Biotin-avidin binding kinetics measured by single-molecule imaging

Rapid isolation and recovery of Salmonella using hollow glass microspheres coated with multilayered nanofilms

Timely isolation, recovery, and identification of Salmonella from food samples is essential for prevention and control of foodborne Salmonella outbreaks. Traditional culture-based Salmonella isolation and serotyping techniques are time consuming and labor intensive. Despite the progress of innovative microfluidic or immunomagnetic isolation techniques, sophisticated lab equipment and microfabrication are often needed. Here, we present a novel, rapid yet simple method for isolation and recovery of Salmonella from mixed bacterial populations in food matrices and blood. This method utilizes self-floating hollow glass microspheres (HGMS) coated with biodegradable layer-by-layer (LbL) films and Salmonella specific antibodies. The isolation and recovery process can be completed in less than 2 h, without any sophisticated laboratory equipment or external force. In this study, we demonstrate that Salmonella can be captured due to antigen-antibody interactions on the surface of HGMS, allowing them to float to the top. The HGMS can then be washed and subjected to enzymatic degradation of the LbL film to recover the captured bacteria. The recovered Salmonella can subsequently be grown on selective agar plates for further analysis. Recovery efficiency of up to 22 % and detection limit of 100 CFU/mL were achieved. This method is expected to provide a viable alternative to traditional isolation techniques, especially in resource limited areas.

A Review on Perception of Binding Kinetics in Affinity Biosensors: Challenges and Opportunities

There are challenges associated with design and development of affinity biosensors due to the complicated multiphysics nature of the system. Understanding the binding interaction between target molecules and immobilized receptors and its kinetics is a crucial step to develop robust and reliable biosensor technologies. Evaluation of binding kinetics in biosensors becomes more important and challenging for clinical samples with a complex matrix. Despite drastic advancements in biosensor technologies, having a practical perception of the binding kinetics has remained a critical bottleneck due to limited fundamental understanding. This Review aims to provide a comprehensive discussion on concepts and advances developed so far for the perception of binding kinetics in affinity biosensors. Here, modeling approaches and measurement techniques are presented to characterize the binding interactions in biosensor technologies, while the effect of fouling and secondary factors in the binding interactions will be discussed in the concept of kinetics. This Review will investigate the existing research gaps and potential opportunities in the perception of binding kinetics and challenges to develop robust and reliable biosensors.

Direct Determination of High-Affinity Binding Constants by Continuous Injection Isothermal Titration Calorimetry

Isothermal titration calorimetry (ITC) is a method to determine thermodynamic values (ΔG, ΔH, and ΔS) for ligand-receptor binding in biological and abiological systems. It is challenging to directly determine subnanomolar dissociation constants using a standard incremental injection approach ITC (IIA-ITC) measurement. We recently demonstrated a continuous injection approach ITC (CIA-ITC) [ J. Phys. Chem. B 2021, 125, 8075-8087]enables the estimation of thermodynamic parameters in situ. In this work, we demonstrate a label-free and surface modification-free CIA-ITC to determine the complete binding thermodynamics of a ligand with a subnanomolar dissociation constant KD. The KD for desthiobiotin (DTB)-avidin binding was determined to be 6.5 pM with respect to the ligand by CIA-ITC, a quantity unsuccessfully measured with IIA-ITC and surface plasmon resonance spectroscopy (SPR). This value compares well with literature-reported spectroscopic determination of DTB-avidin binding. Criteria with respect to the concentration of the ligand and receptor and flow rate for obtaining true equilibrium dissociation constants without displacement titration are presented.

In-situ PLL-g-PEG Functionalized Nanopore for Enhancing Protein Characterization

Single-molecule nanopore detection technology has revolutionized proteomics research by enabling highly sensitive and label-free detection of individual proteins. Herein, we designed a small, portable, and leak-free flowcell made of PMMA for nanopore experiments. In addition, we developed an in situ functionalizing PLL-g-PEG approach to produce non-sticky nanopores for measuring the volume of diseases-relevant biomarker, such as the Alpha-1 antitrypsin (AAT) protein. The in situ functionalization method allows continuous monitoring, ensuring adequate functionalization, which can be directly used for translocation experiments. The functionalized nanopores exhibit improved characteristics, including an increased nanopore lifetime and enhanced translocation events of the AAT proteins. Furthermore, we demonstrated the reduction in the translocation event's dwell time, along with an increase in current blockade amplitudes and translocation numbers under different voltage stimuli. The study also successfully measures the single AAT protein volume (253 nm3 ), which closely aligns with the previously reported hydrodynamic volume. The real-time in situ PLL-g-PEG functionalizing method and the developed nanopore flowcell hold great promise for various nanopores applications involving non-sticky single-molecule characterization.

"Clickable" Organic Electrochemical Transistors

Interfacing the surface of an organic semiconductor with biological elements is a central quest when it comes to the development of efficient organic bioelectronic devices. Here, we present the first example of "clickable" organic electrochemical transistors (OECTs). The synthesis and characterization of an azide-derivatized EDOT monomer (azidomethyl-EDOT, EDOT-N₃) are reported, as well as its deposition on Au-interdigitated electrodes through electropolymerization to yield PEDOT-N₃-OECTs. The electropolymerization protocol allows for a straightforward and reliable tuning of the characteristics of the OECTs, yielding transistors with lower threshold voltages than PEDOT-based state-of-the-art devices and maximum transconductance voltage values close to 0 V, a key feature for the development of efficient organic bioelectronic devices. Subsequently, the azide moieties are employed to click alkyne-bearing molecules such as redox probes and biorecognition elements. The clicking of an alkyne-modified PEG₄-biotin allows for the use of the avidin-biotin interactions to efficiently generate bioconstructs with proteins and enzymes. In addition, a dibenzocyclooctyne-modified thrombin-specific HD22 aptamer is clicked on the PEDOT-N₃-OECTs, showing the application of the devices toward the development of organic transistors-based biosensors. Finally, the clicked OECTs preserve their electronic features after the different clicking procedures, demonstrating the stability and robustness of the fabricated transistors.

Can DyeCycling break the photobleaching limit in single-molecule FRET?

