Multiplexed Analysis of Protein–Ligand Interactions by Fluorescence Anisotropy in a Microfluidic Platform

Modulating the Kinetics of a Fluorescence Anisotropy Immunoassay Using Tracer Point Mutations to Measure Human C-Peptide Secretion On-Chip

Fluorescence anisotropy immunoassays (FAIAs) are widely used to quantify the concentration of target proteins based on competitive binding to a monoclonal antibody with a tracer. We recently designed an FAIA to measure mouse C-peptide secretion from living islets in a continuous-flow microfluidic device (InsC-chip). To develop a similar assay for human C-peptide, we selected two monoclonal antibodies (Ab1 and Ab2) that initially showed a low dynamic range and slow kinetics. One option to measure this assay on-chip was to extend the length of the mixing channels. However, this strategy would increase dispersion and ultimately lower the temporal resolution of secreted C-peptide. To shorten the time-to-reach equilibrium for Ab1, we reengineered the tracer based on a comparison between the human and mouse C-peptide sequences, resulting in >30-fold shorter time-to-reach equilibrium. To increase the relatively small dynamic range for Ab2, we used partial epitope mapping and targeted point mutations to increase the dynamic range by 45%. Finally, we validated both FAIAs by measuring depolarization-induced secretion from individual human stem cell-derived islets in our InsC-chip. These data demonstrate a strategy to optimize FAIA kinetics to be measured in continuous-flow microfluidic devices.

Utilizing solid-state nanopore sensing for high-efficiency and precise targeted localization in antiviral drug development

The efficient identification and validation of drug targets are paramount in drug discovery and development. Excessive costs, intricate procedures, and laborious sample handling frequently encumber contemporary methodologies. In this study, we introduce an innovative approach for the expeditious screening of drug targets utilizing solid-state nanopores. These nanopores provide a label-free, ultra-sensitive, and high-resolution platform for the real-time detection of biomolecular interactions. By observing the changes in relative ion currents over time after mixing different peptides with small molecule drugs, and supplementing this with noise analysis, we can pinpoint specific regions of drug action, thereby enhancing both the speed and cost-efficiency of drug development. This research offers novel insights into drug discovery, expands current perspectives, and lays the groundwork for formulating effective therapeutic strategies across a spectrum of diseases.

Sensitivity-improved blocking agent-free fluorescence polarization assay through surface modification using polyethylene glycol

Fluorescence polarization (FP) assays are widely used to quantify biomolecules, and their combination with microfluidic devices has the potential for application in onsite analysis. However, the hydrophobic surface of polydimethylsiloxane (PDMS)-based microfluidic devices and the amphiphilicity of the blocking agents can cause the nonspecific adsorption of biomolecules, which in turn reduces the sensitivity of the FP assay. To address this, we demonstrated an FP assay with improved sensitivity in microfluidic devices using a polyethylene glycol-based surface modification to avoid the use of blocking agents. We evaluated the effectiveness of the modification in inhibiting nonspecific protein adsorption and demonstrated the improved sensitivity of the FP immunoassay (FPIA). Our study addressed the lack of sensitivity of FP assays in microfluidic devices, particularly for the quantification of low-abundance analytes.

Rapid Information Retrieval from DNA Storage with Microfluidic Very Large-Scale Integration Platform

Due to its high information density, DNA is very attractive as a data storage system. However, a major obstacle is the high cost and long turnaround time for retrieving DNA data with next-generation sequencing. Herein, the use of a microfluidic very large-scale integration (mVLSI) platform is described to perform highly parallel and rapid readout of data stored in DNA. Additionally, it is demonstrated that multi-state data encoded in DNA can be deciphered with on-chip melt-curve analysis, thereby further increasing the data content that can be analyzed. The pairing of mVLSI network architecture with exquisitely specific DNA recognition gives rise to a scalable platform for rapid DNA data reading.

Application of Microfluidic Technology in Antibody Screening

Specific antibodies are widely used in the biomedical field. Current screening methods for specific antibodies mainly involve hybridoma technology and antibody engineering techniques. However, these technologies suffer from tedious screening processes, long preparation periods, high costs, low efficiency, and a degree of automation, which have become a bottleneck for the screening of specific antibodies. To overcome these difficulties, microfluidics has been developed as a promising technology for high-throughput screening and high purity of antibody. In this review, we provide an overview of the recent advances in microfluidic applications for specific antibody screening. In particular, hybridoma technology and four antibody engineering techniques (including phage display, single B cell antibody screening, antibody expression, and cell-free protein synthesis) based on microfluidics have been introduced, challenges, and the future outlook of these technologies are also discussed. This article is protected by copyright. All rights reserved.

