Search

There is an urgent need for reliable biosensors to detect nucleic acid of interest in clinical samples. We propose that the accuracy of the present nucleic acid-sensing method can be advanced by avoiding false-positive identifications derived from nonspecific interactions (e.g., nonspecific binding, probe degradation). The challenge is to exploit biosensors that can distinguish false-positive from true-positive samples in nucleic acid screening. In the present study, by learning from the enzymatic cycle in nature, we raise an allostery tool displaying invertible positive/negative cooperativity for reversible or cyclic activity control of the biosensing probe. We demonstrate that the silencing and regeneration of a positive (or negative) allosteric effector can be carried out through toehold displacement or an enzymatic reaction. We, thus, have developed several dynamic biosensors that can repeatedly measure a single nucleic acid sample. The ability to distinguish a false-positive from a true-positive signal is ascribed to the nonspecific interaction presenting equivalent signal variations, while the specific target binding exhibits diverse signal variations according to repeated measurements. Given its precise identification, such consequent dynamic biosensors offer exciting opportunities in physiological and pathological diagnosis.

This study is dealt with the two-phase binding (specific and nonspecific) of drug eluted from a half- embedded drug-eluting stent in presence of atherosclerotic plaque. The specific binding due to the interaction of drug molecules with specific receptors and nonspecific binding caused by the trapping of drug in the extra-cellular matrix have been paid due attention. An idealised wall consisting of a plaque and a healthy tissue region has been considered. Moreover, a Dirichlet release condition is imposed on the strut surface. In this investigation, a two-dimensional model governing drug transport and its two-phase binding in cylindrical polar coordinate system has been solved numerically by a finite-difference method. Our simulation predicts that plaque behaves like a physical barrier in two types of the binding process and there is an inverse relationship between bound drug concentration and plaque thickness. Simulations show that a single peak profile of drug is noted when the struts are situated one-strut radius apart and as the inter-strut distance increases, the peak concentration falls and distinct peak profiles over each strut are visualised. The model also reveals that in the region downstream of a strut, the concentration of both bound drug forms in the plaque and healthy regions increases, and eventually, the saturation length of binding sites increases. Predicted results show for smaller Damköhler number, the rapid saturation of binding sites takes place and the stent having thinner strut may perform well in terms of effectiveness as well as efficacy in the stent-based delivery.

Summary Powered by renewable electricity, biological | inorganic hybrids employ water-splitting electrocatalysis and generate H2 as reducing equivalents for microbial catalysis. The approach integrates the beauty of biocatalysis with the energy efficiency of inorganic materials for sustainable chemical production. Yet a successful integration requires delicate control of the hybrid's extracellular chemical environment. Such an argument is evident in the exemplary case of O2 because biocatalysis has a stringent requirement of O2, but the electrocatalysis may inadvertently perturb the oxidative pressure of biological moieties. Here we report that the addition of perfluorocarbon nanoemulsions promotes a biocompatible O2 microenvironment in an O2-sensitive N2-fixing biological | inorganic hybrid. Langmuir-type nonspecific binding between bacteria and nanoemulsions facilitates O2 transport in a bacterial microenvironment and leads to a 250% increase in efficiency for organic fertilizers within 120 h. Controlling the biological microenvironment with nanomaterials heralds a general approach accommodating the compatibility in biological | inorganic hybrids.

This paper describes a novel route for the preparation and functionalization of perfectly spherical cellulose nanospheres (CNSs), ranging from 100 to 400 nm with a typical diameter of 160–170 nm, for use in theranostics. The method of preparation enables both surface and interior bulk functionalization, and this presumably also makes the CNSs suitable for use in end-use applications other than theranostics. Surface functionalization was here demonstrated by antibody conjugation with an antibody specific toward the epidermal growth factor receptor (EGFR) protein, i.e., facilitating interaction with cancer cells having the EGFR. Besides showing specificity, the CNS–antibody conjugates showed a very low nonspecific binding. The CNSs could easily be bulk functionalized by embedding gold nanoparticles in the cellulose sphere matrix during CNS preparation to provide imaging contrast for diagnostic purposes.

