Unbound Molecules Research Articles

Novel ultrasensitive automated kinetic exclusion assay for measurement of plasma levels of soluble PD-L1, the predictive and prognostic biomarker in cancer patients treated with immune checkpoint inhibitors

Recently, the blood plasma or serum levels of soluble programmed death protein 1 (PD-L1), but not tissue PD-L1 expression level, have been proposed as an effective predictive and prognostic biomarker in patients treated with immune checkpoint inhibitors for different types of cancers. The quantification of soluble PD-L1 in blood will provide a quick evaluation of patients’ immune status; however, the available assays have limitations in their sensitivity, reproducibility, and accuracy for use in clinical settings. To overcome these problems, this study was dedicated to developing an ultrasensitive automated flow-based kinetic exclusion assay (KinExA) for the accurate and precise measurement of soluble PD-L1 in plasma. The assay was developed with the assistance of KinExA™ 3200 biosensor. In this assay, PD-L1 in its calibrator or plasma sample solution was pre-equilibrated with anti-PD-L1 monoclonal antibody. The equilibrated mixture solution was then passed rapidly over PD-L1 protein that has been coated onto polymethylmethacrylate beads consolidated as a microcolumn in the observation cell of the KinExA™ biosensor. The free anti- PD-L1 antibody was bound to the immobilized PD-L1, however, the unbound molecules were removed from the beads microcolumn by flushing the system with phosphate-buffered saline. Fluorescein-labeled secondary antibody was passed rapidly over the beads, and the fluorescence signals were monitored during the flow of the labeled antibody through the beads. The calibration curve was generated by plotting the binding percentages as a function of PD-L1 concentrations in its sample solution. The working range of the assay with very a good correlation coefficient on a 4-parameter equation (r = 0.9992) was 0.5 − 100 pg mL─1. The assay limit of detection and quantitation were 0.15 and 0.5 pg mL─1, respectively. The recovery values of plasma-spiked PD-L1 were in the range of 96.4–104.3 % (±3.7–6.2 %). The precision of the assay was satisfactory; the values of the coefficient of variations did not exceed 6.2 % for both intra- and inter-day precision. The automated analysis by the proposed KinExA facilitates the processing of many specimens in clinical settings. The overall performance of the proposed KinExA is superior to the available assays for plasma levels of soluble PD-L1. The proposed assay is anticipated to have a great value in the measurement of PD-L1 where a more confident result is needed.

Off-the-shelf proximity biotinylation using ProtA-TurboID.

Proximity biotinylation is a commonly used method to identify the in vivo proximal proteome for proteins of interest. This technology typically relies on fusing a bait protein to a biotin ligase using overexpression or clustered regularly interspaced short palindromic repeats (CRISPR)-based tagging, thus prohibiting the use of such assays in cell types that are difficult to transfect or transduce. We recently developed an 'off-the-shelf' proximity biotinylation method that makes use of a recombinant enzyme consisting of the biotin ligase TurboID fused to the antibody-recognizing moiety Protein A. In this method, a bait-specific antibody and the ProteinA-Turbo enzyme are consecutively added to permeabilized fixed or unfixed cells. Following incubation, during which ProteinA-Turbo antibody-antigen complexes are formed, unbound molecules are washed away, after which bait-proximal biotinylation is triggered by the addition of exogenous biotin. Finally, biotinylated proteins are enriched from crude lysates using streptavidin beads followed by mass spectrometry-based protein identification. In principle, any scientist can perform this protocol within 3 days, although generating the proteomics data requires access to a high-end liquid chromatography-mass spectrometry setup. Data analysis and data visualization are relatively straightforward and can be performed using any type of software that converts raw mass spectrometry spectra files into identified and quantified proteins. The protocol has been optimized for nuclear targets but may also be adapted to other subcellular regions of interest.

