A quantitative assessment of heterogeneity for surface-immobilized proteins

High enhancement of sensitivity and reproducibility in label-free SARS-CoV-2 detection with graphene field-effect transistor sensors through precise surface biofunctionalization control

The COVID-19 pandemic has taught us valuable lessons, especially the urgent need for a widespread, rapid and sensitive diagnostic tool. To this, the integration of bidimensional nanomaterials, particularly graphene, into point-of-care biomedical devices is a groundbreaking strategy able to potentially revolutionize the diagnostic landscape. Despite advancements in the fabrication of these biosensors, the relationship between their surface biofunctionalization and sensing performance remains unclear. Here, we demonstrate that the combination of careful sensor fabrication and its precise surface biofunctionalization is crucial for exalting the sensing performances of 2D biosensors. Specifically, we have biofunctionalized Graphene Field-Effect Transistor (GFET) sensors surface through different biochemical reactions to promote either random/heterogeneous or oriented/homogeneous immobilization of the Anti-SARS-CoV-2 spike protein antibody. Each strategy was thoroughly characterized by in-silico simulations, physicochemical and biochemical techniques and electrical characterization. Subsequently, both biosensors were tested in the label-free direct titration of SARS-CoV-2 virus in simulated clinical samples, avoiding sample preprocessing and within short timeframes. Remarkably, the oriented GFET biosensor exhibited significantly enhanced reproducibility and responsiveness, surpassing the detection sensitivity of conventional non-oriented GFET by more than twofold. This breakthrough not only involves direct implications for COVID-19 surveillance and next pandemic preparedness but also clarify an unexplored mechanistic dimension of biosensor research utilizing 2D-nanomaterials.

Gold nanoparticle-powered screening of membrane protein-specific lipids from complex lipid mixtures

Membrane proteins (MPs) are affected by binding of specific lipids. We previously developed a methodology for systematically analyzing MP-lipid interactions leveraging surface plasmon resonance (SPR). In this method, the gold sensor chip surface was modified with a self-assembled monolayer (SAM), which allowed for a larger amount of MP-immobilization. However, the laborious lipid purification step remained a bottleneck. To address this issue, a new strategy has been developed utilizing gold nanoparticles (AuNPs) instead of the gold sensor chip. AuNPs were coated with SAM, on which MP was covalently anchored. The MP-immobilized AuNPs were mixed with a lipid mixture, and the recovered lipids were quantified by LC-MS. Bacteriorhodopsin (bR) was used as an MP to demonstrate this concept. We optimized immobilization conditions and confirmed the efficient immobilization of bR by dynamic light scattering and electron micrographs. Washing conditions for pulldown experiments were optimized to efficiently remove non-specific lipids. A new binding index was introduced to qualitatively reproduce the known affinity of lipids for bR. Consequently, the low-abundant and least-studied lipid S-TeGD was identified as a candidate for bR-specific lipids. This technique can skip the laborious lipid purification process, accelerating the screening of MP-specific lipids from complex lipid mixtures.

Enzymatic Protein Immobilization for Nanobody Array

Antibody arrays play a pivotal role in the detection and quantification of biomolecules, with their effectiveness largely dependent on efficient protein immobilization. Traditional methods often use heterobifunctional cross-linking reagents for attaching functional residues in proteins to corresponding chemical groups on the substrate surface. However, this method does not control the antibody's anchoring point and orientation, potentially leading to reduced binding efficiency and overall performance. Another method using anti-antibodies as intermediate molecules to control the orientation can be used but it demonstrates lower efficiency. Here, we demonstrate a site-specific protein immobilization strategy utilizing OaAEP1 (asparaginyl endopeptidase) for building a nanobody array. Moreover, we used a nanobody-targeting enhanced green fluorescent protein (eGFP) as the model system to validate the protein immobilization method for building a nanobody array. Finally, by rapidly enriching eGFP, this method further highlights its potential for rapid diagnostic applications. This approach, characterized by its simplicity, high efficiency, and specificity, offers an advancement in the development of surface-modified protein arrays. It promises to enhance the sensitivity and accuracy of biomolecule detection, paving the way for broader applications in various research and diagnostic fields.

Nanomaterial surface modification toolkit: Principles, components, recipes, and applications

Surface-functionalized nanostructures are at the forefront of biotechnology, providing new opportunities for biosensors, drug delivery, therapy, and bioimaging applications. The modification of nanostructures significantly impacts the performance and success of various applications by enabling selective and precise targeting. This review elucidates widely practiced surface modification strategies, including click chemistry, cross-coupling, silanization, aldehyde linkers, active ester chemistry, maleimide chemistry, epoxy linkers, and other protein and DNA-based methodologies. We also delve into the application-focused landscape of the nano-bio interface, emphasizing four key domains: therapeutics, biosensing, environmental monitoring, and point-of-care technologies, by highlighting prominent studies. The insights presented herein pave the way for further innovations at the intersection of nanotechnology and biotechnology, providing a useful handbook for beginners and professionals. The review draws on various sources, including the latest research articles (2018-2023), to provide a comprehensive overview of the field.

Superior Binding of Proteins on a Silica Surface: Physical Insight into the Synergetic Contribution of Polyhistidine and a Silica-Binding Peptide

Controllable protein attachment onto solid interfaces is essential for the functionality of proteins with broad applications. Silica-binding peptides (SBPs) have emerged as an important tool enabling convenient binding of proteins onto a silica surface. Surprisingly, we found that removal of polyhistidines, a common tag for protein purification, dramatically decrease the binding affinity of a SBP-tagged nanobody onto a silica surface. We hypothesized that polyhistidines and SBPs can be combined to enhance affinity. Through a series of purposely designed SBPs, we identified that the relative orientation of amino acids is a key factor affecting the surface binding strength. One re-engineered SBP, SBP4, exhibits a 4000-fold improvement compared to the original sequence. Guided by physical insights, the work provides a simple strategy that can dramatically improve affinity between a SBP and a silica surface, promising a new way for controllable immobilization of proteins, as demonstrated using nanobodies.