Environmental DNA (eDNA) is increasingly popular as a useful non-invasive method to monitor and study biodiversity and community structure in freshwater and marine environments. To effectively extract eDNA from the filter surface is a fundamental factor determining the representativeness of the samples. We improved the eDNA extraction efficiency of an established Sterivex method by 12- to 16-fold using a larger volume of lysis buffer mix coupled with backflushing the cartridges. The DNeasy extraction column could be overloaded when the environmental sample input is high, possibly due to a higher nonspecific binding present in environmental samples, thus resulting in a relatively lower quantity measured. Therefore, we included an internal control DNA in the extraction to monitor the extraction and purification efficiencies in field samples, which is crucial for quantification of original eDNA concentration. The use of Takara Probe qPCR Mix supplemented with protein-based additives improved the robustness of the real time PCR assay on inhibitor-rich environmental samples, but prior purification by Qiagen PowerClean Pro Cleanup kit could be essential for inhibitor-rich water samples, even though the recovery rate was unexpectedly low (average 33.0%). The improved extraction and quantification complement the qualitative analyses including metabarcoding and metagenomics in field application.

A hyaluronic acid-degrading enzyme (hyaluronidase; HAase) is involved in tumor growth and inflammation, and consequently, HAase inhibitors have received recent attention as potential pharmaceuticals. Previous studies have discovered a wide range of inhibitors; however, unfortunately, most of them are dissimilar to the original ligand hyaluronic acid, and their mode of inhibition remains ambiguous or seems promiscuous. This situation presents an urgent need for readily available and highly reliable assay systems identifying the promiscuous inhibitory properties of HAase inhibitors. We have previously proposed a unique method to identify promiscuous nonspecific binding inhibitors of HAase by using the DMSO-perturbing effect. Here, to obtain mechanistic insights into the DMSO-perturbing assay, we studied the addition effect of 11 water-compatible chemicals on HAase inhibitory assay. Intriguingly, the perturbing property was found to be highly specific to DMSO. Furthermore, kinetic analyses described characteristic description of the perturbing property of DMSO: DMSO displayed entropy-driven interactions with HAase, whereas nonperturbing agents such as ethanol and urea exhibited enthalpy-driven interactions. The enthalpy-driven tight interactions of ethanol and urea with HAase would lead to the irreversible denaturation of the enzymes, while the entropy-driven weak interactions caused structural and catalytic perturbation, generating nonproductive but nondenatured states of enzymes, that are key species of the perturbation assay. With these mechanistic understandings in hand, the present assay will enable rapid and reliable identification of HAase inhibitors with certain pharmaceutical potential.

Although surface-based biosensors have been widely used in diagnostic applications, these sensors experience reduced sensitivity in the most common detection fluids because of nonspecific binding e...

For the development of immunoassays into sophisticated analyte-sensing methods, it is a priority to suppress nonspecific binding in immunoassays. Herein, we report a one-step surface coating method that can not only optimally immobilize antibodies but also suppress nonspecific binding. Zwitterionic dopamine (

Background: The continual need for the development and validation of ultra-sensitive (low pg/ml) LC–MS/MS assays in the pharmaceutical industry is largely driven by the ultra-low analyte exposure or very low sample volume. Methodology: Strategies and systematic approaches for sensitivity enhancement are provided which cover all aspects of a LC–MS/MS bioanalysis. A case study where such strategies were applied for the validation of a 5.0 pg/ml assay for a STING agonist is discussed. Conclusion: Analytical protocols were developed to extract analytes from large volume of plasma samples (600 and 400 μl) with high throughput. The guidance provided in this publication can serve as a resource to influence LC–MS/MS method development activities.

Background: The specific Intravenous Immunoglobulin (IVIG) for Alzheimer’s Disease (AD) is developing, which contains a high level of naturally occurring autoantibodies against amyloid-β (nAbs-Aβ), and the measure of nAbs-Aβ content is greatly essential. Though Enzyme-Linked Immunosorbent Assay (ELISA) has been widely used in detecting the nAbs-Aβ content, the impact of Aβ aggregates species chosen as antigen in ELISA on this measure has not been evaluated. Objective: To clarify the influence of different Aβ40/42 aggregates as antigen during ELISA on the content of nAbs-Aβ40/42 measured in IVIG. Method: Preparation of various Aβ40/42 aggregates was performed by different aggregation solutions and various lengths of time, and analyzed by western blot. Different Aβ40/42 aggregates as antigen were adopted to measure the nAbs-Aβ40/42 content in IVIG by ELISA, and the control was carried out to reduce interference of nonspecific binding. The Bonferroni and Dunnett’s T3 were used for statistical analysis. Results: The duration for the formation of Aβ40/42 aggregates had more effect on detecting nAbs-Aβ40/42 content in IVIG than the aggregation solution. Higher content of nAbs-Aβ40/42 in the same IVIG was displayed when measured with Aβ40/42 aggregates at day 3, instead of at day 0.5 and day 7.0. The nAbs- Aβ40/42 contents in the same IVIG measured with Aβ40/42 aggregates prepared in different solutions were obviously different, but there was no significant regularity among them. Conclusion: The nAbs-Aβ40/42 content in the same IVIG is significantly different when measured with Aβ40/42 aggregated under different conditions. The nAbs-Aβ40/42 content in IVIG by antigen-dependent measures, like ELISA, is uncertain.