P800SO3-PEG: a renal clearable bone-targeted fluorophore for theranostic imaging

BackgroundDue to the deep tissue penetration and reduced scattering, NIR-II fluorescence imaging is advantageous over conventional visible and NIR-I fluorescence imaging for the detection of bone growth, metabolism, metastasis, and other bone-related diseases.MethodsBone-targeted heptamethine cyanine fluorophores were synthesized by substituting the meso-carbon with a sulfur atom, resulting in a bathochromic shift and increased fluorescence intensity. The physicochemical, optical, and thermal stability of newly synthesized bone-targeted NIR fluorophores was performed in aqueous solvents. Calcium binding, bone-specific targeting, biodistribution, pharmacokinetics, and 2D and 3D NIR imaging were performed in animal models.ResultsThe newly synthesized S-substituted heptamethine fluorophores demonstrated a high affinity for hydroxyapatite and calcium phosphate, which improved bone-specific targeting with signal-background ratios > 3.5. Particularly, P800SO3-PEG showed minimum nonspecific uptake, and most unbound molecules were excreted into the urinary bladder. Histological analyses demonstrated that P800SO3-PEG remained stable in the bone for over two weeks and was incorporated into bone matrices. Interestingly, the flexible thiol ethylene glycol linker on P800SO3-PEG induced a promising photothermal effect upon NIR laser irradiation, demonstrating potential theranostic imaging.ConclusionsP800SO3-PEG shows a high affinity for bone tissues, deeper tissue imaging capabilities, minimum nonspecific uptake in the major organs, and photothermal effect upon laser irradiation, making it optimal for bone-targeted theranostic imaging.

Rapid and Sensitive Identification and Discrimination of Bound/Unbound Ligands on Colloidal Nanocrystals via Direct Analysis in Real-Time Mass Spectrometry.

Direct analysis in real-time mass spectrometry (DART-MS) has been applied to the characterization of colloidal nanocrystal surface ligands. The nanocrystals (NCs) in colloidal suspension were purified and deposited onto a solid substrate, and the solvent was allowed to evaporate. Ligand desorption was thermally stimulated using a temperature ramp from 30 °C up to 530 °C, and the desorbed ligands were introduced into a DART-MS instrument where metastable He atoms provide energy for ionization and fragmentation through the reaction with ambient vapors including O2 and H2O. The method allows the identification of ligand species with various functional groups, even in complex, mixed-ligand samples. Bound and unbound molecules can be distinguished based on the desorption temperature. In ideal cases, the desorption profile for a given molecule can be analyzed according to methods adapted from thermal desorption spectroscopy (TDS) to estimate desorption activation energy for NC-bound ligands. Results are presented and discussed for different nanocrystal and ligand types. The method is a promising complement to the range of existing tools for NC ligand analysis.

Thermodynamics of wetting, prewetting and surface phase transitions with surface binding

In living cells, protein-rich condensates can wet the cell membrane and surfaces of membrane-bound organelles. Interestingly, many phase-separating proteins also bind to membranes leading to a molecular layer of bound molecules. Here we investigate how binding to membranes affects wetting, prewetting and surface phase transitions. We derive a thermodynamic theory for a three-dimensional bulk in the presence of a two-dimensional, flat membrane. At phase coexistence, we find that membrane binding facilitates complete wetting and thus lowers the wetting angle. Moreover, below the saturation concentration, binding facilitates the formation of a thick layer at the membrane and thereby shifts the prewetting phase transition far below the saturation concentration. The distinction between bound and unbound molecules near the surface leads to a large variety of surface states and complex surface phase diagrams with a rich topology of phase transitions. Our work suggests that surface phase transitions combined with molecular binding represent a versatile mechanism to control the formation of protein-rich domains at intra-cellular surfaces.

Radiolabeling Strategies of Nanobodies for Imaging Applications.

Nanobodies are small recombinant antigen-binding fragments derived from camelid heavy-chain only antibodies. Due to their compact structure, pharmacokinetics of nanobodies are favorable compared to full-size antibodies, allowing rapid accumulation to their targets after intravenous administration, while unbound molecules are quickly cleared from the circulation. In consequence, high signal-to-background ratios can be achieved, rendering radiolabeled nanobodies high-potential candidates for imaging applications in oncology, immunology and specific diseases, for instance in the cardiovascular system. In this review, a comprehensive overview of central aspects of nanobody functionalization and radiolabeling strategies is provided.

