Article

Rational design of multivalent biosensor surfaces to enhance viral particle capture

Authors:
To read the full-text of this research, you can request a copy directly from the authors.

Abstract

Viral particles bind to receptors through multivalent protein interactions. Such high avidity interactions on sensor surfaces are less studied. In this work, three polyelectrolytes that can form biosensing surfaces with different interfacial characteristics in probe density and spatial arrangement were designed. Quartz crystal microbalance, interferometry and atomic force microscopy were used to study their surface density and binding behaviors with proteins and virus particles. A multivalent adsorption kinetic model was developed to estimate the number of bonds from the viral particles bound to the polyelectrolyte surfaces. Experimental results show that the heterogeneous 3D surface with jagged forest-like structure enhances the virus capture ability by maximizing the multivalent interactions. As a proof of concept, specific coronavirus detection was achieved in spiked swab samples. These results indicate the importance of both probe density and their spatial arrangement on the sensing performance, which could be used as a guideline for rational biosensing surface design.

No full-text available

Request Full-text Paper PDF

To read the full-text of this research,
you can request a copy directly from the authors.

... 9 QCMD is used to study electrochemistry at battery electrodes 10 as well as contact mechanics at the atomic 11 and macroscopic scales. 12,13 Examples of QCMD applications in biological interfaces are too numerous and broad to list; suffice it to say, they are found at the level of ions, 14 molecules and molecular assemblies, particularly lipids, [15][16][17][18][19][20][21][22] viruses, [23][24][25] cells, [26][27][28][29][30][31][32] bacterial biofilms, 33,34 and tissues. [35][36][37] Finally, as a sensitive method for probing solid-liquid interfaces that can provide information about the organization of the adsorbed material 15 and its solvation, 38,39 QCMD continues to be used for studying adsorption phenomena, 40 as well as protein orientation and organization at various surfaces. ...
Article
Applications of quartz crystal microbalance with dissipation to studying soft and biological interfaces are reviewed. The focus is primarily on data analysis through viscoelastic modeling and a model-free approach focusing on the acoustic ratio. Current challenges and future research and development directions are discussed.
Article
Full-text available
The ongoing highly contagious Coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underlines the fundamental position of diagnostic testing in outbreak control by allowing a distinction of the infected from the non-infected people. Diagnosis of COVID-19 remains largely based on reverse transcription PCR (RT-PCR), identifying the genetic material of the virus. Molecular testing approaches have been largely proposed in addition to infectivity testing of patients via sensing the presence of viral particles of SARS-CoV-2 specific structural proteins, such as the spike glycoproteins (S1, S2) and the nucleocapsid (N) protein. While the S1 protein remains the main target for neutralizing antibody treatment upon infection and the focus of vaccine and therapeutic design, it has also become a major target for the development of point-of care testing (POCT) devices. This review will focus on the possibility of surface plasmon resonance (SPR)-based sensing platforms to convert the receptor-binding event of SARS-CoV-2 viral particles into measurable signals. The state-of-the-art SPR-based SARS-CoV-2 sensing devices will be provided, and highlights about the applicability of plasmonic sensors as POCT for virus particle as well as viral protein sensing will be discussed.
Article
Full-text available
The atomic force microscope (AFM) can measure nanoscale morphology and mechanical properties and has a wide range of applications. The traditional method for measuring the mechanical properties of a sample does so for the longitudinal and transverse properties separately, ignoring the coupling between them. In this paper, a data processing and multidimensional mechanical information extraction algorithm for the composite mode of peak force tapping and torsional resonance is proposed. On the basis of a tip–sample interaction model for the AFM, longitudinal peak force data are used to decouple amplitude and phase data of transverse torsional resonance, accurately identify the tip–sample longitudinal contact force in each peak force cycle, and synchronously obtain the corresponding characteristic images of the transverse amplitude and phase. Experimental results show that the measured longitudinal mechanical characteristics are consistent with the transverse amplitude and phase characteristics, which verifies the effectiveness of the method. Thus, a new method is provided for the measurement of multidimensional mechanical characteristics using the AFM.
Article
Full-text available
Desirable biosensing assays need to be sensitive, specific, cost‐effective, instrument‐free, and versatile. Herein we report a new strategy termed CLIPON (CRISPR and Large DNA assembly Induced Pregnancy strips for signal‐ON detection) that can deliver these traits. CLIPON integrates a commercial pregnancy test strip (PTS) with four biological elements: the human chorionic gonadotropin (hCG), CRISPR‐Cas12a, crRNA and cauliflower‐like large‐sized DNA assemblies (CLD). CLIPON uses the Cas12a/crRNA complex both to recognize a target of interest and to release CLD‐bound hCG so that target presence can translate into a colorimetric signal on the PTS. We demonstrate the versatility of CLIPON through sensitive and specific detection of HPV genomic DNA, SARS‐CoV‐2 genomic RNA and adenosine. We also engineer a cell phone app and a hand‐held microchip to achieve signal quantification. CLIPON represents an attractive option for biosensing and point‐of‐care diagnostics.
Article
Full-text available
The coronavirus disease 2019 (COVID-19) are outbreaking all over the world. To help fight this disease, it is necessary to establish an effective and rapid detection method. The nucleocapsid (N) protein of Severe Acute Respiratory syndrome Coronavirus 2 (SARS-CoV-2) is involved in viral replication, assembly and immune regulation and plays an important role in the viral life cycle. Moreover, the N protein also could be a diagnostic factor and potential drag target. Therefore, by synthesizing the N gene sequence of SARS-CoV-2, constructing the pET-28a (+)-N recombinant plasmid, we expressed the N protein in E.coli and obtained 15 mAbs against SARS-CoV-2-N protein by the hybridomas and ascites, then an immunochromatographic test strip method detecting N antigen was established. In this study, we obtained 14 high-titer and high-specificity monoclonal antibodies, and the test strips exclusively react with the SARS-CoV-2-N protein and no cross-reactivity with other coronavirus and also recognize the recombinant N protein of Delta (B.1.617.2) variant. These mAbs can be used for the early and rapid diagnosis of SARS-CoV-2 infection through serological antigen. This article is protected by copyright. All rights reserved.