Micropatterned Ligand Arrays to Investigate Spatial Regulation of Cellular Signaling Initiated by Clustered Fc Receptors

Cell surface receptors that bind the Fc segment of antibodies to initiate signaling play fundamental roles in immune responses. Multiple, diverse Fc receptors (e.g., Fc gamma, Fc-alpha, and Fc-epsilon) are expressed on different immune cells, including natural killer cells, macrophages, mast cells, and neutrophils. Fc receptors bind particular antibody isotypes (e.g., IgG, IgA, IgE, respectively) thereby sensitizing the cells to their specific antigens. Receptor clustering by antigen or other multivalent ligands induces a signaling cascade that leads to targeted secretion of chemical mediators (e.g., histamine, cytokines, and chemokines) and other cell-specific responses. Spatial targeting and compartmentalization are common mechanisms for regulating Fc receptor signaling. However, the tools for studying these dynamic interactions at cellular levels have been limited due to the nanoscale dimensions of the signaling complexes and their dispersal across the cell surface. To overcome these limitations in our model system, we use microfabricated surfaces containing spatially defined ligands to cluster and activate IgE receptors (FcεRI), which initiate allergic responses by mast cells. Micron-scale control of receptor assemblies allows investigation with conventional fluorescence microscopy of spatially regulated redistributions of intracellular signaling components. This approach in conjunction with biochemical techniques has proven valuable for investigating immune receptor signaling.

Plasmonic Fiberoptic Absorbance Biosensor (P-FAB) for Rapid Detection of SARS-CoV-2 Nucleocapsid Protein

SARS-CoV-2 nucleocapsid protein-based COVID-19 diagnosis is a promising alternative to the high-priced, time-consuming, and labor-intensive RT-PCR tests. Here, we developed a rapid, dip-type, wash-free plasmonic fiber optic absorbance biosensor (P-FAB) strategy for the point-of-care detection of SARS-CoV-2 N-protein, expressed abundantly during the infection. P-FAB involves a sandwich assay with plasmonic labels on the surface of a U-bent fiber optic sensor probe with a high evanescent wave absorbance (EWA) sensitivity. The SARS-CoV-2 N-protein is quantified in terms of the change in the intensity of the light propagating through the U-bent sensor probe coupled to a green LED and a photodetector. Firstly, the optical fiber material (silica vs. polymeric optical fiber), was evaluated to realize a sensitive sensor platform. The optimal size of AuNP labels (20, 40, and 60 nm) to achieve high sensitivity and a lower limit of detection (LoD) was investigated. Following the P-FAB strategy, fused silica/glass optical fiber (GOF) U-bent senor probe and citrate-capped AuNP labels (size ~40 nm) gave rise to an LoD down to ~2.5 ng/mL within 10 mins of read-out time. Further, studies on development and validation of a point of care (PoC) read-out device, and preclinical studies are in progress.

Rapid capture of biomolecules from blood via stimuli-responsive elastomeric particles for acoustofluidic separation

The detection of biomarkers in blood often requires extensive and time-consuming sample preparation to remove blood cells and concentrate the biomarker(s) of interest. We demonstrate proof-of-concept for a chip-based, acoustofluidic method that enables the rapid capture and isolation of a model protein biomarker (i.e., streptavidin) from blood for off-chip quantification. Our approach makes use of two key components - namely, soluble, thermally responsive polypeptides fused to ligands for the homogeneous capture of biomarkers from whole blood and silicone microparticles functionalized with similar, tethered, thermally responsive polypeptides. When the two components are mixed together and subjected to a mild thermal trigger, the thermally responsive moieties undergo a phase transition, causing the untethered (soluble) polypeptides to co-aggregate with the particle-bound polypeptides. The mixture is then diluted with warm buffer and injected into a microfluidic channel supporting a bulk acoustic standing wave. The biomarker-bearing particles migrate to the pressure antinodes, whereas blood cells migrate to the pressure node, leading to rapid separation with efficiencies exceeding 90% in a single pass. The biomarker-bearing particles can then be analyzed via flow cytometry, with a limit of detection of 0.75 nM for streptavidin spiked in blood plasma. Finally, by cooling the solution below the solubility temperature of the polypeptides, greater than 75% of the streptavidin is released from the microparticles, offering a unique approach for downstream analysis (e.g., sequencing or structural analysis). Overall, this methodology has promise for the detection, enrichment and analysis of some biomarkers from blood and other complex biological samples.

A controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of multiple repair glycosylases