Rapid Screening for COVID-19 Using Field Effect Transistor Biosensors

In this study, we have developed a platform for the rapid screening of the SARS-CoV-2 virus in saliva. Electrical double layer (EDL) gated field-effect transistors (FET) biosensor is applied in this research to detect the electrical signals in the sample. Nucleocapsid protein is used as the target protein since it is expressed abundantly during infection. The sensor illustrates a lower detection limit compared to recent methods, which shows the potential of our sensor to make a diagnosis in the early stages of the disease. Besides, additional pre-pretreatment is not needed. The sensor is a robust diagnostic tool for rapid screening of COVID-19. Introduction The coronavirus pandemic, also known as COVID-19, is caused by SARS-CoV-2 virus. COVID-19 causes severe acute respiratory syndrome and poses a significant threat to health internationally. The World Health Organization (WHO) declared this as a global pandemic. Symptom-based screening cannot be an effective strategy to identify individuals. The symptoms of mild patients are similar to influenza, which may easily lead to false negative confirmation of disease. Real-time reverse transcriptase-polymerase chain reaction (RT-PCR) is the most well-known method employed for the clinical diagnosis of COVID-19. But, this method is costly and needs a long time to get the result. Hence, a rapid and low-cost diagnosis method is urgently required. Experimental Sensor array fabrication The disposable sensor array chip consists of two gold electrodes. One electrode is connected to the gate voltage supply, defined as the reference electrode. The other one is connected to the gate metal, and considered as the sensing electrode. Functionalization of sensor surface Antibody against SARS-CoV-2 nucleocapsid protein is used as receptor in this study, which is immobilized on the gold gate electrode. Traut’s Reagent (Thermo Scientific, (26101)) introduces sulfhydryl (-SH) groups to the primary amines of antibody. The modified antibody can then covalently bind to Au gate electrode by Au-S Bond. The antibody(1.5mg/mL) and Traut’s reagent (14 mM) are mixed and incubated at room temperature for 1 hour. The mixture is then dropped on the sensor surface and incubated in 4 °C refrigerator for 12 hours. Electrical measurement The sensor array chip is inserted into a portable prototype device with FET LND150. 2V DC bias as the drain-source voltage and a short duration gate pulse are steadily provided. The difference between the two current drains is defined as current gain, which is used as the index in data analysis. Fluorescence experiment After the electrical measurement, the secondary antibody, anti-mouse IgG (DyLight® 594), is added to the sensor to conjugate with the primary antibody. The sensor array chip is incubated for 1 hour at room temperature, and the unbound molecule is washed away by 1X PBS. Fluorescence microscope, (LEICA DM2500 LED) is used to capture the fluorescence image with 100 ms exposure time and quantitative analysis is performed using imageJ software. Result and conclusion When infected with SARS-CoV-2, the body produces antibodies that bind specific to nucleocapsid proteins and other surface antigens to help eliminate the virus. SARS-CoV-2 virus nucleocapsid protein is abundantly expressed during infection and is one of the highly immunogenic proteins. Hence, nucleocapsid protein is used as the target protein in this study. We immobilized antibody for nucleocapsid protein on the sensor. Electrical signal changed as the concentration of nucleocapsid protein increased from 0 to 400 ng/mL. The limit of detection for N protein was established at 0.4ng/mL. Tests that can distinguish between IgM and IgG can provide information about the stage of infection, indicating how long the person has been infected with SARS-CoV-2. In this study, we developed a platform that can help to confirm the infection in patients quickly in saliva. N-protein testing can potentially help us track the spread of the disease and accurately detect the infected individuals so as to control further spreading of the disease. Figure 1

Development of Diffusion Contrast Photo-Activated Localization Microscopy to Detect Sparse Protein Interactions at High Background

Many cellular signaling pathways contain protein binding partners that are expressed at extremely different concentrations. Interactions between these molecules can be difficult to observe using super-resolution microscopy techniques like Photo-Activated Localization Microscopy (PALM) since the overwhelming majority of localizations are from non-interacting molecules. Here, we develop and characterize Diffusion Contrast PALM (dcPALM) to overcome this barrier. By taking advantage of targeted photo-activation and the difference in diffusion coefficients between bound and unbound molecules, dcPALM reduces localizations from non-interacting molecules by 10-fold in yeast and even more in mammalian cells.

Distinct Interaction of Lytic Polysaccharide Monooxygenase with Cellulose Revealed by Computational and Biochemical Studies.