RNAs with biological functions that depend on higher-order structures are vulnerable to forming inactive alternative structures. These alternative, misfolded structures can be stable enough to require intervention by proteins that promote conformational transitions. These RNA chaperone proteins are biologically critical, and they have long been hypothesized to possess nonspecific RNA binding as a general property – empowering a small collection of RNA chaperones to facilitate the folding of a large and diverse transcriptome. To identify new candidates for this nonspecific RNA chaperone activity, we performed affinity purifications of budding yeast RNA-binding proteins, using an exogenous and non-orthologous RNA as bait: the highly structured ribozyme derived from the Tetrahymena thermophila Group I intron. Proteins that co-purified with the RNA were identified by mass spectrometry, and analysis of multiple replicates revealed a sizable consistent population that was highly enriched in RNA-binding proteins. From this pool of nonspecific RBPs, we selected the yeast La protein Lhp1 for further investigation. In vitro kinetic assays with purified Lhp1 showed that it robustly accelerates refolding of the Tetrahymena ribozyme from a stable misfolded state to its catalytically active conformation, suggesting that Lhp1 indeed possesses broad RNA chaperone activity. Comparisons between this ATP-independent RNA chaperone and the ATP-dependent DEAD-box helicase CYT-19 highlighted the surprising efficiency of Lhp1 chaperone activity in single-turnover refolding assays, as well as some significant obstacles attributed to its lack of ATP utilization. Our findings suggest that Lhp1 may rely on other proteins in vivo to rescue activity after cycles of duplex unwinding. Overall, the validation of this candidate from our proteomic survey as a general RNA chaperone encourages us to pursue additional candidates in the future.

Highly abundant serum proteins tend to mask the low- and ultralow-abundance proteins, making low-abundance species detection extremely challenging. While traditional highly abundant protein depletion techniques are effective, they suffer from nonspecific binding problems and laborious sample manipulation procedures, and the kinetics of release of current separation systems is inadequately long, causing dilution of the eluted low-abundance protein samples. Here, we introduce an on-chip light-controlled reusable platform for the direct and fast depletion of highly abundant proteins from serum biosamples. Our nanoarrays display fast and highly selective depletion capabilities, up to 99% depletion of highly abundant protein species, with no undesired depletion effects on the concentration of low-abundance protein biomarkers. Displaying an ultrahigh surface area, ∼3400 m2 g-1, alongside a light-triggerable ultrafast release, this platform allows for a high depletion performance, together with high-yield reusability capabilities. Furthermore, this nanostructured light-controlled separation device could easily be integrated with downstream analytical technologies in a single lab-on-a-chip platform.

Many studies have found that gold nanoparticles with branched surfaces (nanoflowers) are markers for immunosensors that provide higher sensitivity gains than the commonly used spherical gold nanoparticles. Although the analytical characteristics of nanoparticle-using systems vary significantly depending on their size and shape, the question of choosing the best gold nanoflowers remains open. This work presents a comparative study of a panel of 33 preparations of gold nanoflowers formed by varying several parameters: the size of spherical nanoparticles-nuclei, the concentrations of nuclei, and tetrachloroauric acid during growth. The sizes of the resulting particles, their sorption capacity under antibody immobilization, mobility along membranes for lateral flow assays, and the effects of these parameters on the limits of detection of lateral flow immunoassay are characterized. The optimality of preparations obtained by growing a 0.2% v/v solution of nuclei with a diameter of 10 or 20 nm with tetrachloroauric acid at a concentration of 0.12 mM was shown. With their use, lateral flow immune tests were developed to determine markers of acute myocardial infarction—fatty acids binding protein and troponins I and T. The use of gold nanoflowers obtained under the proposed protocols led to significant gains in the limits of detection—3 to 10 times under visual detection and over 100 times under instrumental detection—compared to spherical gold nanoparticles. The significant increase under instrumental detection is due to the label’s low nonspecific binding.