Biomolecular systems, such as proteins, crucially rely on dynamic processes at the nanoscale. Detecting biomolecular nanodynamics is therefore key to obtaining a mechanistic understanding of the energies and molecular driving forces that control biomolecular systems. Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique to observe in real-time how a single biomolecule proceeds through its functional cycle involving a sequence of distinct structural states. Currently, this technique is fundamentally limited by irreversible photobleaching, causing the untimely end of the experiment and thus, a narrow temporal bandwidth of ≤ 3 orders of magnitude. Here, we introduce "DyeCycling", a measurement scheme with which we aim to break the photobleaching limit in smFRET. We introduce the concept of spontaneous dye replacement by simulations, and as an experimental proof-of-concept, we demonstrate the intermittent observation of a single biomolecule for one hour with a time resolution of milliseconds. Theoretically, DyeCycling can provide > 100-fold more information per single molecule than conventional smFRET. We discuss the experimental implementation of DyeCycling, its current and fundamental limitations, and specific biological use cases. Given its general simplicity and versatility, DyeCycling has the potential to revolutionize the field of time-resolved smFRET, where it may serve to unravel a wealth of biomolecular dynamics by bridging from milliseconds to the hour range.

Electronic Supplementary Material

Supplementary material is available for this article at 10.1007/s12274-022-4420-5 and is accessible for authorized users.

Catalytic hairpin DNA assembly-based chemiluminescent assay for the detection of short SARS-CoV-2 target cDNA

Colorimetric sensors are recognized as a promising means for target molecule detection as they provide rapid, cost-effective, and facile sensing visible to the naked eye. Challenges remain though in terms of their detection sensitivity and specificity for short-length target genes. Herein, we demonstrate the successful combination of the catalytic hairpin DNA assembly (CHA) approach with enzyme-linked immunosorbent assay (ELISA)-mimicking techniques for a simple, sensitive, and sequence-specific colorimetric assay to detect short SARS-CoV-2 target cDNA. In the developed CHA-based chemiluminescent assay, a low concentration of target cDNA is continuously recycled to amplify dimeric DNA probes from two biotinylated hairpin DNA until the hairpin DNA is completely consumed. The dimeric DNA probes are effectively immobilized in a neutravidin-coated microplate well and then capture neutravidin-conjugated horseradish peroxidase via biotin-neutravidin interactions, resulting in a sensitive and selective colorless-to-blue color change. The developed sensing system exhibits a high sensitivity with a detection limit of ~1 nM for target cDNA as well as the ability to precisely distinguish a single-base mismatched mutant gene within 2 h. As the proposed system does not require complex protocols or expensive equipment to amplify target cDNA, it has the potential to be utilized as a powerful tool to improve the detection sensitivity of target genes for clinical diagnostics with colorimetric detection.

Probing Biosensing Interfaces With Single Molecule Localization Microscopy (SMLM)

Far field single molecule localization microscopy (SMLM) has been established as a powerful tool to study biological structures with resolution far below the diffraction limit of conventional light microscopy. In recent years, the applications of SMLM have reached beyond traditional cellular imaging. Nanostructured interfaces are enriched with information that determines their function, playing key roles in applications such as chemical catalysis and biological sensing. SMLM enables detailed study of interfaces at an individual molecular level, allowing measurements of reaction kinetics, and detection of rare events not accessible to ensemble measurements. This paper provides an update to the progress made to the use of SMLM in characterizing nanostructured biointerfaces, focusing on practical aspects, recent advances, and emerging opportunities from an analytical chemistry perspective.

Rapid Collection and Aptamer-Based Sensitive Electrochemical Detection of Soybean Rust Fungi Airborne Urediniospores

Plants are the central source of food for humans around the world. Unfortunately, plants can be negatively affected by diverse kinds of diseases that are responsible for major economic losses worldwide. Thus, monitoring plant health and early detection of pathogens are essential to reduce disease spread and facilitate effective management practices. Various detection approaches are currently practiced. These methods mainly include visual inspection and laboratory tests. Nonetheless, these methods are labor-intensive, time-consuming, expensive, and inefficient in the early stages of infection. Thus, it is extremely important to detect diseases at the early stages of the epidemic. Here, we would like to present a fast, sensitive, and reliable electrochemical sensing platform for the detection of airborne soybean rust spores. The suspected airborne soybean rust spores are first collected and trapped inside a carbon 3D electrode matrix by high-capacity air-sampling means. Then, a specific biotinylated aptamer, suitable to target specific sites of soybean rust spores is applied. This aptamer agent binds to the surface of the collected spores on the electrode. Finally, spore-bound aptamer units are incubated with a streptavidin-alkaline phosphatase agent leading to the enzymatic formation of p-nitrophenol, which is characterized by its unique electrochemical properties. Our method allows for the rapid (ca. 2 min), selective, and sensitive collection and detection of soybean rust spores (down to the limit of 100-200 collected spores per cm2 of electrode area). This method could be further optimized for its sensitivity and applied to the future multiplex early detection of various airborne plant diseases.

A Multichannel Microfluidic Sensing Cartridge for Bioanalytical Applications of Monolithic Quartz Crystal Microbalance

Integrating acoustic wave sensors into lab-on-a-chip (LoC) devices is a well-known challenge. We address this challenge by designing a microfluidic device housing a monolithic array of 24 high-fundamental frequency quartz crystal microbalance with dissipation (HFF-QCMD) sensors. The device features six 6-µL channels of four sensors each for low-volume parallel measurements, a sealing mechanism that provides appropriate pressure control while assuring liquid confinement and maintaining good stability, and provides a mechanical, electrical, and thermal interface with the characterization electronics. We validate the device by measuring the response of the HFF-QCMD sensors to the air-to-liquid transition, for which the robust Kanazawa–Gordon–Mason theory exists, and then by studying the adsorption of model bioanalytes (neutravidin and biotinylated albumin). With these experiments, we show how the effects of the protein–surface interactions propagate within adsorbed protein multilayers, offering essentially new insight into the design of affinity-based bioanalytical sensors.

Graphene field-effect transistor biosensor for detection of biotin with ultrahigh sensitivity and specificity

Because avidin and biotin molecules exhibit the most specific and strongest non-covalent interaction, avidin-biotin technology is widely used in ELISA (enzyme-linked immunosorbent assay) kits for the detection of different bio-macromolecules linked to different diseases including cancer and influenza. Combining the outstanding electrical conductivity (200,000 cm²V^-1s^-1) of graphene with the unique avidin and biotin interaction, we demonstrate a novel graphene field-effect transistor (GFET) biosensor for the quantitative detection of bio-macromolecules. The GFET consists of six pairs of interdigital Cr/Au electrodes supported on Si/SiO₂ substrate with an avidin immobilized single layer graphene channel as the sensing platform. By monitoring the real time current change upon the addition of biotin solution in bovine serum albumin (BSA) in the silicone pool preformed onto the GFET, the lowest detectable biotin concentration is estimated to be 90 fg/ml (0.37 pM). The specificity of the GFET is confirmed both by controlled and real sample measurements. From the magnitude of current change upon the addition of different concentrations of biotin solutions, the dissociation constant K_d is estimated to be 1.6 × 10^-11 M. Since biotin is capable of conjugating with proteins, nucleotides and other bio-macromolecules without altering their properties, the present GFET sensor with its ultra-high sensitivity (0.37 pM) and specificity can be tailored to the rapid point-of-care detection of different types of desired biomolecules at very low concentration level through biotinylation as well as the exogenous biotin in blood serum.