Article
Full-text available
Biosensors have acquired much importance in drug discovery, medical diagnostics, food safety, defense, security, and monitoring of environmental conditions. Furthermore, there has been great progress in the potential applications of advanced nanomaterials in biosensors. Every year there are several advances in sensing techniques that can be attributed to nanomaterials, biorecognition elements, or their related fabrication techniques. The further development of nanotechnology-based sensors provides a wide variety of opportunities to modern research. Advanced nanomaterials can provide remarkable optical, electrical, mechanical, and catalytic properties. For example, transition metals and organic polymers have been used in the fabrication of powerful, sensitive, and precise biosensors. The distinctive properties of advanced nanomaterials have been widely incorporated into biosensors. However, fabrication techniques also play important roles in the development of these devices. Therefore, we present a review of some of the advanced nanomaterials that have been widely used over the last few years and discuss their fabrication techniques. The focus of this review is to provide a directional perspective of recently fabricated advanced nanomaterial-based biosensors in the diagnosis of various diseases.
Article
Full-text available
The precise diagnosis of COVID-19 is of outmost importance in order to effectively treat patients and prevent SARS-CoV-2 transmission. Herein, we evaluated the sensitivity and specificity of the COVID-19 Antigen Detection Kit (Colloidal Gold—CG) compared with PCR in nasopharyngeal and nasal samples. A total of 114 positive and 244 negative nasopharyngeal specimens confirmed by PCR were used in this comparative study. When the PCR positive Cycle Threshold (Ct) value was ≤25, CG sensitivity was 100%. When the PCR positive Ct value was ≤33, CG sensitivity was 99%. When the PCR positive Ct value was ≤40, CG sensitivity was 89.47%. Regarding nasal swabs, a total of 109 positive and 250 negative specimens confirmed by PCR were used. When the PCR positive Ct value was ≤25, CG sensitivity was 100%. When the PCR positive Ct value was ≤33, CG sensitivity was 96.12%. When the PCR positive Ct value was ≤37, CG sensitivity was 91.74%. Specificity was above 99% regardless of the Ct value of PCR positivity for both nasopharyngeal and nasal specimens. Overall, the CG showed high sensitivity and specificity when the PCR Ct value was less than 33. Therefore, CG can be used for screening early in the disease course. Confirmatory PCR is essential when a false negative result is suspected.
Article
Full-text available
Correlates of infectiousness The role that individuals with asymptomatic or mildly symptomatic severe acute respiratory syndrome coronavirus 2 have in transmission of the virus is not well understood. Jones et al. investigated viral load in patients, comparing those showing few, if any, symptoms with hospitalized cases. Approximately 400,000 individuals, mostly from Berlin, were tested from February 2020 to March 2021 and about 6% tested positive. Of the 25,381 positive subjects, about 8% showed very high viral loads. People became infectious within 2 days of infection, and in hospitalized individuals, about 4 days elapsed from the start of virus shedding to the time of peak viral load, which occurred 1 to 3 days before the onset of symptoms. Overall, viral load was highly variable, but was about 10-fold higher in persons infected with the B.1.1.7 variant. Children had slightly lower viral loads than adults, although this difference may not be clinically significant. Science , abi5273, this issue p. eabi5273
Article
Full-text available
The influenza A virus (IAV) interacts with the glycocalyx of host cells through its surface proteins hemagglutinin (HA) and neuraminidase (NA). Quantitative biophysical measurements of these interactions may help to understand these interactions at the molecular level with the long-term aim to predict influenza infectivity and answer other biological questions. We developed a method, called multivalent affinity profiling (MAP), to measure virus binding profiles on receptor density gradients to determine the threshold receptor density, which is a quantitative measure of virus avidity toward a receptor. Here, we show that imaging of IAVs on receptor density gradients allows the direct visualization and efficient assessment of their superselective binding. We show how the multivalent binding of IAVs can be quantitatively assessed using MAP if the receptor density gradients are prepared around the threshold receptor density without crowding at the higher densities. The threshold receptor density increases strongly with increasing flow rate, showing that the superselective binding of IAV is influenced by shear force. This method of visualization and quantitative assessment of superselective binding allows not only comparative studies of IAV–receptor interactions, but also more fundamental studies of how superselectivity arises and is influenced by experimental conditions.
Article
Full-text available
Understanding how influenza viruses traverse the mucus and recognize host cells is critical for evaluating their zoonotic potential, and for prevention and treatment of the disease. The surface of the influenza A virus is covered with the receptor‐binding protein hemagglutinin and the receptor‐cleaving enzyme neuraminidase, which jointly control the interactions between the virus and the host cell. These proteins are organized in closely spaced trimers and tetramers to facilitate multivalent interactions with sialic acid‐terminated glycans. This review shows that the individually weak multivalent interactions of influenza viruses allow superselective binding, virus‐induced recruitment of receptors, and the formation of dynamic complexes that facilitate molecular walking. Techniques to measure the avidity and receptor specificity of influenza viruses are reviewed, and the pivotal role of multivalent interactions with their emergent properties in crossing the mucus and entering host cells is discussed. A model is proposed for the initiation of cell entry through virus‐induced receptor clustering. The multivalent interactions of influenza viruses are maintained in a dynamic regime by a functional balance between binding and cleaving.