A distinct interaction pattern of lytic polysaccharide monooxygenases (LPMOs) with their insoluble substrate, cellulose, was revealed through the combination of computational and biochemical approaches. The results indicated that the enzymes can stably bind on the flat hydrophobic surface of cellulose via the interactions of the key residues located in the axis across the conserved distal tyrosine residue and copper ion with two adjacent cellulose chains. Further studies on the correlation of substrate binding and H2O2 accumulation suggested that LPMOs involved in the productive binding on the insoluble polysaccharides not only fail to accumulate H2O2 but also consume the H2O2 produced by the unbound molecules under the lab condition. This was further substantiated by quantum-mechanical calculations. These findings broadened our knowledge of the interaction between enzymes and insoluble substrates and deepened our understanding of the role that H2O2 plays in LPMO activity.

Base-pair ambiguity and the kinetics of RNA folding

BackgroundA folding RNA molecule encounters multiple opportunities to form non-native yet energetically favorable pairings of nucleotide sequences. Given this forbidding free-energy landscape, mechanisms have evolved that contribute to a directed and efficient folding process, including catalytic proteins and error-detecting chaperones. Among structural RNA molecules we make a distinction between “bound” molecules, which are active as part of ribonucleoprotein (RNP) complexes, and “unbound,” with physiological functions performed without necessarily being bound in RNP complexes. We hypothesized that unbound molecules, lacking the partnering structure of a protein, would be more vulnerable than bound molecules to kinetic traps that compete with native stem structures. We defined an “ambiguity index”—a normalized function of the primary and secondary structure of an individual molecule that measures the number of kinetic traps available to nucleotide sequences that are paired in the native structure, presuming that unbound molecules would have lower indexes. The ambiguity index depends on the purported secondary structure, and was computed under both the comparative (“gold standard”) and an equilibrium-based prediction which approximates the minimum free energy (MFE) structure. Arguing that kinetically accessible metastable structures might be more biologically relevant than thermodynamic equilibrium structures, we also hypothesized that MFE-derived ambiguities would be less effective in separating bound and unbound molecules.ResultsWe have introduced an intuitive and easily computed function of primary and secondary structures that measures the availability of complementary sequences that could disrupt the formation of native stems on a given molecule—an ambiguity index. Using comparative secondary structures, the ambiguity index is systematically smaller among unbound than bound molecules, as expected. Furthermore, the effect is lost when the presumably more accurate comparative structure is replaced instead by the MFE structure.ConclusionsA statistical analysis of the relationship between the primary and secondary structures of non-coding RNA molecules suggests that stem-disrupting kinetic traps are substantially less prevalent in molecules not participating in RNP complexes. In that this distinction is apparent under the comparative but not the MFE secondary structure, the results highlight a possible deficiency in structure predictions when based upon assumptions of thermodynamic equilibrium.

Rapid Discovery and Structure-Property Relationships of Metal-Ion Fluorescent Sensors via Macroarray Synthesis

A macroarray immobilisation of fluorophores on filter papers for sensing metal ions by in-situ reductive amination and carbodiimide coupling is reported herein. Chemometric approaches resulted in a rapid discovery of sensors that can synergistically discriminate up to 12 metal ions with great prediction accuracies. Covalently bound on paper, sensoring scaffolds that were synthesised from the macroarray format can readily be adopted as practical paper-based sensors with great reusability and sensitivity, achieving the limit of detection at low nanomolar level with some repeating spotting. Lastly, the discovered scaffolds were also confirmed to be functional as unbound molecules, thus paving the way for more diverse applications.

On how the immune system preferentially interacts with antigen-specific molecules bound to antigen over unbound molecules, with emphasis on B cell receptor signalling.

Antigen-specific molecules of the immune system, namely antibodies, the membrane immunoglobulins (mIgs) of B cells and T cell receptors (TcRs), can all signal their interaction with antigen. There are different mechanisms by which this signalling could occur. These mechanisms can be divided into two general categories: allosteric and non-allosteric. In allosteric mechanisms, the monovalent binding of the antigen to the receptor triggers a conformational change at the binding site that is propagated to an invariant part of the receptor, a change recognized by a sensing unit. We argue allosteric mechanisms are implausible. Non-allosteric mechanisms depend on steric effects due to the antigen's size and/or multivalency. We consider two non-allosteric mechanisms by which the mIg of B cells has been envisaged to signal its interaction with antigen: the popular cross-linking model and the dissociation activation model. We argue, on the basis of both experimental observations and physiological considerations, that the dissociation activation model, developed by Reth and his colleagues, is uniquely plausible.