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Combining the outstanding electrical conductivity of graphene with the unique interaction between avidin and biotin, a novel graphene field-effect transistor (GFET) biosensor for quantitative detection of bio-macromolecules is demonstrated.

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The present biosensor is capable of detecting the biotin with the sensitivity of 90 fg/ml (~0.37 pM) and high specificity.

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Since the biotin is capable of conjugating with protein, nucleotide and other bio-macromolecules without affecting their properties, the present GFET sensor can be tailored to various medical applications.

Micromotor-Based Biosensing Using Directed Transport of Functionalized Beads

Previous micromotor-based biosensing studies used to functionalize the surface of the micromotor with specific molecular probes for binding of target analyte, thus limiting the use of the micromotor for the specific target. In contrast, here, we introduce a novel approach of using a nonfunctionalized micromotor as a generic cargo carrier being able to perform label-free and dynamic loading, transport, and release of functionalized beads. Hence, such an approach enables one to use the same micromotor system for sensing of varying targets via different commercially available functionalized beads, demonstrating the use of micromotors as a practical and versatile means for biosensing. We have also introduced a simplified microfluidic design that can be used for immunosensing or DNA binding tests without necessity for complicated fluid handling (buffer exchange, washing, etc.) steps. We expect this approach to open up new realizations of simplified and generic biosensing platforms.

Brushing the surface: cascade reactions between immobilized nanoreactors

Functionalization of hard or soft surfaces with, for example, ligands, enzymes or proteins, is an effective and practical methodology for the development of new applications. We report the assembly of two types of nanoreactors based upon poly(dimethylsiloxane)-block-poly(2-methyl-2-oxazoline) (PDMS-b-PMOXA) diblock copolymers as scaffold, uricase and lactoperoxidase as bio-catalysts located within the nanoreactors, and melittin as the biopores inserted into the hydrophobic shell. The nanoreactors were immobilized on poly(2-hydroxyethyl methacrylate)-co-poly(2-aminoethyl methacrylate hydrochloride) (PHEMA-co-P(2-AEMA·HCl) brushes-grafted wafer surfaces by utilizing the strong supramolecular interactions between biotin and streptavidin. The (PHEMA-co-P(2-AEMA·HCl) brushes on silicon surfaces were prepared by a surface initiating atom transfer radical polymerization (ATRP) "graft-from" technique. Cascade reactions between different surface-anchored nanoreactors were demonstrated by converting Amplex® Red to the fluorescent probe resorufin by using the H2O2 produced from uric acid and H2O. The detailed properties of the nanoreactors on the functionalized surface including the binding behaviours and cascade reactions were investigated using emission spectroscopy, transmission electron microscopy (TEM), light scattering (LS), atomic force microscopy (AFM) and a quartz crystal microbalance (QCM-D). The results are proof-of-principle for the preparation of catalytically functional engineered surface materials and lay the foundation for applying this advanced functional surface material in biosensing, implanting and antimicrobial materials preparation.

Streptavidin Homologues for Applications on Solid Surfaces at High Temperatures

One of the most commonly used bonds between two biomolecules is the bond between biotin and streptavidin (SA) or streptavidin homologues (SAHs). A high dissociation constant and the consequent high-temperature stability even allows for its use in nucleic acid detection under polymerase chain reaction (PCR) conditions. There are a number of SAHs available, and for assay design, it is of great interest to determine as to which SAH will perform the best under assay conditions. Although there are numerous single studies on the characterization of SAHs in solution or selected solid phases, there is no systematic study comparing different SAHs for biomolecule-binding, hybridization, and PCR assays on solid phases. We compared streptavidin, core streptavidin, traptavidin, core traptavidin, neutravidin, and monomeric streptavidin on the surface of microbeads (10-15 μm in diameter) and designed multiplex microbead-based experiments and analyzed simultaneously the binding of biotinylated oligonucleotides and the hybridization of oligonucleotides to complementary capture probes. We also bound comparably large DNA origamis to capture probes on the microbead surface. We used a real-time fluorescence microscopy imaging platform, with which it is possible to subject samples to a programmable time and temperature profile and to record binding processes on the microbead surface depending on the time and temperature. With the exception of core traptavidin and monomeric streptavidin, all other SA/SAHs were suitable for our investigations. We found hybridization efficiencies close to 100% for streptavidin, core streptavidin, traptavidin, and neutravidin. These could all be considered equally suitable for hybridization, PCR applications, and melting point analysis. The SA/SAH-biotin bond was temperature-sensitive when the oligonucleotide was mono-biotinylated, with traptavidin being the most stable followed by streptavidin and neutravidin. Mono-biotinylated oligonucleotides can be used in experiments with temperatures up to 70 °C. When oligonucleotides were bis-biotinylated, all SA/SAH-biotin bonds had similar temperature stability under PCR conditions, even if they comprised a streptavidin variant with slower biotin dissociation and increased mechanostability.

One-Step Biotinylation of Cellulose Paper by Polymer Coating to Prepare a Paper-Based Analytical Device

Cellulose paper has strong potential as an analytical platform owing to its unique characteristics. In the present study, we investigated a procedure for functionalizing the surface of cellulose paper by dip-coating a mixture of a functional polymer and a perfluoroalkylated surfactant (surfactant 1). The functional polymer comprised a mixture of methyl methacrylate and poly(ethylene glycol) methacrylate monomers. The monomer ratio in the functional polymer affected the hydrophilicity and water absorbance of the cellulose paper after dip-coating. Furthermore, the presence of surfactant 1 during dip-coating promoted the surface segregation of poly(ethylene glycol) (PEG) moieties in the polymer, which enhanced the hydrophilicity, prevented nonspecific protein adsorption, and maintained the water absorbance of the dip-coated cellulose paper. Dip-coating with another functional polymer containing biotin groups produced a cellulose paper with a biotin-decorated surface in a one-step procedure. The displayed biotin groups immobilized avidin on the surface, and the PEG moieties in the polymer prevented nonspecific protein adsorption. We then immobilized a thrombin-binding DNA aptamer on the avidin-immobilized cellulose paper to prepare a paper-based analytical device. It is possible to visualize thrombin in model solutions and serum using the paper-based analytical device.