Genomic oxidation and alkylation are two of the most important forms of cytotoxic damage that may induce mutagenesis, carcinogenicity, and teratogenicity. Human 8-oxoguanine (hOGG1) and alkyladenine DNA glycosylases (hAAG) are responsible for two major forms of oxidative and alkylative damage repair, and their aberrant activities may cause repair deficiencies that are associated with a variety of human diseases, including cancers. Due to their complicated catalytic pathways and hydrolysis mechanisms, simultaneous and accurate detection of multiple repair glycosylases has remained a great challenge. Herein, by taking advantage of unique features of T7-based transcription and the intrinsic superiorities of single-molecule imaging techniques, we demonstrate for the first time the development of a controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of hOGG1 and hAAG. The presence of hOGG1 and hAAG can remove damaged 8-oxoG and deoxyinosine, respectively, from the dumbbell substrate, resulting in breaking of the dumbbell substrate, unfolding of two loops, and exposure of two T7 promoters simultaneously. The T7 promoters can activate symmetric transcription amplifications with the unfolded loops as the templates, inducing efficient transcription to produce two different single-stranded RNA transcripts (i.e., reporter probes 1 and 2). Reporter probes 1 and 2 hybridize with signal probes 1 and 2, respectively, to initiate duplex-specific nuclease-directed cyclic digestion of the signal probes, liberating large amounts of Cy3 and Cy5 fluorescent molecules. The released Cy3 and Cy5 molecules can be simply measured by total internal reflection fluorescence-based single-molecule detection, with the Cy3 signal indicating the presence of hOGG1 and the Cy5 signal indicating the presence of hAAG. This method exhibits good specificity and high sensitivity with a detection limit of 3.52 × 10-8 U μL-1 for hOGG1 and 3.55 × 10-7 U μL-1 for hAAG, and it can even quantify repair glycosylases at the single-cell level. Moreover, it can be applied for the measurement of kinetic parameters, the screening of potential inhibitors, and the detection of repair glycosylases in human serum, providing a new paradigm for repair enzyme-related biomedical research, drug discovery, and clinical diagnosis.

Engineering Af1521 improves ADP-ribose binding and identification of ADP-ribosylated proteins

Protein ADP-ribosylation is a reversible post-translational modification that regulates important cellular functions. The identification of modified proteins has proven challenging and has mainly been achieved via enrichment methodologies. Random mutagenesis was used here to develop an engineered Af1521 ADP-ribose binding macro domain protein with 1000-fold increased affinity towards ADP-ribose. The crystal structure reveals that two point mutations K35E and Y145R form a salt bridge within the ADP-ribose binding domain. This forces the proximal ribose to rotate within the binding pocket and, as a consequence, improves engineered Af1521 ADPr-binding affinity. Its use in our proteomic ADP-ribosylome workflow increases the ADP-ribosylated protein identification rates and yields greater ADP-ribosylome coverage. Furthermore, generation of an engineered Af1521 Fc fusion protein confirms the improved detection of cellular ADP-ribosylation by immunoblot and immunofluorescence. Thus, this engineered isoform of Af1521 can also serve as a valuable tool for the analysis of cellular ADP-ribosylation under in vivo conditions.

Protein-functionalized nanoparticles derived from end-functional polymers and polymer prodrugs for crossing the blood-brain barrier

Nanoparticles may provide a viable way for neuroprotective drugs to cross the blood-brain barrier (BBB), which limits the passage of most drugs from the peripheral circulation to the brain. Heterotelechelic polymer prodrugs comprising a neuroprotective model drug (adenosine) and a maleimide functionality were synthesized by the "drug-initiated" approach and subsequent nitroxide exchange reaction. Nanoparticles were obtained by nanoprecipitation and exhibited high colloidal stability with diameters in the 162-185 nm range and narrow size distributions. Nanoparticles were then covalently surface-conjugated to different proteins (albumin, α2-macroglobulin and fetuin A) to test their capability of enhancing BBB translocation. Their performances in terms of endothelial permeability and cellular uptake in an in vitro BBB model were compared to that of similar nanoparticles with surface-adsorbed proteins, functionalized or not with the drug. It was shown that bare NPs (i.e., NPs not surface-functionalized with proteins) without the drug exhibited significant permeability and cellular uptake, which were further enhanced by NP surface functionalization with α2-macroglobulin. However, the presence of the drug at the polymer chain-end prevented efficient passage of all types of NPs through the BBB model, likely due to adecrease in the hydrophobicity of the nanoparticle surface and alteration of the protein binding/coupling, respectively. These results established a new and facile synthetic approach for the surface-functionalization of polymer nanoparticles for brain delivery purposes.

Atomically Flat Au Nanoplate Platforms Enable Ultraspecific Attomolar Detection of Protein Biomarkers

Atomically flat surfaces of single-crystalline Au nanoplates can maximize the functionality of biomolecules, thus realizing extremely high-performance biosensors. Here, we report both highly specific and supersensitive detection of C-reactive protein (CRP) by employing atomically flat Au nanoplates. CRP is a protein biomarker for inflammation and infection and can be used as a predictive or prognostic marker for various cardiovascular diseases. To maximize the binding capacity for CRP, we carefully optimized the Au nanoplate-Cys3-protein G-anti-CRP structure by observing atomic force microscopy (AFM) images. The optimally anti-CRP-immobilized Au nanoplates allowed extremely specific detection of CRP at the attomolar level. To confirm the binding of CRP onto the Au nanoplate, we assembled Au nanoparticles (NPs) onto the CRP-captured Au nanoplate by sandwich immunoreaction and obtained surface-enhanced Raman scattering (SERS) spectra and scanning electron microscopy (SEM) images. Both the SERS and SEM results showed that we completely eliminated the nonspecific binding of Au NPs onto the optimally anti-CRP-immobilized Au nanoplate. Compared with the anti-CRP-immobilized rough Au film and the randomly anti-CRP-attached Au nanoplate, the optimally anti-CRP-immobilized Au nanoplate provided a highly improved detection limit of 10^-17 M. In this study, it was validated that ultraclean and ultraflat Au nanoplates can maximize the sensing capability of CRP. We expect that these Au nanoplates will enable the feasible detection of many important biomarkers with high specificity and high sensitivity.

