL/P(CTAB-CS)-AuNP/GE, Ag/BSA/scFv/P(CTAB-CS)-AuNP/GE, and Ag/BSA/VL/P(CTAB-CS)-AuNP/GE. The aforementioned characteristics demonstrate that the proposed immune-devices can be used in biological and clinical diagnosis as reliable tools for identifying different oncobiomarkers.

Screen printed electrode-based biosensor functionalized with magnetic cobalt/single-chain antibody fragments for cocaine biosensing in different matrices

On-site detection of substance abuse is an important approach in the preventive and intervention protocols implementations. It is known that the traditional methods are heavy, time-consuming, and need a high level of logistical requirements. As such, biosensors represent great potential to simplify and improve substance abuse detection. In this study, we have designed a functionalized screen-printed electrode (SPE) electrochemical biosensor with cobalt oxide nanoparticles and single-chain antibody fragments (scFvs) for cocaine detection. Different electrochemical techniques such as differential pulse voltammetry, cyclic voltammetry, and electrochemical impedance spectrometry were used to examine the functionality of the designed biosensor. Furthermore, SEM observations were performed to observe the surface changes after functionalization. The results showed that the linearity ranged between 5.0 and 250 ng/mL and a detection limit of 3.6 ng/mL (n = 6). These results were compared to results obtained from Q-TOF/MS where four different matrices (serum, sweat, urine, and saliva) were spiked with 100 ng/mL cocaine and were analyzed by both methods (Biosensor and Q-TOF/MS). Results showed a higher performance of the biosensor compared to traditional methods. In addition, the selectivity of the biosensor was shown in the presence of different interferents where the designed platform showed a specific response to only cocaine. In conclusion, the designed biosensor proposes great potential for portable and on-site substance abuse detection in addition to boasting the capability of reuse of the SPE and thus, reducing the costs related to such applications.

Construction of a Nanobodies Phage Display Library From an Escherichia coli Immunized Dromedary

Background:

Diarrhea caused by Escherichia coli is a major cause of morbidity and mortality in young animals. Few treatment options are available, mainly antibiotic therapy increasingly limited by resistance to commonly used drugs.

Objectives:

The aim of this work was to develop immunotherapy based on the use of camel VHH antibody fragments, or nanobodies, to target pathogenic E. coli surface antigens.

Material and methods:

We immunized a camel with a killed strain we had previously isolated from a diarrheic camel calf and identified as expressing the F17 fimbriae antigen

Results:

The immunized animal developed an anti-E.coli immune response including heavy-chain antibodies. Lymphocytes from this animal were purified and RNA isolated to create a VHH library by phage display with a size of about 10⁹ individual transformants. Panning on live E. coli cells resulted in the isolation of VHH fragments specific to the cell surface antigens.

Conclusion:

The identification of these antigens can lead to the development of new diagnostic and therapeutic tools against diarrhea.

Nanobody: outstanding features for diagnostic and therapeutic applications

Nanobodies (Nbs) have arisen as an alternative to conventional antibodies (Abs) and show great potential when used as tools in different biotechnology fields such as diagnostics and therapy. Different approaches have been described for the production of Nbs and these methods face new challenges focused on improving yield, affinity, and reducing production costs. This review summarizes these challenges, and also the latest advances in the detection of different kinds of molecules, such as proteins and small molecules, and describes their potential use for noninvasive in vivo imaging and for in vitro assays. Moreover, the unique properties of Nbs are outlined like internalization, size, thermal and chemical stability, affinity, blood clearance, and labeling procedures. Concerning therapeutic applications, we highlight some already reported examples about Nbs being used for the treatment of several diseases such as cancer, neurodegenerative or infectious diseases among others. Finally, future trends, opportunities, and disadvantages are also discussed.