Article
Full-text available
We investigate the binding interactions of synthesized multi-walled carbon nanotubes (MWCNTs) with SARS-CoV-2 virus. Two essential components of the SARS-CoV-2 structure i.e. 6LU7 (main protease of SARS-CoV-2) and 6LZG (spike receptor-binding domain complexed with its receptor ACE2) were used for computational studies. MWCNTs of different morphologies (zigzag, armchair and chiral) were synthesized through a thermal chemical vapour deposition process as a function of pyrolysis temperature. A direct correlation between radius to volume ratio of the synthesized MWCNTs and the binding energies for all three (zigzag, armchair and chiral) conformations were observed in our computational studies. Our result suggests that MWCNTs interact with the active sites of the main protease along with the host angiotensin-converting enzyme2 (ACE2) receptors. Furthermore, it is also observed that MWCNTs have significant binding affinities towards SARS-CoV-2. However, the highest free binding energy of −87.09 kcal mol⁻¹ with 6LZG were shown by the armchair MWCNTs with SARS-CoV-2 through the simulated molecular dynamic trajectories, which could alter the SARS-CoV-2 structure with higher accuracy. The radial distribution function also confirms the density variation as a function of distance from a reference particle of MWCNTs for the study of interparticle interactions of the MWCNT and SARS-CoV-2. Due to these interesting attributes, such MWCNTs could find potential application in personal protective equipment (PPE) and diagnostic kits.
Article
Full-text available
It was a long-cherished dream for chemists to take a direct look at chemical bonding, a fundamental component of chemistry. This dream was finally accomplished by the state-of-the-art noncontact atomic force microscopy (NC-AFM) equipped with qPlus force sensors and carbon monoxide (CO) functionalized tips. The resolved interconnectivity between atoms and molecules in NC-AFM frequency shift images is interpreted as chemical bonding, providing essential knowledge of the bond length, bond angle and even bond order. The featured contrast of different chemical bonds can serve as fingerprints for further interpretation of chemical structures toward unknown species synthesized on surfaces. This breakthrough enriches characterization tools for surface science and brings our understanding of on-surface reactions to a new level. Beyond bond imaging, the application of NC-AFM has been extended to quantifying interatomic interactions, identifying three-dimensional nanostructures, manipulating molecules and reactions, as well as determining molecular electronic characteristics. Moreover, some recent efforts address the improvement of the usability and versatility of the bond-resolved NC-AFM technique, including high-resolution molecular investigation on bulk insulators, application-specific tip modification, stable bond imaging above liquid helium temperature and autonomous experimentation implemented by artificial intelligence.
Article
Full-text available
The recent pandemic of the novel coronavirus disease 2019 (COVID‐19) has caused huge worldwide disruption due to the lack of available testing locations and equipment. The use of optical techniques for viral detection has flourished in the past 15 years, providing more reliable, inexpensive, and accurate detection methods. In the current minireview, optical phenomena including fluorescence, surface plasmons, surface‐enhanced Raman scattering (SERS), and colorimetry are discussed in the context of detecting virus pathogens. The sensitivity of a viral detection method can be dramatically improved by using materials that exhibit surface plasmons or SERS, but often this requires advanced instrumentation for detection. Although fluorescence and colorimetry lack high sensitivity, they show promise as point‐of‐care diagnostics because of their relatively less complicated instrumentation, ease of use, lower costs, and the fact that they do not require nucleic acid amplification. The advantages and disadvantages of each optical detection method are presented, and prospects for applying optical biosensors in COVID‐19 detection are discussed.
Article
Full-text available
The performance of current microfluidic methods for exosome detection is constrained by boundary conditions, as well as fundamental limits to microscale mass transfer and interfacial exosome binding. Here, we show that a microfluidic chip designed with self-assembled three-dimensional herringbone nanopatterns can detect low levels of tumour-associated exosomes in plasma (10 exosomes μl ⁻¹ , or approximately 200 vesicles per 20 μl of spiked sample) that would otherwise be undetectable by standard microfluidic systems for biosensing. The nanopatterns promote microscale mass transfer, increase surface area and probe density to enhance the efficiency and speed of exosome binding, and permit drainage of the boundary fluid to reduce near-surface hydrodynamic resistance, thus promoting particle–surface interactions for exosome binding. We used the device for the detection—in 2 μl plasma samples from 20 ovarian cancer patients and 10 age-matched controls—of exosome subpopulations expressing CD24, epithelial cell adhesion molecule and folate receptor alpha proteins, and suggest exosomal folate receptor alpha as a potential biomarker for early detection and progression monitoring of ovarian cancer. The nanolithography-free nanopatterned device should facilitate the use of liquid biopsies for cancer diagnosis. © 2019, The Author(s), under exclusive licence to Springer Nature Limited.
Article
Full-text available
Viruses are pathogenic microorganisms that can inhabit and replicate in human bodies causing a number of widespread infectious diseases such as influenza, gastroenteritis, hepatitis, meningitis, pneumonia, acquired immune deficiency syndrome (AIDS) etc. A majority of these viral diseases are contagious and can spread from infected to healthy human beings. The most important step in the treatment of these contagious diseases and to prevent their unwanted spread is to timely detect the disease-causing viruses. Gravimetric viral diagnostics based on quartz crystal microbalance (QCM) transducers and natural or synthetic receptors are miniaturized sensing platforms that can selectively recognize and quantify harmful virus species. Herein, a review of the label-free QCM virus sensors for clinical diagnostics and point of care (POC) applications is presented with major emphasis on the nature and performance of different receptors ranging from the natural or synthetic antibodies to selective macromolecular materials such as DNA and aptamers. A performance comparison of different receptors is provided and their limitations are discussed.
Article
Full-text available
Viral diseases are perpetual threats to human and animal health. Detection and characterization of viral pathogens require accurate, sensitive, and rapid diagnostic assays. For field and clinical samples, the sample preparation procedures limit the ultimate performance and utility of the overall virus diagnostic protocols. This study presents the development of a microfluidic device embedded with porous silicon nanowire (pSiNW) forest for label‐free size‐based point‐of‐care virus capture in a continuous curved flow design. The pSiNW forests with specific interwire spacing are synthesized in situ on both bottom and sidewalls of the microchannels in a batch process. With the enhancement effect of Dean flow, this study demonstrates that about 50% H5N2 avian influenza viruses are physically trapped without device clogging. A unique feature of the device is that captured viruses can be released by inducing self‐degradation of the pSiNWs in physiological aqueous environment. About 60% of captured viruses can be released within 24 h for virus culture, subsequent molecular diagnosis, and other virus characterization and analyses. This device performs viable, unbiased, and label‐free virus isolation and release. It has great potentials for virus discovery, virus isolation and culture, functional studies of virus pathogenicity, transmission, drug screening, and vaccine development.