High-sensitive immunosensing of protein biomarker based on interfacial recognition-induced homogeneous exponential transcription

A novel and versatile immunosensing strategy was developed for ultrasensitive and specific detection of proteins by organically integrating interfacial specific target recognition and homogeneous transcription amplification. In principle, classic antigen-antibody sandwich structure on the microplate could realize the specific identification of target protein. Biotinylated DNA probe was subsequently introduced by streptavidin-biotin system as a bridge linking interfacial and homogeneous reaction. The biotinylated DNA initiated exponential transcription amplification in the solution, which converted per target recognition event on the interface to numerous single-stranded RNA products in solution for highly sensitive fluorescence immunosensing. The proposed immunoassay based on interfacial recognition-induced homogeneous exponential transcription (IR-HET) for vascular endothelial growth factor (VEGF) detection showed a good linear range from 0.01 to 1000 pg/mL and the limit of detection as low as 1 fg/mL, which was 3 orders lower than traditional ELISA method. The established strategy was also successfully applied to directly detect VEGF from culture supernatants of tumor cells and clinical body fluid samples, proving very high sensitivity, selectivity and low matrix effect. Therefore, IR-HET-based immunosensing strategy might become a potential powerful tool be applied in ultrasensitive detection of low abundance protein biomarker for clinical early diagnosis, treatment and prognosis.

Sensing by Molecularly Imprinted Polymer: Evaluation of the Binding Properties with Different Techniques

The possibility of investigating the binding properties of the same molecularly imprinted polymer (MIP), most probably heterogeneous, at various concentration levels by different methods such as batch equilibration and sensing, is examined, considering two kinds of sensors, based respectively on electrochemical and surface plasmon resonance (SPR) transduction. As a proof of principle, the considered MIP was obtained by non-covalent molecular imprinting of 2-furaldehyde (2-FAL). It has been found that different concentration ranges of 2-FAL in aqueous matrices can be measured by the two sensing methods. The SPR sensor responds in a concentration range from 1 × 10⁻⁴ M down to about 1 × 10⁻⁷ M, while the electrochemical sensor from about 5 × 10⁻⁶ M up to about 9 × 10⁻³ M. The binding isotherms have been fit to the Langmuir adsorption model, in order to evaluate the association constant. Three kinds of sites with different affinity for 2-FAL have been detected. The sites at low affinity are similar to the interaction sites of the corresponding NIP since they have a similar association constant. This is near to the affinity evaluated by batch equilibration too. The same association constant has been evaluated in the same concentration range. The sensing methods have been demonstrated to be very convenient for the characterization of the binding properties of MIP in comparison to the batch equilibration, in terms of reproducibility and low amount of material required for the investigation.

Gold-Iron oxide yolk-shell nanoparticles (YSNPs) as magnetic probe for fluorescence-based detection of 3 base mismatch DNA

Seed-mediated Gold-Iron oxide yolk-shell nanoparticles (YSNPs) were synthesized and functionalized with cy5 attached- thiolated single strand DNA probe for the detection of mutated DNA. The optimum concentration of thiolated DNA determined from a bathochromic shift of surface plasmon resonance (SPR) peak, was 0.177μM. The effect of pH (2-10), temperature (4, 37, 60 and 100 °C), and ionic strengths (1 M to 4 M) on the stability of ssDNA probe tethered YSNPs, studied with the assistance of flocculation parameter. The detection of mutation in DNA was possible using such ssDNA probe functionalized and stabilized nanoparticles. The hybridization of the oligonucleotide probe with the complementary, non-complementary and mutated DNA strands are determined via their respective intensities of the fluorescence of cy5, an efficient fluorescent marker. The intensities help in the comprehension of the specificity of the system. The report predicts controlled efficiency of hybridization with the aid of Hamaker constant, which is determined as 1.15 × 10^-20 J for DNA functionalized YSNPs. The minimum concentration of target DNA detected using this methodology was 1.2 × 10^-11 mol/L.

Point-of-Care Compatibility of Ultra-Sensitive Detection Techniques for the Cardiac Biomarker Troponin I-Challenges and Potential Value

Cardiac biomarkers are frequently measured to provide guidance on the well-being of a patient in relation to cardiac health with many assays having been developed and widely utilised in clinical assessment. Effectively treating and managing cardiovascular disease (CVD) relies on swiftly responding to signs of cardiac symptoms, thus providing a basis for enhanced patient management and an overall better health outcome. Ultra-sensitive cardiac biomarker detection techniques play a pivotal role in improving the diagnostic capacity of an assay and thus enabling a better-informed decision. However, currently, the typical approach taken within healthcare depends on centralised laboratories performing analysis of cardiac biomarkers, thus restricting the roll-out of rapid diagnostics. Point-of-care testing (POCT) involves conducting the diagnostic test in the presence of the patient, with a short turnaround time, requiring small sample volumes without compromising the sensitivity of the assay. This technology is ideal for combatting CVD, thus the formulation of ultra-sensitive assays and the design of biosensors will be critically evaluated, focusing on the feasibility of these techniques for point-of-care (POC) integration. Moreover, there are several key factors, which in combination, contribute to the development of ultra-sensitive techniques, namely the incorporation of nanomaterials for sensitivity enhancement and manipulation of labelling methods. This review will explore the latest developments in cardiac biomarker detection, primarily focusing on the detection of cardiac troponin I (cTnI). Highly sensitive detection of cTnI is of paramount importance regarding the rapid rule-in/rule-out of acute myocardial infarction (AMI). Thus the challenges encountered during cTnI measurements are outlined in detail to assist in demonstrating the drawbacks of current commercial assays and the obstructions to standardisation. Furthermore, the added benefits of introducing multi-biomarker panels are reviewed, several key biomarkers are evaluated and the analytical benefits provided by multimarkers-based methods are highlighted.