3D biosensors in advanced medical diagnostics of high mortality diseases

Cardiovascular diseases, cancer, and diabetes are high mortality diseases, which account for almost two thirds of all deaths worldwide. Their early detection and continuous evaluation are fundamental for an improved patient prognosis and reduced socioeconomic impact. Current biosensor technologies are typically based on the analysis of whole blood samples from patients for the detection of disease-specific biomarkers. However, these technologies display serious shortcomings, such as reduced sensitivity and dynamic range, limited in vivo applicability, and lack of continuous monitoring. There is the urgent need for new diagnostic and treatment follow-up tools, which allow for the early detection of the pathology as well as for the continuous monitoring of the physiological responses to specific therapies. During the last years, a new generation of biosensor technologies with improved performance has emerged in the biomedical sector. The combination of advanced biomaterial methods, biochemical tools, and micro/nanotechnology approaches has resulted in the development of innovative three-dimensional (3D) biosensor platforms for advanced medical diagnosis. In this review, we report the most recent advances in the field of 3D biosensors for clinical applications, focusing on the diagnosis and monitoring of cardiovascular diseases, cancer, and diabetes. We discuss about their clinical performance compared to standard biosensor technologies, their implantable capability, and their integration into microfluidic devices to develop clinically-relevant models. Overall, we anticipate that 3D biosensors will drive us toward a new paradigm in medical diagnosis, resulting in real-time in vivo biosensors capable to significantly improve patient prognosis.

The effects of antigen size, binding site valency, and flexibility on fab-antigen binding near solid surfaces

Next generation antibody microarray devices have the potential to outperform current molecular detection methods and realize new applications in medicine, scientific research, and national defense. However, antibody microarrays, or arrays of antibody fragments ("fabs"), continue to evade mainstream use in part due to persistent reliability problems despite improvements to substrate design and protein immobilization strategies. Other factors could be disrupting microarray performance, including effects resulting from antigen characteristics. Target molecules embody a wide range of sizes, shapes, number of epitopes, epitope accessibility, and other physical and chemical properties. As a result, it may not be ideal for microarray designs to utilize the same substrate or immobilization strategy for all of the capture molecules. This study investigates how three antigen properties, such as size, binding site valency, and molecular flexibility, affect fab binding. The work uses an advanced, experimentally validated, coarse-grain model and umbrella sampling to calculate the free energy of ligand binding and how this energy landscape is different on the surface compared to in the bulk. The results confirm that large antigens interact differently with immobilized fabs compared to smaller antigens. Analysis of the results shows that despite these differences, tethering fabs in an upright orientation on hydrophilic surfaces is the best configuration for antibody microarrays.

Sandwich pair nanobodies, a potential tool for electrochemical immunosensing serum prostate-specific antigen with preferable specificity

Prostate-Specific Antigen (PSA) is a crucial biomarker for screening prostate cancer, but a sensitive and selective immunosensor for rapid quantification of serum PSA remains to be developed. In this study, a sandwich pair of nanobodies (Nbs) (i.e., Nb2 and Nb40) against PSA surface antigen was obtained from an alpaca-derived immune phage display library. A sandwich-type immunosensor for the sensitive and selective detection of PSA in serum samples was ingeniously designed based on the pair of Nbs. The small size of Nb40 allowed high capture densities on the surface of reduced graphene oxide (rGO) nanocomposed with massive Au nanoparticles (rGO@AuNPs), which significantly improved the conductivity and provided a large area to anchor many primary antibodies. The secondary antibody Nb2 fused with streptavidin -binding peptide (SBP) cooperated with Nb40 for PSA sandwiching. Accompanying introduction of horseradish peroxidase-streptavidin (HRP-SA) coupled with Nb2-SBP, the faradaic current was linearly correlated with the logarithm of PSA concentration in a range of 0.1-100 ng mL^-1. More importantly, this immunosensor exhibited excellent selectivity, stability, and reproducibility due to the sandwich pair Nbs. The proposed immunosensor was successfully applied in determining PSA in serum samples and could be used for the sensitive and specific detection of PSA.

The effects of tether placement on antibody stability on surfaces

Despite their potential benefits, antibody microarrays have fallen short of performing reliably and have not found widespread use outside of the research setting. Experimental techniques have been unable to determine what is occurring on the surface of an atomic level, so molecular simulation has emerged as the primary method of investigating protein/surface interactions. Simulations of small proteins have indicated that the stability of the protein is a function of the residue on the protein where a tether is placed. The purpose of this research is to see whether these findings also apply to antibodies, with their greater size and complexity. To determine this, 24 tethering locations were selected on the antibody Protein Data Bank (PDB) ID: 1IGT. Replica exchange simulations were run on two different surfaces, one hydrophobic and one hydrophilic, to determine the degree to which these tethering sites stabilize or destabilize the antibody. Results showed that antibodies tethered to hydrophobic surfaces were in general less stable than antibodies tethered to hydrophilic surfaces. Moreover, the stability of the antibody was a function of the tether location on hydrophobic surfaces but not hydrophilic surfaces.