Forces during cellular uptake of viruses and nanoparticles at the ventral side

Many intracellular pathogens, such as mammalian reovirus, mimic extracellular matrix motifs to specifically interact with the host membrane. Whether and how cell-matrix interactions influence virus particle uptake is unknown, as it is usually studied from the dorsal side. Here we show that the forces exerted at the ventral side of adherent cells during reovirus uptake exceed the binding strength of biotin-neutravidin anchoring viruses to a biofunctionalized substrate. Analysis of virus dissociation kinetics using the Bell model revealed mean forces higher than 30 pN per virus, preferentially applied in the cell periphery where close matrix contacts form. Utilizing 100 nm-sized nanoparticles decorated with integrin adhesion motifs, we demonstrate that the uptake forces scale with the adhesion energy, while actin/myosin inhibitions strongly reduce the uptake frequency, but not uptake kinetics. We hypothesize that particle adhesion and the push by the substrate provide the main driving forces for uptake.

Many intracellular pathogens mimic extracellular matrix motifs to specifically interact with the host membrane which may influences virus particle uptake. Here authors use single molecule tension sensors to reveal the minimal forces exerted on single virus particles and demonstrate that the uptake forces scale with the adhesion energy.

Self-Assembled Human Adipose-Derived Stem Cell-Derived Extracellular Vesicle-Functionalized Biotin-Doped Polypyrrole Titanium with Long-Term Stability and Potential Osteoinductive Ability

Mesenchymal stem cell-derived extracellular vesicles (MSC-EVs), containing proteins or microRNAs (miRNAs), possessing various biological activity and low immunogenicity, are considered promising for surface modification of bone grafts. However, the modification efficiency is not satisfied yet, resulting in compromised therapy effects. Here, we report a novel immobilized method by self-assembling biotinylated MSC-EVs onto the surface of biotin-doped polypyrrole titanium (Bio-Ppy-Ti) to improve its biofunctions in vitro and in vivo. Using this method, the amount of human adipose-derived stem cell-EVs (hASC-EVs) anchored onto the Bio-Ppy-Ti surface was 185-fold higher than that of pure Ti after ultrasonic concussion for 30 s and it remained stable on the Bio-Ppy-Ti surface for 14 days at 4 °C. Compared to pristine Ti, EV-Bio-Ppy-Ti exhibited enhanced cell compatibility and osteoinductivity for osteoblasts in vitro and anti-apoptosis ability in the ectopic bone formation mode. Gene chip analysis further demonstrated that several osteoinductive miRNAs were encapsulated in hASC-EVs, which may explain the high bone regeneration ability of EV-Bio-Ppy-Ti. Thus, this MSC-EV biotin-immobilized method appears to be highly efficient and long-term stable for bone graft bioactive modification, demonstrating its potential for clinical metal implants.

Spatiotemporal material functionalization via competitive supramolecular complexation of avidin and biotin analogs

Spatiotemporal control over engineered tissues is highly desirable for various biomedical applications as it emulates the dynamic behavior of natural tissues. Current spatiotemporal biomaterial functionalization approaches are based on cytotoxic, technically challenging, or non-scalable chemistries, which has hampered their widespread usage. Here we report a strategy to spatiotemporally functionalize (bio)materials based on competitive supramolecular complexation of avidin and biotin analogs. Specifically, an injectable hydrogel is orthogonally post-functionalized with desthiobiotinylated moieties using multivalent neutravidin. In situ exchange of desthiobiotin by biotin enables spatiotemporal material functionalization as demonstrated by the formation of long-range, conformal, and contra-directional biochemical gradients within complex-shaped 3D hydrogels. Temporal control over engineered tissue biochemistry is further demonstrated by timed presentation and sequestration of growth factors using desthiobiotinylated antibodies. The method's universality is confirmed by modifying hydrogels with biotinylated fluorophores, peptides, nanoparticles, enzymes, and antibodies. Overall, this work provides a facile, cytocompatible, and universal strategy to spatiotemporally functionalize materials.

Quantitative Measurement of Spatial Effects of DNA Origami on Molecular Binding Reactions Detected using Atomic Force Microscopy

DNA origami is a ubiquitous nanostructure that can be used as a universal scaffold for constructing molecular motors, nanosensors, nanodrugs, and optical devices. Understanding the inherent heterogeneity of DNA origami structures is crucial for optimizing the design of high-efficiency nanosized-devices. Here, we investigated the spatial effects of the DNA origami on binding reactions using atomic force microscopy. Protein complexes formed more efficiently at the vertex and rim than on the surface of the DNA origami; surprisingly, the maximum difference in biotin-streptavidin binding efficiency was over 80%, and the change in the binding rate was approximately 40-fold, suggesting the presence of distinct microenvironments at different locations of the DNA origami. Our findings are not only useful for the potential applications of the DNA origami, but also for clarifying differences in nanomaterials caused by nonuniform distribution or defects.

Detailed characterization of the solution kinetics and thermodynamics of biotin, biocytin and HABA binding to avidin and streptavidin

The high affinity (K_D ~ 10⁻¹⁵ M) of biotin for avidin and streptavidin is the essential component in a multitude of bioassays with many experiments using biotin modifications to invoke coupling. Equilibration times suggested for these assays assume that the association rate constant (k_on) is approximately diffusion limited (10⁹ M^-1s^-1) but recent single molecule and surface binding studies indicate that they are slower than expected (10⁵ to 10⁷ M^-1s^-1). In this study, we asked whether these reactions in solution are diffusion controlled, which reaction model and thermodynamic cycle describes the complex formation, and if there are any functional differences between avidin and streptavidin. We have studied the biotin association by two stopped-flow methodologies using labeled and unlabeled probes: I) fluorescent probes attached to biotin and biocytin; and II) unlabeled biotin and HABA, 2-(4’-hydroxyazobenzene)-benzoic acid. Both native avidin and streptavidin are homo-tetrameric and the association data show no cooperativity between the binding sites. The k_on values of streptavidin are faster than avidin but slower than expected for a diffusion limited reaction in both complexes. Moreover, the Arrhenius plots of the k_on values revealed strong temperature dependence with large activation energies (6–15 kcal/mol) that do not correspond to a diffusion limited process (3–4 kcal/mol). Accordingly, we propose a simple reaction model with a single transition state for non-immobilized reactants whose forward thermodynamic parameters complete the thermodynamic cycle, in agreement with previously reported studies. Our new understanding and description of the kinetics, thermodynamics, and spectroscopic parameters for these complexes will help to improve purification efficiencies, molecule detection, and drug screening assays or find new applications.