A critical insight into the development pipeline of microfluidic immunoassay devices for the sensitive quantitation of protein biomarkers at the point of care

The latest clinical procedures for the timely and cost-effective diagnosis of chronic and acute clinical conditions, such as cardiovascular diseases, cancer, chronic respiratory diseases, diabetes or sepsis (i.e. the biggest causes of death worldwide), involve the quantitation of specific protein biomarkers released into the blood stream or other physiological fluids (e.g. urine or saliva). The clinical thresholds are usually in the femtomolar to picolomar range, and consequently the measurement of these protein biomarkers heavily relies on highly sophisticated, bulky and automated equipment in centralised pathology laboratories. The first microfluidic devices capable of measuring protein biomarkers in miniaturised immunoassays were presented nearly two decades ago and promised to revolutionise point-of-care (POC) testing by offering unmatched sensitivity and automation in a compact POC format; however, the development and adoption of microfluidic protein biomarker tests has fallen behind expectations. This review presents a detailed critical overview into the pipeline of microfluidic devices developed in the period 2005-2016 capable of measuring protein biomarkers from the pM to fM range in formats compatible with POC testing, with a particular focus on the use of affordable microfluidic materials and compact low-cost signal interrogation. The integration of these two important features (essential unique selling points for the successful microfluidic diagnostic products) has been missed in previous review articles and explain the poor adoption of microfluidic technologies in this field. Most current miniaturised devices compromise either on the affordability, compactness and/or performance of the test, making current tests unsuitable for the POC measurement of protein biomarkers. Seven core technical areas, including (i) the selected strategy for antibody immobilisation, (ii) the surface area and surface-area-to-volume ratio, (iii) surface passivation, (iv) the biological matrix interference, (v) fluid control, (vi) the signal detection modes and (vii) the affordability of the manufacturing process and detection system, were identified as the key to the effective development of a sensitive and affordable microfluidic protein biomarker POC test.

Development of a Label-Free Immunosensor for Clusterin Detection as an Alzheimer's Biomarker

Clusterin (CLU) has been associated with the clinical progression of Alzheimer's disease (AD) and described as a potential AD biomarker in blood plasma. Due to the enormous attention given to cerebrospinal fluid (CSF) biomarkers for the past couple of decades, recently found blood-based AD biomarkers like CLU have not yet been reported for biosensors. Herein, we report the electrochemical detection of CLU for the first time using a screen-printed carbon electrode (SPCE) modified with 1-pyrenebutyric acid N-hydroxysuccinimide ester (Pyr-NHS) and decorated with specific anti-CLU antibody fragments. This bifunctional linker molecule contains succinylimide ester to bind protein at one end while its pyrene moiety attaches to the carbon surface by means of π-π stacking. Cyclic voltammetric and square wave voltammetric studies showed the limit of detection down to 1 pg/mL and a linear concentration range of 1-100 pg/mL with good sensitivity. Detection of CLU in spiked human plasma was demonstrated with satisfactory recovery percentages to that of the calibration data. The proposed method facilitates the cost-effective and viable production of label-free point-of-care devices for the clinical diagnosis of AD.

Recent advances on the encoding and selection methods of DNA-encoded chemical library

DNA-encoded chemical library (DEL) has emerged as a powerful and versatile tool for ligand discovery in chemical biology research and in drug discovery. Encoding and selection methods are two of the most important technological aspects of DEL that can dictate the performance and utilities of DELs. In this digest, we have summarized recent advances on the encoding and selection strategies of DEL and also discussed the latest developments on DNA-encoded dynamic library, a new frontier in DEL research.

Local retention of antibodies in vivo with an injectable film embedded with a fluorogen-activating protein

Herein we report an injectable film by which antibodies can be localized in vivo. The system builds upon a bifunctional polypeptide consisting of a fluorogen-activating protein (FAP) and a β-fibrillizing peptide (βFP). The FAP domain generates fluorescence that reflects IgG binding sites conferred by Protein A/G (pAG) conjugated with the fluorogen malachite green (MG). A film is generated by mixing these proteins with molar excess of EAK16-II, a βFP that forms β-sheet fibrils at high salt concentrations. The IgG-binding, fluorogenic film can be injected in vivo through conventional needled syringes. Confocal microscopic images and dose-response titration experiments showed that loading of IgG into the film was mediated by pAG(MG) bound to the FAP. Release of IgG in vitro was significantly delayed by the bioaffinity mechanism; 26% of the IgG were released from films embedded with pAG(MG) after five days, compared to close to 90% in films without pAG(MG). Computational simulations indicated that the release rate of IgG is governed by positive cooperativity due to pAG(MG). When injected into the subcutaneous space of mouse footpads, film-embedded IgG were retained locally, with distribution through the lymphatics impeded. The ability to track IgG binding sites and distribution simultaneously will aid the optimization of local antibody delivery systems.

Flow induced dispersion analysis rapidly quantifies proteins in human plasma samples

Rapid and sensitive quantification of protein based biomarkers and drugs is a substantial challenge in diagnostics and biopharmaceutical drug development. Current technologies, such as ELISA, are characterized by being slow (hours), requiring relatively large amounts of sample and being subject to cumbersome and expensive assay development. In this work a new approach for quantification based on changes in diffusivity is presented. The apparent diffusivity of an indicator molecule interacting with the protein of interest is determined by Taylor Dispersion Analysis (TDA) in a hydrodynamic flow system. In the presence of the analyte the apparent diffusivity of the indicator changes due to complexation. This change in diffusivity is used to quantify the analyte. This approach, termed Flow Induced Dispersion Analysis (FIDA), is characterized by being fast (minutes), selective (quantification is possible in a blood plasma matrix), fully automated, and being subject to a simple assay development. FIDA is demonstrated for quantification of the protein Human Serum Albumin (HSA) in human plasma as well as for quantification of an antibody against HSA. The sensitivity of the FIDA assay depends on the indicator-analyte dissociation constant which in favourable cases is in the sub-nanomolar to picomolar range for antibody-antigen interactions.