Label-Free Bioanalyte Detection from Nanometer to Micrometer Dimensions-Molecular Imprinting and QCMs †

Modern diagnostic tools and immunoassay protocols urges direct analyte recognition based on its intrinsic behavior without using any labeling indicator. This not only improves the detection reliability, but also reduces sample preparation time and complexity involved during labeling step. Label-free biosensor devices are capable of monitoring analyte physiochemical properties such as binding sensitivity and selectivity, affinity constants and other dynamics of molecular recognition. The interface of a typical biosensor could range from natural antibodies to synthetic receptors for example molecular imprinted polymers (MIPs). The foremost advantages of using MIPs are their high binding selectivity comparable to natural antibodies, straightforward synthesis in short time, high thermal/chemical stability and compatibility with different transducers. Quartz crystal microbalance (QCM) resonators are leading acoustic devices that are extensively used for mass-sensitive measurements. Highlight features of QCM devices include low cost fabrication, room temperature operation, and most importantly ability to monitor extremely low mass shifts, thus potentially a universal transducer. The combination of MIPs with quartz QCM has turned out as a prominent sensing system for label-free recognition of diverse bioanalytes. In this article, we shall encompass the potential applications of MIP-QCM sensors exclusively label-free recognition of bacteria and virus species as representative micro and nanosized bioanalytes.

VHH Antibodies: Reagents for Mycotoxin Detection in Food Products

Mycotoxins are the toxic secondary metabolites produced by fungi and they are a worldwide public health concern. A VHH antibody (or nanobody) is the smallest antigen binding entity and is produced by heavy chain only antibodies. Compared with conventional antibodies, VHH antibodies overcome many pitfalls typically encountered in clinical therapeutics and immunodiagnostics. Likewise, VHH antibodies are particularly useful for monitoring mycotoxins in food and feedstuffs, as they are easily genetic engineered and have superior stability. In this review, we summarize the efforts to produce anti-mycotoxins VHH antibodies and associated assays, presenting VHH as a potential tool in mycotoxin analysis.

Iodoacetyl-functionalized pullulan: A supplemental enhancer for single-domain antibody-polyclonal antibody sandwich enzyme-linked immunosorbent assay for detection of survivin

Survivin, an inhibitor of the apoptosis protein family, is a potent tumor marker for diagnosis and prognosis. The enzyme-linked immunosorbent assay (ELISA) is one of the methods that has been used for detection of survivin. However, ELISA has several disadvantages caused by the use of conventional antibodies, and we have therefore been trying to develop a novel ELISA system using camelid single-domain antibodies (VHHs) as advantageous replacements. Here we report a supplemental approach to improve the VHH-polyclonal antibody sandwich ELISA for survivin detection. Iodoacetyl-functionalized pullulan was synthesized, and its thiol reactivity was characterized by a model reaction with l-cysteine. The thiophilic pullulan was applied to an immunoassay asan additive upon coating of standard assay plates with an anti-survivin VHH fusion protein with C-terminal cysteine. The results showed that the mole ratio of the additive to VHH had a significant effect on the consequent response. Mole ratios of 0.07, 0.7, and 7 led to 90% lower, 15% higher, and 69% lower responses, respectively, than the response of a positive control in which no additive was used. The background levels observed in any additive conditions were as low as that of a negative control lacking both VHH and the additive. These results indicate the applicability of the thiol-reactive pullulan as a response enhancer to VHH-based ELISA.

Ultrasensitive Scaffold-Dependent Protease Sensors with Large Dynamic Range

The rational construction of synthetic protein switches with predefined input-output parameters constitutes a key goal of synthetic biology with many potential applications ranging from metabolic engineering to diagnostics. Yet, generally applicable strategies to construct tailor-engineered protein switches have so far remained elusive. Here, we use SpyTag/SpyCatcher-mediated protein ligation to engineer modularly organized, scaffold-dependent protease sensors that exploit a combination of affinity targeting and protease-inducible protein-protein interactions. We use this architecture to create a suite of integrated signal sensing and amplification circuits that can detect the activity of α-thrombin and prostate specific antigen with a dynamic range covering 5 orders of magnitude. We determine the key design features critical for signal transmission between protease-based sensors, transducers, and actuators.

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.