Whole-cell biosensing by siderophore-based molecular recognition and localized surface plasmon resonance

A siderophore-based active bacterial pull-down strategy was integrated in a localized surface plasmon resonance (LSPR) sensing platform and subsequently tested by detecting whole-cell Acinetobacter baumannii. The LSPR-based whole-cell sensing approach was previously demonstrated with aptamer-based molecular recognition motifs, and here it is extended to the powerful siderophore system, which exploits the natural bacterial need to sequester Fe(III). Specifically, a biscatecholate-monohydroxamate mixed ligand siderophore linked to a biotin via three polyethylene glycol repeating units was synthesized and immobilized on Au trigonal nanoprisms of an LSPR sensor. The resulting surface-confined biotinylated siderophore subsequently chelated Fe(III), forming a siderophore-Fe(III) complex which was shown to be competent to recognize A. baumannii. Target bacteria were captured and then detected by measuring wavelength shifts in the LSPR extinction spectrum. This siderophore pull-down LSPR biosensor approach is rapid (≤3 h detection) and sensitive - with a limit of detection (LOD) of 80 bacterial cells and a linear wavelength shift over the range 4 × 10² to 4 × 10⁶ cfu mL^-1. As intended by design, the siderophore-based biosensor was selective for A. baumannii over Pseudomonas aeruginosa, Escherichia coli, and Bacillus cereus, and was stable in ambient conditions for up to 2 weeks.

Tuning the chain length of new pyrene derivatives for site-selective photocleavage of avidin

Rational design of photoreagents with systematic modifications of their structures can provide valuable information for a better understanding of the protein photocleavage mechanism by these reagents. Variation of the length of the linker connecting the photoactive moiety with the protein anchoring-group allowed us to investigate the control of the protein photocleavage site. A series of new photochemical reagents (PMA-1A, PMA-2A and PMA-3A) with increasing chain lengths is examined in the current study. Using avidin as a model system, we examined the interaction of these probes by UV-Vis, fluorescence spectroscopic methods, photocleavage and computational docking studies. Hypochromism of the absorption spectrum was observed for the binding of these new photochemical reagents with estimated binding constants (K_b) of 6.2 × 10⁵, 6.7 × 10⁵ and 4.6 × 10⁵ M^-1, respectively. No significant changes of Stern-Volmer quenching constant (K_sv) with Co(NH₃)₆Cl₃ has been noted and the data indicated that the probes bind near the surface of the protein with sufficient exposure to the solvent. Photoexcitation of the probe-avidin complex, in the presence of Co(NH₃)₆Cl₃, resulted in protein fragmentation, and the cleavage yield decreased with the increase in the linker length, and paralleled with the observed K_sv values. Amino acid sequencing of the photofragments indicated that avidin is cleaved between Thr77 and Val78, as a major cleavage site for all the three photoreagents. This site is proximate to the biotin binding site on avidin, and molecular docking studies indicated that the H-bonding interactions between the polar end-group of the photoreagents and hydrophilic amino acids of avidin were important in positioning the reagent on the protein. The major cleavage site, at residues 77-78, was within 5 Å of the pyrenyl moiety of the probe, and hence, molecular tuning of the linker provided a simple approach to position the photoreagent along the potential photocleavage site.

Design, synthesis, and evaluation of VEGFR-targeted macromolecular MRI contrast agent based on biotin-avidin-specific binding

Developing magnetic resonance imaging (MRI) contrast agents with high relaxivity and specificity was essential to increase MRI diagnostic sensitivity and accuracy. In this study, the MRI contrast agent, vascular endothelial growth factor receptor (VEGFR)-targeted poly (l-lysine) (PLL)-diethylene triamine pentacetate acid (DTPA)-gadolinium (Gd) (VEGFR-targeted PLL-DTPA-Gd, VPDG), was designed and prepared to enhance the MRI diagnosis capacity of tumor. Biotin-PLL-DTPA-Gd was synthesized first, then, VEGFR antibody was linked to biotin-PLL-DTPA-Gd using biotin-avidin reaction. In vitro cytotoxicity study results showed that VPDG had low toxicity to MCF-7 cells and HepG2 cells at experimental concentrations. In cell uptake experiments, VPDG could significantly increase the internalization rates (61.75%±5.22%) in VEGFR-positive HepG2 cells compared to PLL-DTPA-Gd (PDG) (25.16%±4.71%, P<0.05). In MRI studies in vitro, significantly higher T1 relaxivity (14.184 mM^-1 s^-1) was observed compared to Magnevist^® (4.9 mM^-1 s^-1; P<0.01). Furthermore, in vivo MRI study results showed that VPDG could significantly enhance the tumor signal intensity and prolong the diagnostic time (from <1 h to 2.5 h). These results indicated that macromolecular VPDG was a promising MRI contrast agent and held great potential for molecular diagnosis of tumor.

Colloidally Assembled Zinc Ferrite Magnetic Beads: Superparamagnetic Labels with High Magnetic Moments for MR Sensors

Magnetic particles are widely used as labels in magnetoresistive sensors. To use magnetic particles as labels, several important characteristics should be considered, such as superparamagnetism, a high magnetic moment per particle (m), facile surface functionalization and biomolecule immobilization, colloidal stability, and analyte specificity. In this paper, we describe the preparation of magnetic labels with a high m, using colloidal assemblies of superparamagnetic zinc ferrite nanoparticles (ZFNPs, ∼9 nm). Also, several properties of these particles are compared with those of commercially available magnetic beads, Dynabeads and TurboBeads. The colloidally assembled zinc ferrite magnetic beads (ZFMBs, ∼160 nm) were synthesized by assembling ZFNPs via an emulsion-based assembly approach. While retaining superparamagnetism at room temperature, the m of ZFMBs is ∼4000× higher than that of the constituent ZFNPs. Surface functionalization with a layer of polyacrylic acid stabilized the ZFMBs in aqueous solution and enabled conjugation with streptavidin via carbodiimide linking chemistry. The streptavidinated ZFMBs can be suspended in aqueous buffer for ≥24 h, whereas 1.05 μm Dynabeads and 30 nm TurboBeads undergo ballistic deposition and instantaneous aggregation in solution, respectively. Finally, the streptavidinated ZFMBs were employed as labels in an immunoassay for the detection of osteopontin, a potential pancreatic cancer marker, proving superior to the commercial particles in terms of limit of detection and dynamic range. We expect that the work presented in this article can be extended to other biological applications, especially where superparamagnetic particles with a high m and colloidal stability are needed.

Enhancement of binding kinetics on affinity substrates by laser point heating induced transport

Binding of analyte to an affinity substrate is significantly enhanced by laser point heating induced transport.