Article
Full-text available
Exosomes are cell-derived nano-sized vesicles that have been recently recognized as new mediators for many cellular processes and potential biomarkers for non-invasive disease diagnosis and the monitoring of treatment response. To better elucidate the biology and clinical value of exosomes, there is a pressing need for new analytical technologies capable of the efficient isolation and sensitive analysis of such small and molecularly diverse vesicles. Herein, we developed a microfluidic exosome analysis platform based on a new graphene oxide/polydopamine (GO/PDA) nano-interface. To the best of our best knowledge, we report for the first time, the GO-induced formation of a 3D nanoporous PDA surface coating enabled by the microfluidic layer-by-layer deposition of GO and PDA. It was demonstrated that this nanostructured GO/PDA interface greatly improves the efficiency of exosome immuno-capture, while at the same time effectively suppressing non-specific exosome adsorption. Based on this nano-interface, an ultrasensitive exosome ELISA assay was developed to afford a very low detection limit of 50 μL(-1) with a 4 log dynamic range, which is substantially better than the existing methods. As a proof of concept for clinical applications, we adapted this platform to discriminate ovarian cancer patients from healthy controls by the quantitative detection of exosomes directly from 2 μL plasma without sample processing. Thus, this platform could provide a useful tool to facilitate basic and clinical investigations of exosomes for non-invasive disease diagnosis and to aid precision treatment.
Article
Full-text available
Imaging native membrane receptors and testing how they interact with ligands is of fundamental interest in the life sciences but has proven remarkably difficult to accomplish. Here, we introduce an approach that uses force-distance curve-based atomic force microscopy to simultaneously image single native G protein-coupled receptors in membranes and quantify their dynamic binding strength to native and synthetic ligands. We measured kinetic and thermodynamic parameters for individual protease-activated receptor-1 (PAR1) molecules in the absence and presence of antagonists, and these measurements enabled us to describe PAR1's ligand-binding free-energy landscape with high accuracy. Our nanoscopic method opens an avenue to directly image and characterize ligand binding of native membrane receptors.
Article
Full-text available
A novel biosensor interface exploiting the spontaneous surface assembly of a polycationic, polyethylene glycol (PEG)-grafted, biotinylated copolymer is investigated. By means of optical waveguide lightmode spectroscopy (OWLS), streptavidin and avidin are shown to bind specifically to the biotin-functionalized PEG, while the resistance of the remaining PEG chains to protein absorption yields a high specific binding to nonspecific binding ratio. The various components of this model immunoassay are shown to retain their biological activity and the effects of protein charge and the ionic strength of the buffer is explored.
Article
Full-text available
The generation of surfaces and interfaces that are able to withstand protein adsorption is a major challenge in the design of blood-contacting materials for both medical implants and bioaffinity sensors. Poly(ethylene glycol)-derived materials are generally considered to be particularly effective candidates for the fabrication of protein-resistant materials. Most metallic biomaterials are covered by a protective, stable oxide film; converting such oxide surfaces, which are known to strongly interact with proteins, into noninteractive surfaces requires a specific design of the surface/interface architecture. A class of copolymers based on poly(L-lysine)g-poly(ethylene glycol) (PLL g-PEG) was found to spontaneously adsorb from aqueous solutions onto several metal oxide surfaces, such as TiO2, Si0.4Ti0.6O2 and Nb2O5, as measured by the in situ optical waveguide lightmode spectroscopy technique and by ex situ X-ray photoelectron spectroscopy. The resulting adsorbed layers are highly effective in reducing the adsorption both of blood serum and of individual proteins such as fibrinogen, which is known to play a major role in the cascade of events that lead to biomaterial-surface-induced blood coagulation and thrombosis. Adsorbed protein levels as low as <5 ng/cm(2) could be achieved for an optimized polymer architecture. The modified surfaces are stable to desorption under flow conditions at 37 degrees C and pH 7.4 in HEPES [4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid] and PBS (phosphate-buffered saline) buffers. The adsorbed layer of copolymer is thought to form a comblike structure at the surface, with positively charged primary amine groups of the PLL bound to the negatively charged metal oxide surface, while the hydrophilic and uncharged PEG side chains are exposed to the solution phase. Copolymer architecture is an important factor in the resulting protein resistance; it is discussed on the basis of packing-density considerations and the corresponding radii of gyration of the different PEG chain lengths studied. This surface functionalization technology is believed to be of value for use in both the biomaterial and biosensor areas, as the chosen macromolecules are biocompatible and the application is straightforward and cost-effective.
Article
Full-text available
Advances in materials chemistry offer a range of nanostructured shapes and textures for building new biosensors. Previous reports have implied that controlling the properties of sensor substrates can improve detection sensitivities, but the evidence remains indirect. Here we show that by nanostructuring the sensing electrodes, it is possible to create nucleic acid sensors that have a broad range of sensitivities and that are capable of rapid analysis. Only highly branched electrodes with fine structuring attained attomolar sensitivity. Nucleic acid probes immobilized on finely nanostructured electrodes appear more accessible and therefore complex more rapidly with target molecules in solution. By forming arrays of microelectrodes with different degrees of nanostructuring, we expanded the dynamic range of a sensor system from two to six orders of magnitude. The demonstration of an intimate link between nanoscale sensor structure and biodetection sensitivity will aid the development of high performance diagnostic tools for biology and medicine.