Designing monoclonal antibody fragment-based affinity resins with high binding capacity by thiol-directed immobilisation and optimisation of pore/ligand size ratio

Monoclonal antibody (mAb) based affinity resins usually suffer from low binding capacity, most probably as a result of steric hindrance by the large 150kDa size of the mAb and a random immobilisation approach. The present work investigates the influence of a variety of factors on dynamic binding capacity (DBC) such as pore/ligand size ratio, accessibility of ligand and ligand density. The effect of pore/ligand size ratio was investigated using Fab and scFv fragments on various resins with different pore sizes. The accessibility of the ligand was investigated by a site-directed immobilisation approach, where three C-terminal tags, PPKPPK, FLAG™ and Cys, were introduced into the Fab fragments for immobilisation on resins via amino-, carboxyl- and thiol-groups, respectively. The scFv fragments were tagged at the C-terminal only with FLAG™ to enable a straight forward purification procedure, and were immobilised to resins via amino- and carboxyl-groups. The target protein had a molecular weight (MW) of 50kDa. A 3-fold higher dynamic binding capacity at 100% breakthrough (DBC_100%) was observed for Fab wild-type (wt) on CNBr-activated Sepharose 4 FF relative to mAb on same resin at the same ligand density. However, no major difference in DBC_100% was observed between Fab wt and scFv immobilised on CNBr-activated Sepharose 4 FF at the same ligand density. Thus, further increase of pore/ligand size ratio from Fab to scFv on a resin with average pore size of 300Å, did not seem to be beneficial. Among the tested tags, only the C-terminal Cys tag proved to site-direct the ligands during immobilisation as it allowed the DBC_100% to increase 1.6-fold as compared to Fab wt immobilised via amino-groups on CNBr-activated Sepharose 4 FF and Actigel ALD Superflow at the same ligand density. The influence of ligand density was investigated by selecting immobilised Fab Cys on Sulfhydryl-reactive resin. Increasing ligand density from 0.103 to 0.202μmol/mL resulted in the same utilisation yield (82-85%), whereas a further increase in ligand density from 0.202 to 0.328μmol/mL resulted in a 20%-unit decrease in utilisation yield and less steep breakthrough curve, suggesting steric hindrance in the pores of the resin. In addition, site-directed affinity ligands resulted in a more pronounced, sigmoid-shaped breakthrough curve, leading to more efficient use of capacity. The highest DBC_100% was obtained for Fab Cys on Sulfhydryl-reactive resin and scFv on Actigel ALD Superflow; 11mg/mL and 10mg/mL, respectively, as compared to the DBC_100% of 0.8mg/mL for mAb on CNBr-activated Sepharose 4 FF. Pore/ligand size ratio of 3, which was achieved for Fab ligands on the studied resins, was shown to be feasible for capturing a protein in MW of 50kDa. Totally, a 13.8-fold improvement in DBC_100% was achieved with the Fab-based affinity resin coupled via the C-terminal Cys as compared to the mAb-based affinity resin.

Nanoparticle-Templated Molecular Recognition Platforms for Detection of Biological Analytes

Molecular recognition of biological analytes with optical nanosensors provides both spatial and temporal biochemical information. A recently developed sensing platform exploits near-infrared fluorescent single-wall carbon nanotubes combined with electrostatically pinned heteropolymers to yield a synthetic molecular recognition technique that is maximally transparent through biological matter. This molecular recognition technique is known as corona phase molecular recognition (CoPhMoRe). In CoPhMoRe, the specificity of a folded polymer toward an analyte does not arise from a pre-existing polymer-analyte chemical affinity. Rather, specificity is conferred through conformational changes undergone by a polymer that is pinned to the surface of a nanoparticle in the presence of an analyte and the subsequent modifications in fluorescence readout of the nanoparticles. The protocols in this article describe a novel single-molecule microscopy tool (near-infrared fluorescence and total internal reflection fluorescence [nIRF TIRF] hybrid microscope) to visualize the CoPhMoRe recognition process, enabling a better understanding of synthetic molecular recognition. We describe this requisite microscope for simultaneous single-molecule visualization of optical molecular recognition and signal transduction. We elaborate on the general procedures for synthesizing and identifying single-walled carbon nanotube-based sensors that employ CoPhMoRe via two biologically relevant examples of single-molecule recognition for the hormone estradiol and the neurotransmitter dopamine. © 2016 by John Wiley & Sons, Inc.