Nanoprobe-Initiated Enzymatic Polymerization for Highly Sensitive Electrochemical DNA Detection

Electrochemical DNA (E-DNA) sensors have been greatly developed and play an important role in early diagnosis of different diseases. To determine the extremely low abundance of DNA biomarkers in clinical samples, scientists are making unremitting efforts toward achieving highly sensitive and selective E-DNA sensors. Here, a novel E-DNA sensor was developed taking advantage of the signal amplification efficiency of nanoprobe-initiated enzymatic polymerization (NIEP). In the NIEP based E-DNA sensor, the capture probe DNA was thiolated at its 3'-terminal to be immobilized onto gold electrode, and the nanoprobe was fabricated by 5'-thiol-terminated signal probe DNA conjugated gold nanoparticles (AuNPs). Both of the probes could simultaneously hybridize with the target DNA to form a "sandwich" structure followed by the terminal deoxynucleotidyl transferase (TdT)-catalyzed elongation of the free 3'-terminal of DNA on the nanoprobe. During the DNA elongation, biotin labels were incorporated into the NIEP-generated long single-stranded DNA (ssDNA) tentacles, leading to specific binding of avidin modified horseradish peroxidase (Av-HRP). Since there are hundreds of DNA probes on the nanoprobe, one hybridization event would generate hundreds of long ssDNA tentacles, resulting in tens of thousands of HRP catalyzed reduction of hydrogen peroxide and sharply increasing electrochemical signals. By employing nanoprobe and TdT, it is demonstrated that the NIEP amplified E-DNA sensor has a detection limit of 10 fM and excellent differentiation ability for even single-base mismatch.

Recognition kinetics of biomolecules at the surface of different-sized spheres

Bead-based assay is widely used in many bioanalytical applications involving the attachment of proteins and other biomolecules to the surface. For further understanding of the formation of a sphere-biomolecule complex and easily optimizing the use of spheres in targeted biological applications, it is necessary to know the kinetics of the binding reaction at sphere/solution interface. In our presented work, a simple fluorescence analysis method was employed to measure the kinetics for the binding of biotin to sphere surface-bound FITC-SA, based on the fact that the fluorescence intensity of FITC was proportionally enhanced by increasing the binding amount of biotin. By monitoring the time-dependent changes of FITC fluorescence, it was found that the binding rate constant of biotin to sphere surface-immobilized FITC-SA was much smaller than that of biotin to freely diffusing FITC-SA. This can be attributed to the decreased encounter frequency of the reaction pair, restricted motion of the attached biomolecule, and the weakened steric accessibility of the binding site. These factors would become more obvious when increasing the size of the sphere upon which the FITC-SA was immobilized. Additionally, the effect of nanoparticles on the diffusion-controlled bimolecular binding reaction was more evident than that on the chemical recognition-controlled binding reaction.

Molecular screening of cancer-derived exosomes by surface plasmon resonance spectroscopy

We report on a generic method to detect and identify the molecular profile of exosomes either derived from cultured cell lines or isolated from biofluids. Exosomes are nanovesicles shed by cells into their microenvironment and carry the molecular identity of their mother cells. These vesicles are actively involved in intercellular communication under physiological conditions and ultimately in the spread of various diseases such as cancer. As they are accessible in most biofluids (e.g., blood, urine, or saliva), these biological entities are promising tools for cancer diagnostics, offering a non-invasive and remote access to the molecular state of the disease. The composition of exosomes derived from cancer cells depends on the sort and state of the tumor, requiring a screening of multiple antigens to fully characterize the disease. Here, we exploited the capacity of surface plasmon resonance biosensing to detect simultaneously multiple exosomal and cancer biomarkers on exosomes derived from breast cancer cells. We developed an immunosensor surface which provides efficient and specific capture of exosomes, together with their identification through their distinct molecular profiles. The successful analysis of blood samples demonstrated the suitability of our bioanalytical procedure for clinical use.

Determination of multivalent protein-ligand binding kinetics by second-harmonic correlation spectroscopy

Binding kinetics of the multivalent proteins peanut agglutinin (PnA) and cholera toxin B subunit (CTB) to a GM1-doped 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid bilayer were investigated by both second-harmonic correlation spectroscopy (SHCS) and a traditional equilibrium binding isotherm. Adsorption and desorption rates, as well as binding affinity and binding free energy, for three bulk protein concentrations were determined by SHCS. For PnA binding to GM1, the measured adsorption rate decreased with increasing bulk PnA concentration from (3.7 ± 0.3) × 10(6) M(-1)·s(-1) at 0.43 μM PnA to (1.1 ± 0.1) × 10(5) M(-1)·s(-1) at 12 μM PnA. CTB-GM1 exhibited a similar trend, decreasing from (1.0 ± 0.1) × 10(9) M(-1)·s(-1) at 0.5 nM CTB to (3.5 ± 0.2) × 10(6) M(-1)·s(-1) at 240 nM CTB. The measured desorption rates in both studies did not exhibit any dependence on initial protein concentration. As such, 0.43 μM PnA and 0.5 nM CTB had the strongest measured binding affinities, (3.7 ± 0.8) × 10(9) M(-1) and (2.8 ± 0.5) × 10(13) M(-1), respectively. Analysis of the binding isotherm data suggests there is electrostatic repulsion between protein molecules when PnA binds GM1, while CTB-GM1 demonstrates positive ligand-ligand cooperativity. This study provides additional insight into the complex interactions between multivalent proteins and their ligands and showcases SHCS for examining these complex yet technologically important protein-ligand complexes used in biosensors, immunoassays, and other biomedical diagnostics.

Solid-phase single molecule biosensing using dual-color colocalization of fluorescent quantum dot nanoprobes

The development of solid-phase surface-based single molecule imaging technology has attracted significant interest during the past decades. Here we demonstrate a sandwich hybridization method for highly sensitive detection of a single thrombin protein at a solid-phase surface based on the use of dual-color colocalization of fluorescent quantum dot (QD) nanoprobes. Green QD560-modified thrombin binding aptamer I (QD560-TBA I) were deposited on a positive poly(l-lysine) assembled layer, followed by bovine serum albumin blocking. It allowed the thrombin protein to mediate the binding of the easily detectable red QD650-modified thrombin binding aptamer II (QD650-TBA II) to the QD560-TBA I substrate. Thus, the presence of the target thrombin can be determined based on fluorescent colocalization measurements of the nanoassemblies, without target amplification or probe separation. The detection limit of this assay reached 0.8 pM. This fluorescent colocalization assay has enabled single molecule recognition in a separation-free detection format, and can serve as a sensitive biosensing platform that greatly suppresses the nonspecific adsorption false-positive signal. This method can be extended to other areas such as multiplexed immunoassay, single cell analysis, and real time biomolecule interaction studies.