Article
Full-text available
We report on the design and characterization of a class of biomolecular interfaces based on derivatized poly(l-lysine)-grafted poly(ethylene glycol) copolymers adsorbed on negatively charged surfaces. As a model system, we synthesized biotin-derivatized poly(l-lysine)-grafted poly(ethylene glycol) copolymers, PLL-g-[(PEGm)((1-x)) (PEG-biotin)(x)], where x varies from 0 to 1. Monolayers were produced on titanium dioxide substrates and characterized by x-ray photoelectron spectroscopy. The specific biorecognition properties of these biotinylated surfaces were investigated with the use of radiolabeled streptavidin alone and within complex protein mixtures. The PLL-g-PEG-biotin monolayers specifically capture streptavidin, even from a complex protein mixture, while still preventing nonspecific adsorption of other proteins. This streptavidin layer can subsequently capture biotinylated proteins. Finally, with the use of microfluidic networks and protein arraying, we demonstrate the potential of this class of biomolecular interfaces for applications based on protein patterning.
Article
Full-text available
The past decade has seen researchers develop and apply novel technologies for biomolecular detection, at times approaching hard limits imposed by physics and chemistry. In nearly all sensors, the transport of target molecules to the sensor can play as critical a role as the chemical reaction itself in governing binding kinetics, and ultimately performance. Yet rarely does an analysis of the interplay between diffusion, convection and reaction motivate experimental design or interpretation. Here we develop a physically intuitive and practical understanding of analyte transport for researchers who develop and employ biosensors based on surface capture. We explore the qualitatively distinct behaviors that result, develop rules of thumb to quickly determine how a given system will behave, and derive order-of-magnitude estimates for fundamental quantities of interest, such as fluxes, collection rates and equilibration times. We pay particular attention to collection limits for micro- and nanoscale sensors, and highlight unexplained discrepancies between reported values and theoretical limits.
Article
The COVID-19 pandemic demonstrated the public health benefits of reliable and accessible point-of-care (POC) diagnostic tests for viral infections. Despite the rapid development of gold-standard reverse transcription polymerase chain reaction (RT-PCR) assays for SARS-CoV-2 only weeks into the pandemic, global demand created logistical challenges that delayed access to testing for months and helped fuel the spread of COVID-19. Additionally, the extreme sensitivity of RT-PCR had a costly downside as the tests could not differentiate between patients with active infection and those who were no longer infectious but still shedding viral genomes. To address these issues for the future, we propose a novel membrane-based sensor that only detects intact virions. The sensor combines affinity and size based detection on a membrane-based sensor and does not require external power to operate or read. Specifically, the presence of intact virions, but not viral debris, fouls the membrane and triggers a macroscopically visible hydraulic switch after injection of a 40 μL sample with a pipette. The device, which we call the μSiM-DX (microfluidic device featuring a silicon membrane for diagnostics), features a biotin-coated microslit membrane with pores ∼2-3× larger than the intact virus. Streptavidin-conjugated antibody recognizing viral surface proteins are incubated with the sample for ∼1 hour prior to injection into the device, and positive/negative results are obtained within ten seconds of sample injection. Proof-of-principle tests have been performed using preparations of vaccinia virus. After optimizing slit pore sizes and porous membrane area, the fouling-based sensor exhibits 100% specificity and 97% sensitivity for vaccinia virus (n = 62). Moreover, the dynamic range of the sensor extends at least from 105.9 virions per mL to 1010.4 virions per mL covering the range of mean viral loads in symptomatic COVID-19 patients (105.6-107 RNA copies per mL). Forthcoming work will test the ability of our sensor to perform similarly in biological fluids and with SARS-CoV-2, to fully test the potential of a membrane fouling-based sensor to serve as a PCR-free alternative for POC containment efforts in the spread of infectious disease.
Article
In this study, an artificial neural network has been developed to predict the boundary layer flow of a single-walled carbon nanotubes nanofluid towards three different nonlinear thin isothermal needles of paraboloid, cone and cylinder shapes with convective boundary conditions. Different effects of particle diameter and solid-fluid interface coating have been taken into account in the thermal conductivity model of nanofluid in which ethylene glycol has been used as the base fluid. Single and dual phase approach is used to establish the management model under the phenomenon of zero heat and mass flux. A data set has been developed for different scenarios of the fluid model by changing the relevant parameters with the Runge-Kutta based shooting technique. Two different artificial neural network models have been developed to predict Nusselt number and skin friction coefficient values. The values obtained from artificial neural network models have been compared with the numerical data, which are the target values. In addition, mean square error and R values have also been examined in order to analyze the prediction performance of artificial neural network models more comprehensively. The calculated R values for Nusselt number and skin friction coefficient were obtained as 0.9999. The results obtained showed that artificial neural network can predict Nusselt number and skin friction coefficient values with high accuracy.
Article
The current ongoing outbreak of Coronavirus Disease 2019 (COVID-19) has globally affected the lives of more than one hundred million people. RT-PCR based molecular test is recommended as the gold standard method for diagnosing current infections. However, transportation and processing of the clinical sample for detecting virus require an expert operator and long processing time. Testing device enables on-site virus detection could reduce the sample-to-answer time, which plays a central role in containing the pandemic. In this work, we proposed an intelligent face mask, where a flexible immunosensor based on high density conductive nanowire array, a miniaturized impedance circuit, and wireless communication units were embedded. The sub-100 nm size and the gap between the neighbored nanowires facilitate the locking of nanoscale virus particles by the nanowire arrays and greatly improve the detection efficiency. Such a point-of-care (POC) system was demonstrated for coronavirus ‘spike’ protein and whole virus aerosol detection in simulated human breath. Detection of viral concentration as low as 7 pfu/mL from the atomized sample of coronavirus aerosol mimic was achieved in only 5 mins. The POC systems can be readily applied for preliminary screening of coronavirus infections on-site and may help to understand the COVID-19 progression while a patient is under prescribed therapy.