Correlation of Capture Efficiency with the Geometry, Transport, and Reaction Parameters in Heterogeneous Immunosensors

Higher capture efficiency of biomarkers in heterogeneous immunosensors would enable early detection of diseases. Several strategies are used to improve the capture efficiency of these immunosensors including the geometry of the system along with the transport and reaction parameters. Having a prior knowledge of the behavior of the above parameters would facilitate the design of an efficient immunosensor. While the contributions of the transport and reaction parameters toward understanding of the mechanism involved in capture have been well studied in the literature, their effect in combination with the geometry of the sensors has not been explored until now. In this work, we have experimentally demonstrated that the capture efficiency of the antigen-antibody systems is inversely related to the size of the sensor patch. The experimental system was simulated in order to get an in-depth understanding of the mechanism behind the experimental observation. Further, the extent of heterogeneity in the system was analyzed using the Sips isotherm to obtain the heterogeneity index (α) and the reaction rate constant (K(D)) as fitted parameters for a sensor patch of 1.5 mm radius. The experimental kinetic data obtained for the same sensor patch matched reasonably with the simulation results by considering K(D) as the global affinity constant, which indicated that our system can be considered to be homogeneous. Our simulation results associated with the size dependency of the capture efficiency were in agreement with the trends obtained in our experimental observations where an inverse relation was observed owing to the fact that the mass-transfer limitation decreases with the decrease in the size of the sensor patch. The possible underlying mechanism associated with size dependency of capture efficiency was discussed based on the time-dependent radial variation of captured antigens obtained from our simulation results. A study on the parametric variation was further conducted for the nonmixed and mixed systems on the transport (Deff), reaction (K(D)), and geometric parameters (R). Two different correlations were established for the nonmixed and mixed systems between the capture efficiency (f) and a nondimensional number (t(D)/t(R)) consisting of the above-mentioned parameters. Such unified relations will be useful in designing heterogeneous immunosensors and can be extended to microfluidic immunosensors.

Direct ultrasensitive electrochemical biosensing of pathogenic DNA using homogeneous target-initiated transcription amplification

Sensitive and specific methodologies for detection of pathogenic gene at the point-of-care are still urgent demands in rapid diagnosis of infectious diseases. This work develops a simple and pragmatic electrochemical biosensing strategy for ultrasensitive and specific detection of pathogenic nucleic acids directly by integrating homogeneous target-initiated transcription amplification (HTITA) with interfacial sensing process in single analysis system. The homogeneous recognition and specific binding of target DNA with the designed hairpin probe triggered circular primer extension reaction to form DNA double-strands which contained T7 RNA polymerase promoter and served as templates for in vitro transcription amplification. The HTITA protocol resulted in numerous single-stranded RNA products which could synchronously hybridized with the detection probes and immobilized capture probes for enzyme-amplified electrochemical detection on the biosensor surface. The proposed electrochemical biosensing strategy showed very high sensitivity and selectivity for target DNA with a dynamic response range from 1 fM to 100 pM. Using salmonella as a model, the established strategy was successfully applied to directly detect invA gene from genomic DNA extract. This proposed strategy presented a simple, pragmatic platform toward ultrasensitive nucleic acids detection and would become a versatile and powerful tool for point-of-care pathogen identification.

Study on the bio-functionalization of memristive nanowires for optimum memristive biosensors

Semiconductor nanowires are emerging as promising building blocks for biosensors enabling direct electrical detection of various biomolecules.

Genetic fusion of single-chain variable fragments to partial spider silk improves target detection in micro- and nanoarrays

Immobilizing biomolecules with retained functionality and stability on solid supports is crucial for generation of sensitive immunoassays. However, upon use of conventional immobilization strategies, a major portion of the biomolecules (e.g. antibodies) frequently tends to lose their bioactivity. In this study, we describe a procedure to immobilize human single-chain variable fragment (scFv) via genetic fusion to partial spider silk, which have a high tendency to adhere to solid supports. Two scFvs, directed towards serum proteins, were genetically fused to partial spider silk proteins and expressed as silk fusion proteins in E. coli. Antigen binding ability of scFvs attached to a partial silk protein denoted RC was investigated using microarray analysis, whereas scFvs fused to the NC silk variant were examined using nanoarrays. Results from micro- and nanoarrays confirmed the functionality of scFvs attached to both RC and NC silk, and also for binding of targets in crude serum. Furthermore, the same amount of added scFv gives higher signal intensity when immobilized via partial spider silk compared to when immobilized alone. Together, the results suggest that usage of scFv-silk fusion proteins in immunoassays could improve target detection, in the long run enabling novel biomarkers to be detected in crude serum proteomes.

Osteogenic Surface Modification Based on Functionalized Poly-P-Xylylene Coating

The biotechnology to immobilize biomolecules on material surfaces has been developed vigorously due to its high potentials in medical applications. In this study, a simple and effective method was designed to immobilize biomolecules via amine-N-hydroxysuccinimide (NHS) ester conjugation reaction using functionalized poly-p-xylylene coating on material surfaces. The NHS ester functionalized coating is synthesized via chemical vapor deposition, a facile and solvent-less method, creating a surface which is ready to perform a one-step conjugation reaction. Bone morphogenetic protein 2 (BMP-2) is immobilized onto material surfaces by this coating method, forming an osteogenic environment. The immobilization process is controlled at a low temperature which does not damage proteins. This modified surface induces differentiation of preosteoblast into osteoblast, manifested by alkaline phosphatase (ALP) activity assay, Alizarin Red S (ARS) staining and the expression of osteogenic gene markers, Alpl and Bglap3. With this coating technology, immobilization of growth factors onto material surface can be achieved more simply and more effectively.