Microfluidic Device for Screening for Target Cell-Specific Binding Molecules by Using Adherent Cells.

This paper proposes a microfluidic device for screening molecules such as aptamers, antibodies, proteins, etc. for target cell-specific binding molecules. The discovery of cancer cell-specific binding molecules was the goal of this study. Its functions include filtering non-target cell-binding molecules, trapping molecules on the surface of target cells, washing away unbound molecules, and collecting target cell-specific binding molecules from target cells. These functions were effectively implemented by using our previously developed micro pillar arrays for cell homogeneous dispersion and pneumatic microvalves for tall microchannels. The device was also equipped with serially connected filter chambers in which non-target cells were cultured to reduce the molecules binding to non-target cells as much as possible. We evaluated the performance of the device using cancer cell lines (N87 cells as target cells and HeLa cells as non-target cells) and two fluorescent dye-labeled antibodies: Anti-human epidermal growth factor receptor 2 (anti-HER2) antibody that binds to target cells and anti-integrin antibody that binds to non-target cells. The results showed that the device could reduce anti-integrin antibodies to the detection limit of fluorescent measurement and collect anti-HER2 antibodies from the target cells.

An Aptamer against the Matrix Binding Domain on the Hepatitis B Virus Capsid Impairs Virion Formation.

The hepatitis B virus (HBV) particle is an icosahedral nucleocapsid surrounded by a lipid envelope containing viral surface proteins. A small domain (matrix domain [MD]) in the large surface protein L and a narrow region (matrix binding domain [MBD]) including isoleucine 126 on the capsid surface have been mapped, in which point mutations such as core I126A specifically blocked nucleocapsid envelopment. It is possible that the two domains interact with each other during virion morphogenesis. By the systematic evolution of ligands by exponential enrichment (SELEX) method, we evolved DNA aptamers from an oligonucleotide library binding to purified recombinant capsids but not binding to the corresponding I126A mutant capsids. Aptamers bound to capsids were separated from unbound molecules by filtration. After 13 rounds of selections and amplifications, 16 different aptamers were found among 73 clones. The four most frequent aptamers represented more than 50% of the clones. The main aptamer, AO-01 (13 clones, 18%), showed the lowest dissociation constant (Kd) of 180 ± 82 nM for capsid binding among the four molecules. Its Kd for I126A capsids was 1,306 ± 503 nM. Cotransfection of Huh7 cells with AO-01 and an HBV genomic construct resulted in 47% inhibition of virion production at 3 days posttransfection, but there was no inhibition by cotransfection of an aptamer with a random sequence. The half-life of AO-01 in cells was 2 h, which might explain the incomplete inhibition. The results support the importance of the MBD for nucleocapsid envelopment. Inhibiting the MD-MBD interaction with a low-molecular-weight substance might represent a new approach for an antiviral therapy. Approximately 240 million people are persistently infected with HBV. To date, antiviral therapies depend on a single target, the viral reverse transcriptase. Future additional targets could be viral protein-protein interactions. We selected a 55-base-long single-stranded DNA molecule (aptamer) which binds with relatively high affinity to a region on the HBV capsid interacting with viral envelope proteins during budding. This aptamer inhibits virion formation in cell culture. The results substantiate the current model for HBV morphogenesis and show that the capsid envelope interaction is a potential antiviral target.

On the energy components governing molecular recognition in the framework of continuum approaches.

Molecular recognition is a process that brings together several biological macromolecules to form a complex and one of the most important characteristics of the process is the binding free energy. Various approaches exist to model the binding free energy, provided the knowledge of the 3D structures of bound and unbound molecules. Among them, continuum approaches are quite appealing due to their computational efficiency while at the same time providing predictions with reasonable accuracy. Here we review recent developments in the field emphasizing on the importance of adopting adequate description of physical processes taking place upon the binding. In particular, we focus on the efforts aiming at capturing some of the atomistic details of the binding phenomena into the continuum framework. When possible, the energy components are reviewed independently of each other. However, it is pointed out that rigorous approaches should consider all energy contributions on the same footage. The two major schemes for utilizing the individual energy components to predict binding affinity are outlined as well.