Article
Bacterial pili are proteinaceous motorized nanomachines that play various functional roles including surface adherence, bacterial motion, and virulence. The surface-contact sensor type IVc (or Tad) pilus is widely distributed in both Gram-positive and Gram-negative bacteria. In Caulobacter crescentus, this nanofilament, though crucial for surface colonization, has never been thoroughly investigated at the molecular level. As Caulobacter assembles several surface appendages at specific stages of the cell cycle, we designed a fluorescence-based screen to selectively study single piliated cells and combined it with atomic force microscopy and genetic manipulation to quantify the nanoscale adhesion of the type IVc pilus to hydrophobic substrates. We demonstrate that this nanofilament exhibits high stickiness compared to the canonical type IVa/b pili, resulting mostly from multiple hydrophobic interactions along the fiber length, and that it features nanospring mechanical properties. Our findings may be helpful to better understand the structure-function relationship of bacterial pilus nanomachines.
Article
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and pathogenic coronavirus that emerged in late 2019 and has caused a pandemic of acute respiratory disease, named ‘coronavirus disease 2019’ (COVID-19), which threatens human health and public safety. In this Review, we describe the basic virology of SARS-CoV-2, including genomic characteristics and receptor use, highlighting its key difference from previously known coronaviruses. We summarize current knowledge of clinical, epidemiological and pathological features of COVID-19, as well as recent progress in animal models and antiviral treatment approaches for SARS-CoV-2 infection. We also discuss the potential wildlife hosts and zoonotic origin of this emerging virus in detail. In this Review, Shi and colleagues summarize the exceptional amount of research that has characterized acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease 2019 (COVID-19) since this virus has swept around the globe. They discuss what we know so far about the emergence and virology of SARS-CoV-2 and the pathogenesis and treatment of COVID-19.
Article
We have developed a new three-dimensional (3D) surface for use in biosensors that is based on modified novel thorns-like polyelectrolytes (3D-PETx), which comprises of poly-l-lysine (PLL) appended with multitude oligo (ethylene glycol) (OEG) and biotin moieties. It tethered to the sensor surface by PLL, while the OEG-biotin chains are forced to stretch away from the surface for target detections. Due to its 3D structure, the number of the OEG-biotin per surface unit is markedly increased compared to conventional 2D polyelectrolytes (2D-PET) coating. Their antifouling property and sensing performance for human IgG and PSA were compared with the 2D-PET by BioLayer Interferometry (Blitz), Surface Plasmon Resonance (SPR), microfluidic devices and Enzyme-Linked ImmunoSorbent Assay (ELISA). Experimental results show that 3D-PETx presents higher sensitivity for biomarker detection both in buffer and in serum and provides an almost non-fouling surface even in undiluted serum. In addition, a sensitive PSA detection was achieved in undiluted serum with a LOD down to 0.6 ng/mL. The successful immunosensing in undiluted serum demonstrate the potential of the 3D-PETx coating for real clinical applications.
Article
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its associated Coronavirus disease 2019 (COVID-19) pandemic has demanded rapid upscaling of in-vitro diagnostic assays to enable mass screening and testing of high-risk groups, and simultaneous ascertainment of robust data on past SARS-CoV-2 exposure at an individual and population level. To meet the exponential demand in testing, there has been an accelerated development of both molecular and serological assays across a plethora of platforms. In the present review, we discuss the current literature on these modalities including the nucleic acid amplification tests, direct viral antigen tests and the rapidly expanding laboratory based and point of care serological tests. This suite of complementary tests will inform crucial decisions by healthcare providers and policy makers and understanding their strengths and limitations will be critical to their judicious application for the development of algorithmic approaches to treatment and public health strategies.
Article
Today self-assembled monolayer (SAM) approach for surface functionalization especially in biomolecules immobilization and fabrication of novel supramolecular architecture is regarded as highly versatile and compelling. Most of the scientific articles published these days on biosensors use the concept of SAM to generate different surface functional groups for the immobilization of biomolecules such as antibodies, proteins, enzymes and so on. The simplicity in the formation process with no requirement of the costly instrument makes this approach prominent among the researchers working in the field of surface functionalization and biosensing devices. Herein, we have reviewed a wide range of literature on electronic devices such as chemical sensors, biosensors and organic film transistors that uses SAM concept for their purposes. In this review article, attention has been made to provide the information about the SAM functionalization procedure i.e. technique used, molarity of SAM solution and other physical/chemical conditions involved. Moreover, the fundamental concept of monolayer, types of monolayers on air/water interface, techniques used for SAM formation on solid substrate and SAM for patterning have been discussed.
Article
Inflammation is a pathophysiological response of innate immunity to infection or tissue damage. This response is among others triggered by factors released by damaged or dying cells, termed damage-associated molecular pattern (DAMP) molecules that act as danger signals. DAMPs interact with pattern recognition receptors (PRRs) to contribute to the induction of inflammation. However, how released peroxiredoxins (PRDXs) are able to activate PRRs, such as Toll-like receptors (TLRs), remains elusive. Here, we used force-distance curve-based atomic force microscopy to investigate the molecular mechanisms by which extracellular human PRDX5 can activate a proinflammatory response. Single-molecule experiments demonstrated that PRDX5 binds to purified TLR4 receptors, on macrophage-differentiated THP-1 cells, and on human TLR4-transfected CHO cells. These findings suggest that extracellular PRDX5 can specifically trigger a proinflammatory response. Moreover, our work also revealed that PRDX5 binding induces a cellular mechanoresponse. Collectively, this study provides insights into the role of extracellular PRDX5 in innate immunity.
Article
In this work, gigahertz solidly mounted resonators (SMRs) (2.5 GHz) were designed and fabricated to construct a novel particle-resonator system to achieve the biomolecular stiffness sensing in real time. The positive frequency shift of the system was used to estimate the stiffness of biomolecules connecting between the SMR and attached particles. The working principle was revealed by the mathematical analysis of the general block-spring model of the system. Further interpretations about the mechanism of such elastic interaction from the perspective of acoustic resonant modes of SMRs were given by finite element method. Biotin-streptavidin, antibody and antigen binding system were used as model molecular linkers to study the frequency shift varied with different particle diameters and particle densities. Different linker stiffness was realized by adjusting the concentrations of antigens connected with particles which form specific binding with antibodies immobilized on the SMR. The results fairly agree with the simulation results demonstrating the proposed particle-resonator system as an effective method to realize the real-time biomolecular stiffness detection.