Single-molecule fluorescence imaging of DNA at a potential-controlled interface

Many interfacial chemical phenomena are governed in part by electrostatic interactions between polyelectrolytes and charged surfaces; these phenomena can influence the performance of biosensors, adsorption of natural polyelectrolytes (humic substances) on soils, and production of polyelectrolyte multilayer films. In order to understand electrostatic interactions that govern these phenomena, we have investigated the behavior of a model polyelectrolyte, 15 kbp fluorescently labeled plasmid DNA, near a polarized indium tin oxide (ITO) electrode surface. The interfacial population of DNA was monitored in situ by imaging individual molecules through the transparent electrode using total-internal-reflection fluorescence microscopy. At applied potentials of +0.8 V versus Ag/AgCl, the DNA interfacial population near the ITO surface can be increased by 2 orders of magnitude relative to bulk solution. The DNA molecules attracted to the interface do not adsorb to ITO, but rather they remain mobile with a diffusion coefficient comparable to free solution. Ionic strength strongly influences the sensitivity of the interfacial population to applied potential, where the increase in the interfacial population over a +300 mV change in potential varies from 20% in 30 mM ionic strength to over 25-fold in 300 μM electrolyte. The DNA accumulation with applied potential was interpreted using a simple Boltzmann model to predict average ion concentrations in the electrical double layer and the fraction of interfacial detection volume that is influenced by applied potential. A Gouy-Chapman model was also applied to the data to account for the dependence of the ion population on distance from the electrode surface, which indicates that the net charge on DNA responsible for interactions with the polarized surface is low, on the order of one excess electron. The results are consistent with a small fraction of the DNA plasmid being resident in the double-layer and with counterions screening much of the DNA excess charge.

MUC-1 aptamer-conjugated dye-doped silica nanoparticles for MCF-7 cells detection

In this work, we have prepared three types of aptamer-conjugated Rubpy-doped silica nanoparticles for Human breast carcinoma MCF-7 cells labeling. Probe A is prepared through covalent conjugation between amine-labeled MUC-1 aptamer and carboxyl-modified Rubpy-doped NPs (NPs-aptamer). Probe B is prepared based on the interaction between biotin-labeled MUC-1 aptamer and avidin-conjugated Rubpy-doped NPs (NPs-avidin-biotin-aptamer). For Probe C, there is a PEG with flexible long chain as the bridge between avidin and the NPs (NPs-PEG-avidin-biotin-aptamer). In addition, we further investigate the practical number of MUC-1 aptamers on an NP of each probe using hoechst33258 dye. The binding efficiency of MUC-1 aptamer on the three types of probes as follows: Probe A < Probe B < Probe C. In addition, microscopic fluorescence imaging shows that Probe C containing the PEG molecules can be effectively applied for the recognition of MUC-1 protein in human breast carcinoma MCF-7 cells thus demonstrates that the PEG with flexible long chain as the bridge between the aptamer and NP can greatly enhances the freedom of MUC-1 aptamer. Compared with common organic dyes, the dye-doped silica nanoparticles serve as a stable bioprobe because of their facile conjugation with the desirable biomolecules, and have exhibited great potential in bioanalysis.

Continuous flow multi-stage microfluidic reactors via hydrodynamic microparticle railing

"Multi-stage" fluidic reactions are integral to diverse biochemical assays; however, such processes typically require laborious and time-intensive fluidic mixing procedures in which distinct reagents and/or washes must be loaded sequentially and separately (i.e., one-at-a-time). Microfluidic processors that enable multi-stage fluidic reactions with suspended microparticles (e.g., microbeads and cells) to be performed autonomously could greatly extend the efficacy of lab-on-a-chip technologies. Here we present a single-layer microfluidic reactor that utilizes a microfluidic railing methodology to passively transport suspended microbeads and cells into distinct, adjacent laminar flow streams for rapid fluidic mixing and assaying. Four distinct molecular synthesis processes (i.e., consisting of 48 discrete fluidic mixing stages in total) were accomplished on polystyrene microbead substrates (15 μm in diameter) in parallel, without the need for external observation or regulation during device operation. Experimental results also revealed successful railing of suspended bovine aortic endothelial cells (approximately 13 to 17 μm in diameter). The presented railing system provides an effective continuous flow methodology to achieve bead-based and cell-based microfluidic reactors for applications including point-of-care (POC) molecular diagnostics, pharmacological screening, and quantitative cell biology.

Direct biomolecule binding on nonfouling surfaces via newly discovered supramolecular self-assembly of lysozyme under physiological conditions

When lysozyme is dissolved in a neutral HEPES buffer solution (pH = 7.4) with 0.001-0.050 M TCEP added, a fast phase transition process occurs and the resulting novel fiber-like hierarchical supramolecular assemblies made by primary spherical-particle aggregation can function as a "superglue" that binds strongly and quickly onto non-fouling coatings. This binding is highly selective towards lysozyme, and excludes synthetic, chemical/physical activation/deactivation (blocking) steps. By using biotinylated lysozyme, such a phase transition quickly creates a perfect biotinylated surface on non-fouling surfaces for avidin binding, showing great potential for the development of low-cost and practical biochips.

Angiogenic efficacy of Heparin on chick chorioallantoic membrane

Heparin is an anticoagulant agent known to have diverse effects on angiogenesis with some reports suggesting that it can induce angiogenesis while a few have indicated of its inhibitory property. Cancer patients treated for venous thromboembolism with low molecular heparin had a better survival than the unfractionated heparin (UFH). Heparin is known to interact with various angiogenic growth factors based on its sulfation modifications within the glycosaminoglycan chains. Therefore it is important to study the mechanism of action of heparin of different molecular weight to understand its angiogenic property. In this concern, we examined the angiogenic response of higher molecular weight Heparin (15 kDa) of different concentrations using late CAM assay. Growth of blood vessels in terms of their length and size was measured and thickness of the CAM was calculated morphometrically. The observed increase in the thickness of the CAM is suggestive of the formation of capillary like structures at the treated region. Analysis of the diffusion pattern showed internalized action of heparin that could affect gene expression leading to proliferation of endothelial cells. Angiogenesis refers to formation of new blood vessels from the existing ones and occurrence of new blood vessels at the treated area strongly confirms that heparin of 15 kDa molecular weight has the ability to induce angiogenesis on CAM vascular bed in a dose dependent manner. The results demonstrate the affinity of heparin to induce angiogenesis and provide a novel mechanism by which heparin could be used in therapeutics such as in wound healing process.