Concentration-Dependent Thermophoretic Accumulation for the Detection of DNA Using DNA-Functionalized Nanoparticles

Thermophoresis is a phenomenon about the migration of particles along a temperature gradient and is sensitive to the properties of particles and the surrounding medium. While a few studies have investigated its mechanisms and effects on particle motion in recent years, the applications of thermophoresis in biosensing has not been well explored. In this study, we demonstrate a thermophoresis-based method for detecting DNA. We use DNA-functionalized gold nanoparticles and fluorescent DNA probes to capture target DNA in free solution, and we demonstrate that the hybridization between the specially designed capture probes and the target DNA significantly changes the thermophoretic properties of the fluorescent probes. As a result, the target DNA can be specifically detected in serum-containing buffers based on the spatial distribution of the fluorescent probes in a laser-induced temperature gradient. The optical setup consists of only a laser and an epifluorescence microscope, and the detection does not rely on any micro- or nanofabricated devices. In addition, because the detection is based on the thermophoretic motion of molecules in free solution, no capture probes need to be immobilized on a fixed surface before detection, and no channels or pumps are needed for washing away unbound molecules. The thermophoresis-based biosensing method is found to be simple and effective for detecting DNA.

The Effect of Age on the Glycosylation of Human Alpha-2-Macroglobulin

Introduction: Alpha-2-macroglobulin (a2m) is a plasma glycoprotein capable of inhibiting all classes of serine proteases. Within the coagulation and fibrinolytic systems, a2m inhibits several critical factors, including thrombin, plasmin, and activated protein C. Previous studies have shown that coagulation factor concentrations are highly variable with age. Notably, a2m levels are approximately twice as high in newborns compared to adults. Elevated levels of a2m in newborns may, in part, contribute to a resistance towards thrombotic events observed in this population. Protein glycosylation is known to affect protein activity as well as pharmacodynamics. The glycosylation profile of adult a2m has previously been analyzed and shown to contain 8 potential sites of N-linked glycosylation. Information regarding glycosylation of a2m in other age groups has yet to be elucidated. Therefore, the purpose of this study is to examine the differences in the glycosylation profiles between newborn and adult a2m.Methods: Normal adult pooled platelet-poor plasma was obtained commercially. Newborn platelet-poor plasma was isolated by standard methods from umbilical cord blood obtained immediately after delivery of healthy full-term infants. Pooled newborn plasma was constructed from 30 different donors. To evaluate the degree of N-linked glycosylation, plasma samples were enzymatically deglycosylated by peptide N-glycosidase F (PNGaseF). Samples were subjected to SDS polyacrylamide (5%) gel electrophoresis (SDS PAGE) and western blotting to detect a2m in plasma. To evaluate a2m sialic acid content, plasma samples were incubated with Neuraminidase from Clostridium perfringens. Following incubation, samples were subjected to native polyacrylamide (4%) gel electrophoresis and western blotting. To detect the presence of non-sialylated terminal galactose residues, plasma samples were incubated with immobilized Ricinus communis lectin, and lectin-bound molecules were separated from unbound molecules by centrifugation. Bound and unbound fractions were subjected to SDS-PAGE and western blotting as described above to detect a2m.Results: Deglycosylation of both newborn and adult a2m with PNGaseF resulted in a change in migration and apparent molecular weight on SDS-PAGE. There was no significant difference (p=0.28, n=3) between the change in apparent molecular weight for newborn a2m (16.1 ± 0.42 kDa) versus adult a2m (14.5 ± 0.99 kDa). On native polyacrylamide gel electrophoresis, newborn a2m exhibited slightly increased migration compared to adult a2m. This difference in migration was abolished following treatment with neuraminidase, indicating the variation in migration was due to differing sialic acid content. Additionally, a lower proportion of newborn a2m was bound to Ricinus communis compared to adult a2m. This indicates newborn a2m has fewer non-sialylated galactose residues available for binding to this lectin.Conclusions: To our knowledge, this is the first study investigating potential glycan heterogeneity between newborn and adult a2m molecules. The results from PNGaseF analyses indicate that there is no macroheterogeneity in total N-glycan content apparent between newborn and adult a2m. However, the observed increase in sialic acid content of newborn a2m compared to adult a2m may be responsible for age-related differences in pharmacodynamic and pharmacokinetic properties of this important protease inhibitor. DisclosuresNo relevant conflicts of interest to declare.