Optical biosensors for bacteria detection by a peptidomimetic antimicrobial compound

In this work we present a label-free optical biosensor for rapid bacteria detection using a novel peptide-mimetic compound, as the recognition element. The biosensor design is based on an oxidized porous silicon (PSiO2) nanostructure used as the optical transducer, functionalized with the sequence K-[C12K]7 (referred to as K-7α12), which is a synthetic antimicrobial peptide. This compound is a member of a family of oligomers of acylated lysines (OAKs), mimicking the hydrophobicity and charge of natural antimicrobial peptides. The OAK is tethered to the PSiO2 film and the changes in the reflectivity spectrum are monitored upon exposure to Escherichia coli (E. coli) bacterial suspensions and their lysates. We show that capture of bacterial cell fragments induces predictable changes in the reflectivity spectrum, proportional to E. coli concentrations, thereby enabling rapid, sensitive and reproducible detection of E. coli at concentrations as low as 10(3) cells per mL. While for intact bacterial cells, the K-7α12-tethered PSiO2 shows a poor capturing ability, resulting in an insignificant optical response. The biosensor performance is also studied upon exposure to model Gram positive and negative bacterial lysates, suggesting preferential capture of E. coli cell fragments in the presented scheme. These OAK-based biosensors offer significant advantages in comparison with conventional antibody-based assays, in terms of their simple and cost-effective production, while providing numerous possible sequence combinations for designing new detection schemes.

Nanobody-derived nanobiotechnology tool kits for diverse biomedical and biotechnology applications

Owing to peculiar properties of nanobody, including nanoscale size, robust structure, stable and soluble behaviors in aqueous solution, reversible refolding, high affinity and specificity for only one cognate target, superior cryptic cleft accessibility, and deep tissue penetration, as well as a sustainable source, it has been an ideal research tool for the development of sophisticated nanobiotechnologies. Currently, the nanobody has been evolved into versatile research and application tool kits for diverse biomedical and biotechnology applications. Various nanobody-derived formats, including the nanobody itself, the radionuclide or fluorescent-labeled nanobodies, nanobody homo- or heteromultimers, nanobody-coated nanoparticles, and nanobody-displayed bacteriophages, have been successfully demonstrated as powerful nanobiotechnological tool kits for basic biomedical research, targeting drug delivery and therapy, disease diagnosis, bioimaging, and agricultural and plant protection. These applications indicate a special advantage of these nanobody-derived technologies, already surpassing the “me-too” products of other equivalent binders, such as the full-length antibodies, single-chain variable fragments, antigen-binding fragments, targeting peptides, and DNA-based aptamers. In this review, we summarize the current state of the art in nanobody research, focusing on the nanobody structural features, nanobody production approach, nanobody-derived nanobiotechnology tool kits, and the potentially diverse applications in biomedicine and biotechnology. The future trends, challenges, and limitations of the nanobody-derived nanobiotechnology tool kits are also discussed.

Fluorescence enhancement aided by metal ion displacement

Immunosensors are one of the most common platform used in clinical laboratories, in particular the class based on Enzyme Linked Fluorescent Assays (ELFA) takes advantage of the amplification step of the enzyme, usually the alkaline phosphatase, that catalyzes the hydrolysis of a fluorescent substrate leading it to fluoresce. Anyway, they suffer in sensitivity if compared to molecular diagnostic or more modern in vitro diagnostic devices. In our work, a simple and effective mechanism to enhance the fluorescent signal, and hence the sensitivity of the system, is presented. It is based on the metal ion displacement principle in which a second fluorophore, in our case Calcein Blue, quenched by a cobalt ion is add to the first one (4-MUP), and, in presence of inorganic phosphate, it will be progressively activated by the inorganic phosphate itself leading to the metal displacement. In this way Calcein Blue, newly free to fluoresce, contributes to global fluorescent signal generated by 4-MU. We have tested our proof of principle on a currently used immunoanalyzer, that is VIDAS® system (bioMérieux, Marcy l'Etoile, France) obtaining a fluorescence enhancement of about 50% for each concentration of hydrolyzed 4-MUP tested.

Aptamers, antibody scFv, and antibody Fab' fragments: An overview and comparison of three of the most versatile biosensor biorecognition elements

The choice of biosensing elements is crucial for the development of the optimal biosensor. Three of the most versatile biosensing elements are antibody single-chain Fv fragments (scFv), antibody fragment-antigen binding (Fab') units, and aptamers. This article provides an overview of these three biorecognition elements with respects to their synthesis/engineering, various immobilization techniques, and examples of their use in biosensors. Furthermore, the final section of the review compares and contrasts their characteristics (time/cost of development, ease and variability of immobilization, affinity, stability) illustrating their advantages and disadvantages. Overall, scFv fragments are found to display the highest customizability (i.e. addition of functional groups, immobilizing peptides, etc.) due to recombinant synthesis techniques. If time and cost are an issue in the development of the biosensor, Fab' fragments should be chosen as they are relatively cheap and can be developed quickly from whole antibodies (several days). However, if there are sufficient funds and time is not a factor, aptamers should be utilized as they display the greatest affinity towards their target analytes and are extremely stable (excellent biosensor regenerability).