Non-synonymous amino acid alterations in PfEBA-175 modulate the merozoite ligand's ability to interact with host's Glycophorin A receptor

The pathological outcome of malaria due to Plasmodium falciparum infection depends largely on erythrocyte invasion by blood-stage merozoites which employ a cascade of interactions occurring between parasite ligands and RBC receptors. In a previous study exploring the genetic diversity of region-II of PfEBA-175, a ligand that plays a crucial part in parasite's RBC entry through Glycophorin A (GPA) receptor, we demonstrated that F2 domain of region-II underwent positive selection in Indian P. falciparum population through the accumulation of non-synonymous polymorphisms. Here, we examine the functional impact of two highly prevalent non-synonymous alterations in F2, namely Q584E & E592A, using a battery of molecular, biophysical and in-silico techniques. Application of circular dichroism, FTIR, fluorescence spectroscopy reveals that secondary and three-dimensional folding of recombinant-F2 protein carrying 584E and 592A residues (F2-Mut) differs significantly from that carrying 584Q and 592E (F2-3D7). A comparison of spectroscopic and thermodynamic parameters shows that F2-Mut is capable of forming a complex with GPA with higher efficiency compared to F2-3D7. In silico docking predicts both artemisinin and artesunate possess the capacity of slipping into the GPA binding crevices of PfEBA-175 and disrupt PfEBA-GPA association. However, the estimated affinity of artesunate towards PfEBA-175 with 584E and 592A residues is higher than that of artemisinin. Thermodynamic parameters computed using isotherms are concordant with this in-silico prediction. Together, our data suggest that the presence of amino acid alterations in F2 provide structural and functional stability favoring PfEBA-GPA interaction and artesunate can efficiently disrupt the interaction between GPA and PfEBA-175 even carrying altered amino acid residues. The present study alerts the malaria research community by presenting evidence that the parasite is gaining evolutionary fitness by cultivating genetic alterations in many of its proteins.

Microfluidic approaches for the analysis of protein-protein interactions in solution

Exploration and characterisation of the human proteome is a key objective enabling a heightened understanding of biological function, malfunction and pharmaceutical design. Since proteins typically exhibit their behaviour by binding to other proteins, the challenge of probing protein-protein interactions has been the focus of new and improved experimental approaches. Here, we review recently developed microfluidic techniques for the study and quantification of protein-protein interactions. We focus on methodologies that utilise the inherent strength of microfluidics for the control of mass transport on the micron scale, to facilitate surface and membrane-free interrogation and quantification of interacting proteins. Thus, the microfluidic tools described here provide the capability to yield insights on protein-protein interactions under physiological conditions. We first discuss the defining principles of microfluidics, and methods for the analysis of protein-protein interactions that utilise the diffusion-controlled mixing characteristic of fluids at the microscale. We then describe techniques that employ electrophoretic forces to manipulate and fractionate interacting protein systems for their biophysical characterisation, before discussing strategies that use microdroplet compartmentalisation for the analysis of protein interactions. We conclude by highlighting future directions for the field, such as the integration of microfluidic experiments into high-throughput workflows for the investigation of protein interaction networks.

Analysis of deoxyribonuclease activity by conjugation-free fluorescence polarisation in sub-nanolitre droplets

We report the analysis of deoxyribonuclease (DNase) activity by conjugation-free fluorescence polarisation in a droplet-based microfluidic chip. DNase is a DNA cleaving enzyme and its activity is important in the maintenance of normal cellular functions. Alterations in DNase activity have been implicated as the cause of various cancers and autoimmune diseases. To date, various methods for the analysis of DNase activity have been reported. However, they are not cost effective due to the requirement of large sample volumes and the need for the conjugation of fluorescent dyes. In this study, we have used ethidium bromide (EtBr), a DNA intercalating reagent, as a fluorescent reporter without any prior conjugation or modification of DNA. Degradation of DNA by DNase 1 was monitored at a steady state by making changes in the fluorescence polarisation of EtBr in droplets with a volume of 330 picolitre at a 40 hertz frequency under visible light. Using this technique, we successfully determined the half-maximal inhibitory concentration (IC₅₀) of ethylenediaminetetraacetic acid (EDTA) for the inhibition of DNase 1 activity to be 1.56 ± 0.91 mM.