Real-time immuno-polymerase chain reaction in a 384-well format: Detection of vascular endothelial growth factor and epidermal growth factor-like domain 7

Immuno-polymerase chain reaction (immuno-PCR) combines the specificity of antibodies with the amplification power of PCR to detect low levels of proteins. Here, we describe the development of a 384-well immuno-PCR method that uses streptavidin coated on a PCR plate to capture complexes of biotinylated capture antibody, antigen, and DNA-labeled detection antibody. Unbound molecules are removed by a wash step using a standard plate washer. Antibody–DNA molecules in bound complexes are then detected directly on the plate using real-time PCR. Circulating human vascular endothelial growth factor concentrations measured by this method correlated with measurements obtained from enzyme-linked immunosorbent assay (ELISA). Using this method, we developed an assay for human epidermal growth factor-like domain 7 (EGFL7), an extracellular matrix-bound angiogenic factor. EGFL7 is expressed at a higher level in certain cancers, although endogenous EGFL7 concentrations have not been reported. Our 384-well EGFL7 immuno-PCR assay can detect 0.51pM EGFL7 in plasma, approximately 16-fold more sensitive than the ELISA, utilizing the same antibodies. This assay detected EGFL7 in lysates of non-small-cell lung cancer and hepatocellular carcinoma cell lines and also hepatocellular carcinoma, breast cancer, and ovarian cancer tissues. This 384-well immuno-PCR method can be used to develop high-throughput biomarker assays.

Ir-spectrometric investigation on cluster composition of two-component solid films of nitrogen-ethanol

Studies that were carried out previously investigating the properties of the cry condensed films of weak two-component solutions of ethanol in nitrogen found that the state of the film is not stable. A slight increase in temperature of solid nitrogen cryomatrix leads to changes in the vibrational spectrum of ethanol. This article is a continuation of this research and is aimed at studying the cluster composition of thin films of ethanol cry vacuum condensates in weak solutions with nitrogen. Measurements were carried out in a temperature range from 12 to 40 K, the pressure in the vacuum chamber was less than 5 × 10-8Torr. The concentration of ethanol in nitrogen was varied in the range from 0.5% to 3%. Based on the analysis of the vibrational spectra, it is assumed that the two-component nitrogen-ethanol film contains clusters of various compositions, from dimers to polyaggregates. An increase in cryomatrixtemperature leads to transformations in these polyaggregates with formation of more stable forms, as demonstrated by changes in the fine structure of the considered bands. The presence in the spectra of the absorption bands, which frequencies correspond to the existence of ethanol dimers and monomers in nitrogen matrix, can be explained as follows. Part of the ethanol molecules forming polyaggregates may not be combined via hydrogen bonds with neighboring molecules, forming a broken chain. Thus, they form a set of quasi-free molecules with corresponding absorption bands of these states. It is assumed that the quasi-free unbound molecules are preferably arranged in the surface area of the clusters.

A microfluidic linear node array for the study of protein-ligand interactions.

We have developed a microfluidic device for the continuous separation of small molecules from a protein mixture and demonstrated its practical use in the study of protein-ligand binding, a crucial aspect in drug discovery. Our results demonstrated dose-dependent binding between bovine serum albumin (BSA) and its small-molecule site marker, Eosin Y (EY), and found that the binding reached a plateau when the BSA : EY ratio was above 1, which agreed with the eosin binding capacity of BSA reported in literature. By streamline control using a combination of two fundamental building blocks (R and L nodes) with a microdevice operated at a high flow rate (up to 1300 μL h(-1)), a solution barrier was created to "filter" off protein/protein-ligand complexes such that the small unbound molecules were isolated and quantified easily. The percentage decrease of small molecules with increasing protein concentration indicated the presence of binding events. Several fluorophores with different molecular weights were used to test the performance of the microfluidic "filter", which was tunable by 1) the total flow rate, and/or 2) the flow distribution ratio between the two device inlets; both were easily controllable by changing the syringe pump settings. Since the microdevice was operated at a relatively high flow rate, aliquots were easily recovered from the device outlets to facilitate off-chip detection. This microfluidic design is a novel and promising tool for preliminary drug screening.