Article
This paper reports a surface functionalization strategy for protein detections based on biotin-derivatized poly(L-lysine)-grafted oligo-ethylene glycol (PLL-g-OEGx-Biotin) copolymers. Such strategy can be used to attach the biomolecule receptors in a reproducible way simply by incubation of the transducer element in a solution containing such copolymers which largely facilitated the sensor functionalization at an industrial scale. As the synthesized copolymers are cationic in physiology pH, surface biotinylation can be easily achieved via electrostatic adsorption on negatively charged sensor surface. Biotinylated receptors can be subsequently attached through well-defined biotin-streptavidin interaction. In this work, the bioactive sensor surfaces were applied for mouse IgG and prostate specific antigen (PSA) detections using quartz crystal microbalance (QCM), optical sensor (BioLayer Interferometry) and conventional ELISA test (colorimetry). A limit of detection (LOD) of 0.5 nM was achieved for PSA detections both in HEPES buffer and serum dilutions in ELISA tests. The synthesized PLL-g-OEGx-Biotin copolymers with different OEG chain length were also compared for their biosensing performance. Moreover, the surface regeneration was achieved by pH stimulation to remove the copolymers and the bonded analytes, while maintaining the sensor reusability as well. Thus, the developed PLL-g-OEGx-Biotin surface assembling strategy is believed to be a versatile surface coating method for protein detections with multi-sensor compatibility.
Article
The number of bonds formed between one single bionanoparticle and many surface receptors is an important object to be studied but seldom quantitatively investigated. A new evaluation of the correlation between binding kinetics and number of bonds is presented by varying ligand density and receptor density. An experimental system was developed using measurements with surface plasmon resonance spectroscopy. A corresponding multi-site adsorption model elucidated the correlation. The results show that with the increase of the receptor density, the adsorption rate first decreased when the number of bonds was below a maximum value and then increased when the number of bonds stayed at this maximum value. The investigation on ligand density variation suggests that the coating density on top of the bionanoparticle surface may have a particular value below which more ligand will accelerate the adsorption rate. The ratio of ligand amount bound by the receptors to the total ligand amount associated with a single bionanoparticle will remain finally constant even if one attaches more ligands to a bionanoparticle. We envision that the bionanoparticle desorption will not depend on density changes from either ligand or receptor when the number of bonds reaches a specific efficient value.
Article
AlN thin film bulk acoustic resonators (FBARs) with a resonant frequency of 575 MHz have been fabricated to function as an epithelial tumor marker mucin 1 (MUC1) biosensor. Streptavidin was assembled on the sensitive area of FBAR. After the recognition between aptamers–AuNP conjugates and MUC1, biotin, along with the conjugates, was captured by streptavidin onto the surface of FBARs. Therefore, the target MUC1 could be sensitively detected. This biosensor exhibited a good linear relationship between the frequency shifts and the concentrations of MUC1 ranging from 30 to 500 nM, which indicated the sensitivity is about 818.6 Hz nM−1. The frequency shift remained relatively stable when the concentration of MUC1 was greater than 500 nM since the binding between MUC1 and aptamers–AuNP conjugates reached saturation. The selectivity experiment demonstrated that this biosensor can precisely detect MUC1 with good specificity. The positive results suggest that FBAR is an attractive alternative to a new approach for the detection of MUC1.
Article
A new surface functionalization scheme for nano-Bio field effect transistors (FETs) using biocompatible polyelectrolyte thin films (PET) is developed. PET assemblies on Si nanowires (Si-NWs) are driven by electrostatic interactions between the positively charged polymer backbone and negatively charged Si/SiO2 surface. Such assemblies can be directly coated from PET aqueous solutions and result in a uniform nanoscale thin film, which is more stable compared to the conventional amine silanization. Short oligo-ethylene glycol chains are grafted on the PETs to prevent nonspecific protein binding. Moreover, the reactive groups of the polymer chains can be further functionalized to other chemical groups in specific stoichiometry for biomolecules detection. Therefore, it opens a new strategy to precisely control the functional group densities on various biosensor surfaces at the molecular level. In addition, such assemblies of the polymers together with the bound analytes can be removed with the pH stimulation resulting in regeneration of a bare sensor surface without compromising the integrity and performance of the Si-NWs. Thus, it is believed that the developed PET coating and sensing systems on Si-NW FETs represent a versatile, promising approach for regenerative biosensors which can be applied to other biosensors and will benefit real device applications, enhancing sensor lifetime, reliability, and repeatability.
Article
The surprising properties of biomaterials are the results of billions of years of evolution. Generally, biomaterials are assembled under mild conditions with very limited supply of constituents available for living organism, and their amazing properties largely result from the sophisticated hierarchical structures. Following the biomimetic principles to prepare manmade materials has drawn great research interests in materials science and engineering. In this review, we summarize the recent progress in fabricating bioinspired materials with the emphasis on mimicking the structure from one to three dimensions. Selected examples are described with a focus on the relationship between the structural characters and the corresponding functions. For one-dimensional materials, spider fibers, polar bear hair, multichannel plant roots and so on have been involved. Natural structure color and color shifting surfaces, and the antifouling, antireflective coatings of biomaterials are chosen as the typical examples of the two-dimensional biomimicking. The outstanding protection performance, and the stimuli responsive and self-healing functions of biomaterials based on the sophisticated hierarchical bulk structures are the emphases of the three-dimensional mimicking. Finally, a summary and outlook are given.