Oriented Immobilization of Fab Fragments by Site-Specific Biotinylation at the Conserved Nucleotide Binding Site for Enhanced Antigen Detection

Oriented immobilization of antibodies and antibody fragments has become increasingly important as a result of the efforts to reduce the size of diagnostic and sensor devices to miniaturized dimensions for improved accessibility to the end-user. Reduced dimensions of sensor devices necessitate the immobilized antibodies to conserve their antigen binding activity for proper operation. Fab fragments are becoming more commonly used in small-scaled diagnostic devices due to their small size and ease of manufacture. In this study, we used the previously described UV-NBS(Biotin) method to functionalize Fab fragments with IBA-EG11-Biotin linker utilizing UV energy to initiate a photo-cross-linking reaction between the nucleotide binding site (NBS) on the Fab fragment and IBA-Biotin molecule. Our results demonstrate that immobilization of biotinylated Fab fragments via UV-NBS(Biotin) method generated the highest level of immobilized Fab on surfaces when compared to other typical immobilization methods while preserving antigen binding activity. UV-NBS(Biotin) method provided 432-fold, 114-fold, and 29-fold improved antigen detection sensitivity than physical adsorption, NHS-Biotin, and ε-NH3(+), methods, respectively. Additionally, the limit of detection (LOD) for PSA utilizing Fab fragments immobilized via UV-NBS(Biotin) method was significantly lower than that of the other immobilization methods, with an LOD of 0.4 pM PSA. In summary, site-specific biotinylation of Fab fragments without structural damage or loss in antigen binding activity provides a wide range of application potential for UV-NBS immobilization technique across numerous diagnostic devices and nanotechnologies.

Nature of immobilization surface affects antibody specificity to placental alkaline phosphatase

Retention of native conformation of immobilized protein is essential for various applications including selection and detection of specific recombinant antibodies (scFvs). Placental alkaline phosphatase (PAP), an onco-fetal antigen expressed on the surface of several tumors, was immobilized on supermagnetic particles for selection of recombinant antibodies from a human phage display antibody library. The isolated antibodies were found to be cross-reactive to either of the isozymes of alkaline phosphatase, i.e., bone alkaline phosphatase (BAP) or intestinal alkaline phosphatase (IAP) and could not be used for tumor targeting. A specific anti-PAP monoclonal antibody H17E2 was tested for retention of specificity under these conditions. Binding of the antibody to magnetic beads conjugated IAP and BAP along with PAP and the ability of the two isozymes to inhibit its binding to PAP depicted the loss of isozyme specificity of the antibody. However, the antibody retained its specificity to PAP immobilized on polyvinyl chloride (PVC) surface. Enzyme activity was observed on both surfaces. This demonstrates that nature of immobilization may affect antigen-antibody binding in subtle ways, resulting in alteration of conformation of the epitopes. This may have consequences for determining the specificity of antibody binding for proteins that share a high degree of homology.

Direct detection of protein biomarkers in human fluids using site-specific antibody immobilization strategies

Design of an optimal surface biofunctionalization still remains an important challenge for the application of biosensors in clinical practice and therapeutic follow-up. Optical biosensors offer real-time monitoring and highly sensitive label-free analysis, along with great potential to be transferred to portable devices. When applied in direct immunoassays, their analytical features depend strongly on the antibody immobilization strategy. A strategy for correct immobilization of antibodies based on the use of ProLinker™ has been evaluated and optimized in terms of sensitivity, selectivity, stability and reproducibility. Special effort has been focused on avoiding antibody manipulation, preventing nonspecific adsorption and obtaining a robust biosurface with regeneration capabilities. ProLinker™-based approach has demonstrated to fulfill those crucial requirements and, in combination with PEG-derivative compounds, has shown encouraging results for direct detection in biological fluids, such as pure urine or diluted serum. Furthermore, we have implemented the ProLinker™ strategy to a novel nanoplasmonic-based biosensor resulting in promising advantages for its application in clinical and biomedical diagnosis.

Theoretical analysis of a magnetophoresis-diffusion T-sensor immunoassay

We present the analytical investigation of a microfluidic homogeneous competitive immunoassay that incorporates antibody-conjugated superparamagnetic nanoparticles and magnetophoretic transport to enhance the limits of detection and dynamic range. The analytical model considers the advective, diffusive, and magnetophoretic transport of the antibody-coated nanoparticles relative to the labeled and sample antigens of interest in a T-sensor configuration. The magnetophoresis-diffusion immunoassay identified clear improvements to the assay response and reductions to the limit of detection for increased magnetophoretic velocities and larger nanoparticles. The externally applied magnetophoretic transport enriched the antibody-antigen accumulation region, while larger nanoparticles led to decreased diffusive peak broadening. The integration of nanoparticles to the diffusion immunoassay (NP-DIA) demonstrated an approximately 3-fold improvement to the limit of detection of the basic antibody/antigen system, while the integration of superparamagnetic nanoparticles and magnetophoretic transport (MIA) established an order of magnitude improvement in sensitivity as well as means to greatly reduce response time. The implementation of an external magnetic force enabled the detectable antigen size spectrum to extend from small molecules i.e., 10's Da to 100's Da, up to large proteins and macromolecules, i.e., 50 kDa to 150 kDa, for a single class of binding species, i.e., superparamagnetic nanoparticle. This investigation provides guidelines for the design and development of a magnetophoresis-diffusion T-sensor immunoassay, and clearly identifies the regimes for optimal operation.