Micro Magnetic Gyromixer for Speeding up Reactions in Droplets

We report a novel micro magnetic gyromixer designed for accelerating mixing hence reactions in droplets. The gyromixer is fabricated with magnetite-PDMS composite using soft lithography. The mixer spins and balances itself on the droplet surface through the gyroscopic effect, rapidly homogenizing the enclosed reagents by stretching and folding internal fluid streamlines to enhance mixing. We examined the capability of the gyromixer for improving biochemical reactions in droplets by monitoring the biotin-streptavidin binding as a linker in a quantum dot fluorescence resonant energy transfer (QD-FRET) sensing system. The remotely controlled gyromixer exhibits high flexibility and potential for integration in a variety of droplet-based miniaturized total analysis systems (μTAS) to reduce turnaround times.

Application of a biotin functionalized QD assay for determining available binding sites on electrospun nanofiber membrane

BACKGROUND

The quantification of surface groups attached to non-woven fibers is an important step in developing nanofiber biosensing detection technologies. A method utilizing biotin functionalized quantum dots (QDs) 655 for quantitative analysis of available biotin binding sites within avidin immobilized on electrospun nanofiber membranes was developed.

RESULTS

A method for quantifying nanofiber bound avidin using biotin functionalized QDs is presented. Avidin was covalently bound to electrospun fibrous polyvinyl chloride (PVC 1.8% COOH w/w containing 10% w/w carbon black) membranes using primary amine reactive EDC-Sulfo NHS linkage chemistry. After a 12 h exposure of the avidin coated membranes to the biotin-QD complex, fluorescence intensity was measured and the total amount of attached QDs was determined from a standard curve of QD in solution (total fluorescence vs. femtomole of QD 655). Additionally, fluorescence confocal microscopy verified the labeling of avidin coated nanofibers with QDs. The developed method was tested against 2.4, 5.2, 7.3 and 13.7 mg spray weights of electrospun nanofiber mats. Of the spray weight samples tested, maximum fluorescence was measured for a weight of 7.3 mg, not at the highest weight of 13.7 mg. The data of total fluorescence from QDs bound to immobilized avidin on increasing weights of nanofiber membrane was best fit with a second order polynomial equation (R(2) = .9973) while the standard curve of total fluorescence vs. femtomole QDs in solution had a linear response (R(2) = .999).

CONCLUSION

A QD assay was developed in this study that provides a direct method for quantifying ligand attachment sites of avidin covalently bound to surfaces. The strong fluorescence signal that is a fundamental characteristic of QDs allows for the measurement of small changes in the amount of these particles in solution or attached to surfaces.

Analysis of IP3 receptors in and out of cells

BACKGROUND

Inositol 1,4,5-trisphosphate receptors (IP3R) are expressed in almost all animal cells. Three mammalian genes encode closely related IP3R subunits, which assemble into homo- or hetero-tetramers to form intracellular Ca2+ channels.

SCOPE OF THE REVIEW

In this brief review, we first consider a variety of complementary methods that allow the links between IP3 binding and channel gating to be defined. How does IP3 binding to the IP3-binding core in each IP3R subunit cause opening of a cation-selective pore formed by residues towards the C-terminal? We then describe methods that allow IP3, Ca2+ signals and IP3R mobility to be examined in intact cells. A final section briefly considers genetic analyses of IP3R signalling.

MAJOR CONCLUSIONS

All IP3R are regulated by both IP3 and Ca2+. This allows them to initiate and regeneratively propagate intracellular Ca2+ signals. The elementary Ca2+ release events evoked by IP3 in intact cells are mediated by very small numbers of active IP3R and the Ca2+-mediated interactions between them. The spatial organization of these Ca2+ signals and their stochastic dependence on so few IP3Rs highlight the need for methods that allow the spatial organization of IP3R signalling to be addressed with single-molecule resolution.

GENERAL SIGNIFICANCE

A variety of complementary methods provide insight into the structural basis of IP3R activation and the contributions of IP3-evoked Ca2+ signals to cellular physiology. This article is part of a Special Issue entitled Biochemical, biophysical and genetic approaches to intracellular calcium signaling.

In situ monitoring of single molecule binding reactions with time-lapse atomic force microscopy on functionalized DNA origami

Individual biomolecular binding events were recorded in situ by combining time-lapse atomic force microscopy and DNA origami. Single streptavidin molecules bound to specifically biotinyated DNA origami were simply counted as a function of time to obtain a direct measure of the binding rate.

Nanogel surface coatings for improved single-molecule imaging substrates

Surfaces that resist protein adsorption are important for many bioanalytical applications. Bovine serum albumin (BSA) coatings and multi-arm poly(ethylene glycol) (PEG) coatings display low levels of non-specific protein adsorption and have enabled highly quantitative single-molecule (SM) protein studies. Recently, a method was developed for coating a glass with PEG-BSA nanogels, a promising hybrid of these two low-background coatings. We characterized the nanogel coating to determine its suitability for SM protein experiments. SM adsorption counting revealed that nanogel-coated surfaces exhibit lower protein adsorption than covalently coupled BSA surfaces and monolayers of multi-arm PEG, so this surface displays one of the lowest degrees of protein adsorption yet observed. Additionally, the nanogel coating was resistant to DNA adsorption, underscoring the utility of the coating across a variety of SM experiments. The nanogel coating was found to be compatible with surfactants, whereas the BSA coating was not. Finally, applying the coating to a real-world study, we found that single ligand molecules could be tethered to this surface and detected with high sensitivity and specificity by a digital immunoassay. These results suggest that PEG-BSA nanogel coatings will be highly useful for the SM analysis of proteins.

Competitive surface-enhanced Raman scattering assay for the 1,25-dihydroxy metabolite of vitamin D3

This paper describes the development and preliminary testing of a competitive surface-enhanced Raman scattering (SERS) immunoassay for calcitriol, the 1,25-dihydroxy metabolite (1,25-(OH)(2)-D(3)) of vitamin D(3). Deficiencies in 1,25-(OH)(2)-D have been linked to renal disease, while elevations are linked to hypercalcemia. Thus, there has been a sharp increase in the clinical demand for measurements of this metabolite. The work herein extends the many attributes of SERS-based sandwich immunoassays that have been exploited extensively in the detection of large biolytes (e.g., DNA, proteins, viruses, and microorganisms) into a competitive immunoassay for the low level determination of a small biolyte, 1,25-(OH)(2)-D(3) (M(w) = 416 g mol(-1)). The assay uses surface modified gold nanoparticles as SERS labels, and has a dynamic range of 10-200 pg mL(-1) and a limit of detection of 8.4 ± 1.8 pg mL(-1). These analytical performance metrics match those of tests for 1,25-(OH)(2)-D(3) that rely on radio- or enzyme-labels, while using a much smaller sample volume and eliminating the disposal of radioactive wastes. Moreover, the SERS-based data from pooled-patient sera show strong agreement with that from radioimmunoassays. The merits and potential utility of this new assay are briefly discussed.