Article
Affinity chromatography and membrane adsorption are highly promising methods for the downstream processing of cell culture-derived influenza virus. For the optimization of this separation process, it is desirable to quantify the kinetics of virus adsorption. For this reason, the adsorption kinetics of the influenza A virus (Puerto Rico/8/34 (H1N1)) on a surface with the immobilized ligand Euronymus europaeus lectin (EEL) was investigated. The adsorption kinetics was experimentally monitored in a microfluidic flow cell by surface plasmon resonance (SPR) spectroscopy. The boundary layer theory was applied to analyze the convective and diffusive mass transport of the virus particles in the SPR flow cell. A multi-site kinetic adsorption model was found to describe the experimentally recorded adsorption curves adequately. According to the proposed model, under the applied experimental conditions, the number of sites (galactose residuals) binding one single virus particle to the EEL surface is in the range of 300 to 460, which is in average about 4% of the total number of sites available on the virus surface. The avidity of individual virus particles to the EEL surface was estimated to be in the order of magnitude of 106 M−1s−1
Article
Metal centers in metalloproteins involve multiple metal-ligand bonds. The release of metal ions from metalloproteins can have significant biological consequences so understanding of the mechanisms by which metal ion dissociates has broad implications. By definition, the release of metal ions from metalloproteins involves the disruption of multiple metal-ligand bonds, and this process is often accompanied by unfolding of the protein. Detailed pathways for metal ion release from metalloproteins have been difficult to elucidate by classical ensemble techniques. Here we combine single molecule force spectroscopy and protein engineering techniques to investigate the mechanical dissociation mechanism of iron from the active site of the simplest iron-sulfur protein, rubredoxin, at the single molecule level. Our results reveal that the mechanical rupture of this simplest iron center is stochastic and follows multiple, complex pathways that include concurrent rupture of multiple ferric-thiolate bonds as well as sequential rupture of ferric-thiolate bonds that leads to the formation of intermediate species. Our results uncover the surprising complexity of the rupture process of the seemingly simple iron center in rubredoxin and provide the first unambiguous experimental evidence concerning the detailed mechanism of mechanical disruption of a metal center in its native protein environment in aqueous solution. This study opens up a new avenue to investigating the rupture mechanism of metal centers in metalloproteins with unprecedented resolution by using single molecule force spectroscopy techniques.
Article
Tailoring the surface of biometallic implants with protein-resistant polymer brushes represents an efficient approach to improve the biocompability and mechanical compliance with soft human tissues. A general approach utilizing electropolymerization to form initiating group (-Br) containing poly(3,4-ethylenedioxythiophen)s (poly(EDOT)s) is described. After the conducting polymer is deposited, neutral poly((oligo(ethylene glycol) methacrylate), poly(OEGMA), and zwitterionic poly([2-(methacryloyloxy)ethyl]dimethyl-(3-sulfopropyl)ammonium hydroxide), poly(SBMA), brushes are grafted by surface-initiated atom transfer radical polymerization. Quartz crystal microbalance (QCM) experiments confirm protein resistance of poly(OEGMA) and poly(SBMA)-grafted poly(EDOT)s. The protein binding properties of the surface are modulated by the density of polymer brushes, which is controlled by the feed content of initiator-containing monomer (EDOT-Br) in the monomer mixture solution for electropolymerization. Furthermore, these polymer-grafted poly(EDOT)s also prevent cells to adhere on the surface.
Article
The ability to control cell-surface interactions in order to achieve binding of specific cell types is a major challenge for microfluidic immunoaffinity cell capture systems. In the majority of existing systems, the functionalized capture surface is constructed of solid materials, where flow stagnation at the solid-liquid interface is detrimental to the convection of cells to the surface. We study the use of ultra-high porosity (99%) nanoporous micro-posts in microfluidic channels for enhancing interception efficiency of particles in flow. We show using both modelling and experiment that nanoporous posts improve particle interception compared to solid posts through two distinct mechanisms: the increase of direct interception, and the reduction of near-surface hydrodynamic resistance. We provide initial validation that the improvement of interception efficiency also results in an increase in capture efficiency when comparing nanoporous vertically aligned carbon nanotube (VACNT) post arrays with solid PDMS post arrays of the same geometry. Using both bacteria (∼1 μm) and cancer cell lines (∼15 μm) as model systems, we found capture efficiency increases by 6-fold and 4-fold respectively. The combined model and experimental platform presents a new generation of nanoporous microfluidic devices for cell isolation.
Article
Solid materials, such as silicon, glass, and polymers, dominate as structural elements in microsystems including microfluidics. Porous elements have been limited to membranes sandwiched between microchannel layers or polymer monoliths. This paper reports the use of micropatterned carbon-nanotube forests confined inside microfluidic channels for mechanically and/or chemically capturing particles ranging over three orders of magnitude in size. Nanoparticles below the internanotube spacing (80 nm) of the forest can penetrate inside the forest and interact with the large surface area created by individual nanotubes. For larger particles (>80 nm), the ultrahigh porosity of the nanotube elements reduces the fluid boundary layer and enhances particle-structure interactions on the outer surface of the patterned nanoporous elements. Specific biomolecular recognition is demonstrated using cells (≈10 μm), bacteria (≈1 μm), and viral-sized particles (≈40 nm) using both effects. This technology can provide unprecedented control of bioseparation processes to access bioparticles of interest, opening new pathways for both research and point-of-care diagnostics.
Article
Self-assembled monolayers (SAMs) have aroused much interest due to their potential applications in biosensors, biomolecular electronics and nanotechnology. This has been largely attributed to their inherent ordered arrangement and controllable properties. SAMs can be formed by chemisorption of organic molecules containing groups like thiols, disulphides, amines, acids or silanes, on desired surfaces and can be used to fabricate biomolecular electronic devices. We focus on recent applications of organosulphur compounds (thiols) based SAMs to biomolecular electronic devices in the last about 3 years.
Article
The use of self-assembled monolayers (SAMs) in various fields of research is rapidly growing. In particular, many biomedical fields apply SAMs as an interface-layer between a metal surface and a solution or vapour. This review summarises methods for the formation of SAMs upon the most commonly used materials and techniques used for monolayer characterisation. Emphasis will lie on uniform, mixed and functionalised monolayers applied for immobilisation of biological components including (oligo-)nucleotides, proteins, antibodies and receptors as well as polymers. The application of SAMs in today’s research, together with some applications will be discussed.