Solution-phase vs surface-phase aptamer-protein affinity from a label-free kinetic biosensor

Aptamers are selected DNA ligands that target biomolecules such as proteins. In recent years, they are showing an increasing interest as potential therapeutic agents or recognition elements in biosensor applications. In both cases, the need for characterizing the mating between the target and the aptamer either in solution or immobilized on a surface, is pressing. In this context, we have developed a kinetic biosensor made of micro-arrayed anti-thrombin aptamers to assess the kinetic parameters of this interaction. The binding of label-free thrombin on the biosensor was monitored in real-time by Surface Plasmon Resonance imaging. Remarkable performances were obtained for the quantification of thrombin without amplification (sub-nanomolar limit of detection and linear range of quantification to two orders of magnitude). The independent determinations of both the solution- and surface-phase affinities, respectively K_D^Sol and K_D^Surf, revealed distinct values illustrating the importance of probes, targets or surface interactions in biosensors. Interestingly, K_D^Surf values depend on the aptamer grafting density and linearly extrapolate towards K_D^Sol for highly diluted probes. This suggests a lesser impact of the surface compared to the probe or target cooperativity interactions since the latter decrease with a reduced grafting density.

FACS-sorted particles reduce the data variance in optical tweezers-assisted dynamic force spectroscopy measurements

By combining optical tweezers-assisted dynamic force spectroscopy experiments with fluorescence activated cell sorting (FACS), we demonstrate a new approach to reducing the data variance in measuring receptor-ligand interactions on a single molecule level by ensuring similar coating densities. Therefore, the carboxyfluorescein-labelled monophosphorylated peptide tau226-240[pThr231] is anchored on melamine resin beads and these beads are sorted by FACS to achieve a homogeneous surface coverage. To quantify the impact of the fluorescence dye on the bond parameters between the phosphorylated peptide and the corresponding phosphorylation specific anti-human tau monoclonal antibody HPT-104, we perform dynamic force spectroscopy and compare the results to data using unsorted beads covered with the non-fluorescence peptide analogue. Finally, we demonstrate that the data variance of the relative binding frequency is significantly decreased by a factor of 3.4 using pre-sorted colloids with a homogeneous ligand coating compared to using unsorted colloids.

Oriented antibody immobilization by site-specific UV photocrosslinking of biotin at the conserved nucleotide binding site for enhanced antigen detection

The nucleotide binding site (NBS) is an under-utilized, highly conserved binding site found within the variable region of nearly all antibody Fab arms. Here, we describe an NBS specific UV photocrosslinking biotinylation method (UV-NBS(Biotin)) for the oriented immobilization of antibodies to streptavidin-coated surfaces, such that the antigen binding activity remains unaffected. An optimal UV exposure of 1J/cm(2) yielded an average conjugation efficiency of ≈ 1 biotin per antibody resulting in significant immobilization efficiency while maintaining maximal antigen binding activity. With the continued push for miniaturization of medical diagnostics to reduce cost and increase patient accessibility the ever shrinking on chip detection areas necessitate the highest level of immobilized antibody activity to maximize assay detection capabilities. The UV-NBS(Biotin) method yielded surfaces with significantly enhanced antigen detection capabilities, improved antigen detection sensitivity and the highest amount of active surface immobilized antibody when compared to other common immobilization methods including: ε-NH3(+) surface conjugation, NHS-Biotin, and direct physical adsorption. Taken together, the UV-NBS(Biotin) method provides a universal, site-specific immobilization method that is amenable to any available assay detection modality with potential significant implications in the development of miniaturized medical diagnostics and lab on a chip technologies.

Selective photocrosslinking of functional ligands to antibodies via the conserved nucleotide binding site

The conserved nucleotide binding site (NBS), found in the Fab variable domain of all antibody isotypes, remains a not-so-widely known and under-utilized site. Here, we describe a UV photocrosslinking method (UV-NBS) that utilizes the NBS for site-specific covalent functionalization of antibodies, while preserving antibody activity. We identified a small molecule, indole-3-butyric acid (IBA), which has affinity for the NBS (K(d) = 1-8 μM) and can be photocrosslinked to antibodies upon UV energy exposure. By synthesizing their IBA conjugated versions, we have successfully photocrosslinked various types of functional ligands to antibodies at the NBS, including affinity tags (biotin), fluorescent molecules (FITC), peptides (iRGD), and chemotherapeutics (paclitaxel). An optimal UV exposure of 1-2 J/cm(2) yielded the most efficient photocrosslinking and resulted in 1-2 conjugations per antibody, while preserving the antigen binding activity and Fc related functions. Analysis of the photocrosslinked conjugates using western blotting, mass spectrometry, and computational docking simulations demonstrated that the photocrosslinking specifically takes place at the Y/F42 residue in framework region 2 of the antibody light chain. Taken together, the UV-NBS method provides a practical, site-specific, and chemically efficient method to functionalize antibodies with significant implications in diagnostic and therapeutic settings.

A comparison of binding surfaces for SPR biosensing using an antibody-antigen system and affinity distribution analysis

The application of optical biosensors in the study of macromolecular interactions requires immobilization of one binding partner to the surface. It is often highly desirable that the immobilization is uniform and does not affect the thermodynamic and kinetic binding parameters to soluble ligands. To achieve this goal, a variety of sensor surfaces, coupling strategies and surface chemistries are available. Previously, we have introduced a technique for determining the distribution of affinities and kinetic rate constants from families of binding and dissociation traces acquired at different concentrations of soluble ligand. In the present work, we explore how this affinity distribution analysis can be useful in the assessment and optimization of surface immobilization. With this goal, using an antibody-antigen interaction as a model system, we study the activity, thermodynamic and kinetic binding parameters, and heterogeneity of surface sites produced with different commonly used sensor surfaces, at different total surface densities and with direct immobilization or affinity capture.