Aim: Accurate and reliable quantification of oligonucleotides can be difficult, which has led to an increased focus on bioanalytical methods for more robust analyses. Recent advances toward mitigating sample losses on liquid chromatography (LC) systems have produced recovery advantages for oligonucleotide separations. Results & methodology: LC instruments and columns constructed from MP35N metal alloy and stainless steel columns were compared against LC hardware modified with hybrid inorganic-organic silica surfaces. Designed to minimize metal-analyte adsorption, these surfaces demonstrated a 73% increase in 25-mer phosphorothioate oligonucleotide recovery using ion-pairing reversed-phase LC versus standard LC surfaces, most particularly upon initial use. Conclusion: Hybrid silica chromatographic surfaces improve the performance, detection limits and reproducibility of oligonucleotide bioanalytical assays.

Introduction: Plasma protein binding (PPB) remains a controversial topic in drug discovery and development. Fraction unbound (fu) is a critical parameter that needs to be measured accurately, because it has significant impacts on the predictions of drug-drug interactions (DDI), estimations of therapeutic indices (TI), and developments of PK/PD relationships. However, it is generally not advisable to change PPB through structural modifications, because PPB on its own has little relevance for in vivo efficacy.Areas covered: PPB fundamentals are discussed including the three main classes of drug binding proteins (i.e., albumin, alpha1-acid glycoprotein, and lipoproteins) and their physicochemical properties, in vivo half-life, and synthesis rate. State-of-the-art methodologies for PPB are highlighted. Applications of PPB in drug discovery and development are presented.Expert opinion: PPB is an old topic in pharmacokinetics, but there are still many misconceptions. Improving the accuracy of PPB for highly bound compounds is an ongoing effort in the field with high priority. As the field continues to generate high quality data, the regulatory agencies will increase their confidence in our ability to accurately measure PPB of highly bound compounds, and experimental fu values below 0.01 will more likely be used for DDI predictions in the future.

This study described a simple, specific, and sensitive method using immunoaffinity magnetic purification coupled with high-performance liquid chromatography-fluorescence (HPLC-FL) detection for determination of bovine lactoferrin (bLf) in dairy products. BLf was selectively extracted from dairy products using immunoaffinity beads and then detected by HPLC-FL with its intrinsic fluorescence. During the analysis, standard solutions of bLf were pretreated with Tween 20, an anti-adsorptive agent, for blocking the nonspecific binding of bLf to polypropylene tubes. The calibration curve was linear over the range of 0.8-30 μg mL-1. The validated method was successfully applied to measure bLf at the intact level in dairy products.

A radioimmunoassay (RIA) method for progesterone has been developed. It has been validated for the determination of progesterone in cow skim milk. The main reagents used in the development work were prepared and characterized in-house. The assay uses a radioiodinated tracer purified by gel filtration on Sephadex G-25, standards prepared in skim milk and coated tubes with specific antibodies as the solid phase (separation system). The radiochemical purity of the tracer was greater than 95%, the maximum binding using solid phase reached 43% and the nonspecific binding didn't exceed 5%. Series of progesterone standards using milk matrix with concentration ranging from 0 to 40ng/mL were prepared. Detection limit of the assay was 0.13ng/mL and the precision evaluation gives an intra and inter-assay coefficient variations between 4.94% and 12.66%. The recovery obtained with skim milk samples was 84% to 119% and the parallelism test indicated good linearity (R2 > 0.99). The clinical tests give high correlation coefficient (r = 0.998) between progesterone concentrations of cow's skim milk assayed using developed progesterone RIA kit and commercial progesterone RIA kit.

Non-specific binding (NSB) is a key parameter in optimizing PET imaging tracers. We compared the ability of three available methods to predict NSB: LIMBA, rat fu,brain and CHI(IAM). Even though NSB is often associated with lipophilicity, we observed that logD does not correlate with any of these assays, clearly indicating that lipophilicity, while influencing NSB, is insufficient to predict it. A cross-comparison of the methods showed that all three correlate and are useful predictors of NSB. The three assays however rank the molecules slightly differently, illustrating the challenge of comparing molecules within a narrow chemical space. We also noted that CHI(IAM) values more effectively predict VNS, a measure of in vivo NSB in the human brain. CHI(IAM) measurements might be a closer model of the actual physicochemical interaction between PET tracer candidates and cell membranes, and seems to be the method of choice for the optimization of in vivo NSB.