An embedded microretroreflector-based microfluidic immunoassay platform

We present a microfluidic immunoassay platform based on the use of linear microretroreflectors embedded in a transparent polymer layer as an optical sensing surface, and micron-sized magnetic particles as light-blocking labels. Retroreflectors return light directly to its source and are highly detectable using inexpensive optics. The analyte is immuno-magnetically pre-concentrated from a sample and then captured on an antibody-modified microfluidic substrate comprised of embedded microretroreflectors, thereby blocking reflected light. Fluidic force discrimination is used to increase specificity of the assay, following which a difference imaging algorithm that can see single 3 μm magnetic particles without optical calibration is used to detect and quantify signal intensity from each sub-array of retroreflectors. We demonstrate the utility of embedded microretroreflectors as a new sensing modality through a proof-of-concept immunoassay for a small, obligate intracellular bacterial pathogen, Rickettsia conorii, the causative agent of Mediterranean Spotted Fever. The combination of large sensing area, optimized surface chemistry and microfluidic protocols, automated image capture and analysis, and high sensitivity of the difference imaging results in a sensitive immunoassay with a limit of detection of roughly 4000 R. conorii per mL.

Single-domain antibody based thermally stable electrochemical immunosensor

Conventional monoclonal and polyclonal antibodies are sensitive to changes in environmental factors such as temperature, pH, humidity, etc. This limits the current cost-effective and portable electrochemical immunosensors in harsh environments. Using Ricin Chain-A, a naturally occurring toxin, as a model analyte we report fabrication of a thermally stable electrochemical immunosensor. Single-domain antibodies (sdAb) or nanobodies have been employed as recognition elements for direct detection of Ricin at temperatures great than 4°C. Immunosensor fabricated using the conventional Ricin monoclonal and polyclonal antibodies have also been demonstrated for comparison. In the case of sdAb immunosensor, Ricin was detected in a linear range of 1log(fg/mL)-1log(μg/mL) with a sensitivity of 0.07μA/log(g/mL)/cm(2) using cyclic voltammetry. The fabricated miniaturized sensors have demonstrated higher shelf life and stability at temperatures up to 40°C. Therefore these electrochemical sensors can be integrated as a part of a portable device for point-of-care immunosensing.

Microfluidics Integrated Biosensors: A Leading Technology towards Lab-on-a-Chip and Sensing Applications

A biosensor can be defined as a compact analytical device or unit incorporating a biological or biologically derived sensitive recognition element immobilized on a physicochemical transducer to measure one or more analytes. Microfluidic systems, on the other hand, provide throughput processing, enhance transport for controlling the flow conditions, increase the mixing rate of different reagents, reduce sample and reagents volume (down to nanoliter), increase sensitivity of detection, and utilize the same platform for both sample preparation and detection. In view of these advantages, the integration of microfluidic and biosensor technologies provides the ability to merge chemical and biological components into a single platform and offers new opportunities for future biosensing applications including portability, disposability, real-time detection, unprecedented accuracies, and simultaneous analysis of different analytes in a single device. This review aims at representing advances and achievements in the field of microfluidic-based biosensing. The review also presents examples extracted from the literature to demonstrate the advantages of merging microfluidic and biosensing technologies and illustrate the versatility that such integration promises in the future biosensing for emerging areas of biological engineering, biomedical studies, point-of-care diagnostics, environmental monitoring, and precision agriculture.

HIV-1 Tat biosensor: Current development and trends for early detection strategies

Human immunodeficiency virus (HIV) has infected almost 35 million people worldwide. Various tests have been developed to detect the presence of HIV during the early stages of the disease in order to reduce the risk of transmission to other humans. The HIV-1 Tat protein is one of the proteins present in HIV that are released abundantly approximately 2-4 weeks after infection. In this review, we have outlined various strategies for detecting the Tat protein, which helps transcribe the virus and enhances replication. Detection strategies presented include immunoassays, biosensors and gene expression, which utilize antibodies or aptamers as common probes to sense the presence of Tat. Alternatively, measuring the levels of gene transcription is a direct method of analysing the HIV gene to confirm the presence of Tat. By detection of the Tat protein, virus transmission can be detected in high-risk individuals in the early stages of the disease to reduce the risk of an HIV pandemic.