Simultaneous detection of large viruses has been a great obstacle in the field of molecular imprinting. In this work, for the first time, a multifunctional molecularly imprinted sensor for single or simultaneous determination of hepatitis A virus (HAV) and hepatitis B virus (HBV) is provided. Visual detection was realized due to the color of green and red quantum dots that varied with the concentration of the target substance. The combination of hydrophilic monomers and metal chelation reduced the nonspecific binding and enhanced the specificity of adsorption. As a result, satisfactory selectivity and sensitivity were obtained for the detection of the two viruses, with imprinting factors of 3.70 and 3.35 for HAV and HBV, and limits of detection of 3.4 and 5.3 pmol/L, respectively, that were achieved within 20 min. The excellent recoveries during simultaneous detection and single detection modes indicate the prominent ability of the proposed sensor to detect HAV and HBV in human serum and the potential ability to simultaneously detect multiple viruses in real applications.

Digital enzyme-linked immunosorbent assay (ELISA) is a powerful analytical method for highly sensitive protein biomarker detection. The current protocol of digital ELISA requires multiple washing steps and signal amplification using an enzyme, which could be the potential drawback in in vitro diagnosis. In this study, we propose a digital immunoassay method, which we call "Digital HoNon-ELISA" (digital homogeneous non-enzymatic immunosorbent assay) for highly sensitive detection without washing and signal amplification. Target antigen molecules react with antibody-coated magnetic nanoparticles, which are then magnetically pulled into femtoliter-sized reactors. The antigens on the particles are captured by antibodies anchored on the bottom surface of the reactor via molecular tethers. Magnetic force enhances the efficiency of particle encapsulation in the reactors. Subsequent physical compartmentalization of the particles enhances the binding efficiency of antigen-carrying particles to the antibodies. The tethered particles show characteristic Brownian motion within a limited space by the molecular tethering, which is distinct from free diffusion or nonspecific binding of antigen-free particles. The number of tethered particles directly correlates with the concentration of the target antigen. Digital HoNon-ELISA was used with a prostate-specific antigen to achieve a detection of 0.093 pg/mL, which is over 9.0-fold the sensitivity of commercialized highly sensitive ELISA (0.84 pg/mL) and comparable to digital ELISA (0.055 pg/mL). This digital immunoassay strategy has sensitivity similar to digital ELISA with simplicity similar to homogeneous assay. Such similarity allows for potential application in rapid and simple digital diagnostic tests without the need for washing and enzymatic amplification.

Aggregation of amyloid-β (Aβ) peptides from soluble monomers to insoluble amyloid fibrils has been hypothesized to be one of the crucial steps in the progression of Alzheimer’s disease (AD). Due to the disordered nature of Aβ peptides, identifying aggregation inhibitors as potential drug candidates against AD has been a great challenge. In this communication, we report an atomistic simulation study of the inhibition mechanism of two small molecules, homotaurine and scyllo-inositol, which are AD drug candidates currently under investigation. Using a replica exchange molecular dynamics method to extensively explore the conformational space of Aβ42 monomer with and without the presence of the small molecule agents, we found that both drug candidates reduce the β-strand propensity of the C-terminus region (I31-A42) and promote a conformational change of Aβ42 monomer toward a more collapsed phase through a non-specific binding mechanism. These findings provide atomistic-level insights into understanding of the inhibitory mechanisms of the two potential small-molecule drug candidates for AD treatment in the future.

A sheep single-chain antibody-fragment library (Griffin.1, UK) was used to obtain miniantibodies to the lipopolysaccharide of Herbaspirillum seropedicae Z78. Using electro-optical analysis and electron microscopy, we recorded a biospecific interaction of antigenic determinants on the cell surface with phage antibodies against the LPS of H. seropedicae Z78 (mini-AbsLPS). Control experiments were run to rule out nonspecific binding of the mini-AbsLPS to cells of Azospirillum brasilense Sp245. Use of the highly specific mini-AbsLPS enabled the lipopolysaccharide of H. seropedicae Z78 to be detected in a mixture of bacterial cells by electro-optical means (analysis time, ∼5 min). This report is the first to show the possibility of rapid detection of Herbaspirillum on the basis of electro-optical analysis coupled with the use of mini-AbsLPS. The results are promising for the development of biosensor-based methods to detect potentially human-harmful prokaryotes whose structures either have not been studied or are absent from commercial databases.

Historically, cancer was seen and treated as a single disease. Over the years, this image has shifted, and it is now generally accepted that cancer is a complex and dynamic disease that engages multiple progression pathways in each patient. The shift from treating cancer as single disease to tailoring the therapy based on the individual's characteristic cancer profile promises to improve the clinical outcome and has also given rise to the field of personalized cancer treatment. To advise a suitable therapy plan and adjust personalized treatment, a reliable and fast diagnostic strategy is required. The advances in nanotechnology, microfluidics, and biomarker research have spurred the development of powerful miniaturized diagnostic systems that show high potential for use in personalized cancer treatment. These devices require only minute sample volumes and have the capability to create instant cancer snapshots that could be used as tool for cancer risk indication, early detection, tumor classification, and recurrence. Miniaturized systems can combine a whole sample-to-answer workflow including sample handling, preparation, analysis, and detection. As such, this concept is also often referred to as "lab-on-a-chip". An inherit challenge of monitoring personalized cancer treatment using miniaturized systems is that cancer biomarkers are often only detectable at trace concentrations present in a complex biological sample rich in interfering molecules, necessitating highly specific and sensitive biosensing strategies. To address the need for trace level detection, highly sensitive fluorescence, absorbance, surface-enhanced Raman spectroscopy (SERS), electrochemical, mass spectrometric, and chemiluminescence approaches were developed. To reduce sample matrix interferences, ingenious device modifications including coatings and nanoscopic fluid flow manipulation have been developed. Of the latter, our group has exploited the use of alternating current electrohydrodynamic (ac-EHD) fluid flows as an efficient strategy to reduce nonspecific nontarget biosensor binding and speed-up assay times. ac-EHD provides fluid motion induced by an electric field with the ability to generate surface shear forces in nanometer distance to the biosensing surface (known as nanoshearing phenomenon). This is ideally suited to increase the collision frequency of cancer biomarkers with the biosensing surface and shear off nontarget molecules thereby minimizing nonspecific binding. In this Account, we review recent advancements in miniaturized diagnostic system development with potential use in personalized cancer treatment and monitoring. We focus on integrated microfluidic structures for controlled sample flow manipulation followed by on-device biomarker interrogation. We further highlight the progress in our group, emphasis fundamentals and applications of ac-EHD-enhanced miniaturized systems, and outline promising detection concepts for comprehensive cancer biomarker profiling. The advances are discussed based on the type of cancer biomarkers and cover circulating tumor cells, proteins, extracellular vesicles, and nucleic acids. The potential of miniaturized diagnostic systems for personalized cancer treatment and monitoring is underlined with representative examples including device illustrations. In the final section, we critically discuss the future of personalized diagnostics and what challenges should be addressed to make these devices clinically translatable.

In chemistry and drug discovery, compound promiscuity is a controversial issue and often viewed differently. On the one hand, promiscuity has a clear-cut negative connotation, as promiscuous behavior of small molecules is often associated with nonspecific binding or assay artifacts. On the other hand, it is also well-established that compounds frequently interact with multiple targets including distantly related or unrelated proteins. In drug discovery, multitarget activity of small molecules receives increasing attention because it is therapeutically relevant, giving rise to desired or undesired pharmacological effects. Exploration of compound promiscuity is far from being simple because true and artificial activities are often difficult to discern. In light of these complications, X-ray structures of ligand–target complexes provide a wealth of information about molecular promiscuity, which is just beginning to be recognized and explored. Systematic analysis of structurally confirmed binding events invol...

A new method is demonstrated for preparing antifouling and low nonspecific adsorption surfaces on poorly reactive hydrophobic substrates, without the need for energy-intensive or environmentally aggressive pretreatments. The surface-active protein hydrophobin was covalently modified with a controlled radical polymerization initiator and allowed to self-assemble as a monolayer on hydrophobic surfaces, followed by the preparation of antifouling surfaces by Cu(0)-mediated living radical polymerization of poly(ethylene glycol) methyl ether acrylate (PEGA) performed in situ. By taking advantage of hydrophobins to achieve at the same time the immobilization of protein A, this approach allowed to prepare surfaces for IgG1 binding featuring greatly reduced nonspecific adsorption. The success of the surface modification strategy was investigated by contact angle, XPS, and AFM characterization, while the antifouling performance and the reduction of nonspecific binding were confirmed by QCM-D measurements.

Compound promiscuity is often attributed to nonspecific binding or assay artifacts. On the other hand, it is well-known that many pharmaceutically relevant compounds are capable of engaging multiple targets in vivo, giving rise to polypharmacology. To explore and better understand promiscuous binding characteristics of small molecules, we have searched X-ray structures (and very few qualifying solution structures) for ligands that bind to multiple distantly related or unrelated target proteins. Experimental structures of a given ligand bound to different targets represent high-confidence data for exploring promiscuous binding events. A total of 192 ligands were identified that formed crystallographic complexes with proteins from different families and for which activity data were available. These "multifamily" compounds included endogenous ligands and were often more polar than other bound compounds and active in the submicromolar range. Unexpectedly, many promiscuous ligands displayed conserved or similar binding conformations in different active sites. Others were found to conformationally adjust to binding sites of different architectures. A comprehensive analysis of ligand-target interactions revealed that multifamily ligands frequently formed different interaction hotspots in binding sites, even if their bound conformations were similar, thus providing a rationale for promiscuous binding events at the molecular level of detail. As a part of this work, all multifamily ligands we have identified and associated activity data are made freely available.

Nanomaterials have extensive applications in the life sciences and in clinical diagnosis. We have developed magnetic nanoparticles with high dispersibility and extremely low nonspecific binding to biomolecules and have demonstrated their application in chemical biology (e.g., for the screening of drug receptor proteins). Recently, the excellent properties of nanobeads have made possible the development of novel rapid immunoassay systems and high-precision technologies for exosome detection. For immunoassays, we developed a technology to encapsulate a fluorescent substance in magnetic nanobeads. The fluorescent nanobeads allow the rapid detection of a specific antigen in solution or in tissue specimens. Exosomes, which are released into the blood, are expected to become markers for several diseases, including cancer, but techniques for measuring the absolute quantity of exosomes in biological fluids are lacking. By integrating magnetic nanobead technology with an optical disc system, we developed a novel method for precisely quantifying exosomes in human serum with high sensitivity and high linearity without requiring enrichment procedures. This review focuses on the properties of our magnetic nanobeads, the development of novel biosensors using these nanobeads, and their broad practical applications. Graphical abstract ᅟ.

Context: Butylidenephthalide (Bdph) has been reported to inhibit rat uterine contractions, but significantly potentiate the noradrenaline (NA)-induced contractions in guinea-pig vas deferens (GPVDs). Objective: The present study elucidates the binding specificity of Bdph in GPVD to potentiate contractions. Materials and methods: Electrical field stimulation (EFS, supramaximal voltage, 1 ms and 1 Hz) or exogenous NA (50 μM) was applied to the GPVD in Krebs or 1/10 Mg-Tyrode’s solution, respectively. After the clonidine (10 nM)-induced twitch inhibition or the exogenous NA-induced contractions reached a constant, Bdph (50 µM) was added 2 min prior to the subsequent addition of NA (50 µM). Three experiments were performed. In the presence of Bdph (100 μM), the release of NA in the medium and remaining NA content in the tissues were determined after EFS-stimulation. Results: Bdph (100 μM) significantly antagonized the clonidine (10 nM)-induced twitch inhibition from 22.5 ± 2.1 to –11.4 ± 1.6% (n = 6) and dibutyryl-cAMP (300 μM) from 25.7 ± 3.2 to 7.9 ± 4.0% (n = 8). Bdph (100 μM) significantly increased the electrically stimulated release of NA from 393.0 ± 109.5 to 1000.0 ± 219.1 ng/g (n = 6). Bdph (50 μM) potentiated the exogenous NA (50 μM)-induced contractions from 3.0 ± 0.06 to 3.9 ± 0.06 g (n = 3), but after washout of Bdph, the response to NA gradually curtailed. Discussion and conclusions: Bdph action may be through the nonspecific binding of the butylidene group to prejunctional α2- and postjunctional α1-adrenoceptors to reversibly block K+ channels, and irreversibly block VDCCs on the smooth muscle cell membrane, respectively.

Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems. ISSN:0009-2665 ISSN:1520-6890