Microfluidics-Implemented Biochemical Assays: From the Perspective of Readout

Over the past decades, microfluidics has emerged as an increasingly important tool to perform biochemical assays for diagnosis and healthcare. The precise fluid control and molecule manipulation within microfluidics greatly contribute to developing assays with simplicity and convenience. The advantages of microfluidics, including decreased consumption of reagents and samples, lower operating and analysis time, much lower cost, and higher integration and automation over traditional systems, offer a great platform to meet the needs of point-of-care applications. In this Review, versatile strategies are outlined and recent advances in microfluidics-implemented assays are discussed from the perspective of readout, because a convenient and straightforward readout is what a biochemical assay requires and the end user desires. Functions and properties arising from each readout are reviewed and the advantages and limitations of each readout are discussed together with current challenges and future perspectives.

The interaction mechanism between alkaloids and pepsin based on lum-AuNPs in the chemiluminescence analysis

Herein, novel luminol functional gold nanoparticles (lum-AuNPs) were quickly prepared in an alkaline luminol solution with HAuCl4, which had the unique characteristics of uniform size and excellent luminescence properties. A self-made flow injection-chemiluminescence (FI-CL) system was established to study the interaction between pepsin (Pep) and five alkaloids (anisodamine, berberine, reserpine, jatrorrhizine and matrine) using lum-AuNPs as the CL probe. Based on the abovementioned home-made CL system, the possible interaction mechanisms of Pep with five alkaloids have been comprehensively discussed by molecular docking simulation, chemical thermodynamics and kinetic studies. The results indicated that there were obvious CL enhancement and inhibition effects on the lum-AuNPs CL system for the Pep and the complex of Pep/alkaloids, respectively. The possible mechanism for the interaction of Pep-five alkaloids was mainly mediated by the hydrophobic force. The binding constant K and binding site n for the Pep-alkaloid interaction are consistent with the list of Ber > Res > Ani, Jat > Mat, which is relative to the potential of groups of alkaloids interacting with the active site of Pep.

High-throughput fluorescence polarization immunoassay by using a portable fluorescence polarization imaging analyzer

High-throughput fluorescence polarization immunoassays (FPIAs) for mycotoxin were conducted using a portable FP analyzer with a microdevice. Simultaneous FPIA measurements for 8 different deoxynivalenol (DON) concentrations in 12 chambers (total of 96 samples) and high-throughput FPIA measurements for single DON concentrations in more than 500 chambers were conducted. The results indicated that simultaneous FPIAs for 96 independent samples and for 500 samples were possible by FP imaging. The FP analyzer has a size of 65 cm (W 35 cm × D 15 cm × H 15 cm) and costs less than $5000. The sample volume was 1 nL. Furthermore, it is expected that sample reaction and FP detection can be automatically conducted with the analyzer by changing the microdevice and the software. Its features such as low cost and portability will contribute to on-site measurement and point-of-care testing. Additionally, the high-throughput feature will contribute to the study of molecular interactions based on FP measurements.

Microfluidic-Mass Spectrometry Interfaces for Translational Proteomics

Interfacing mass spectrometry (MS) with microfluidic chips (μchip-MS) holds considerable potential to transform a clinician's toolbox, providing translatable methods for the early detection, diagnosis, monitoring, and treatment of noncommunicable diseases by streamlining and integrating laborious sample preparation workflows on high-throughput, user-friendly platforms. Overcoming the limitations of competitive immunoassays - currently the gold standard in clinical proteomics - μchip-MS can provide unprecedented access to complex proteomic assays having high sensitivity and specificity, but without the labor, costs, and complexities associated with conventional MS sample processing. This review surveys recent μchip-MS systems for clinical applications and examines their emerging role in streamlining the development and translation of MS-based proteomic assays by alleviating many of the challenges that currently inhibit widespread clinical adoption.

Online fluorescence anisotropy immunoassay for monitoring insulin secretion from islets of Langerhans

Insulin secretion from islets of Langerhans is a dynamic process that is essential for maintaining glucose homeostasis. The ability to measure dynamic changes in insulin levels upon glucose stimulation from single islets will allow testing of therapeutics and investigating mechanisms of defective secretion observed in metabolic diseases. Most approaches to date for measurement of rapid changes in insulin levels rely on separations, making the assays difficult to translate to non-specialist laboratories. To enable rapid measurements of secretion dynamics from a single islet in a manner that will be more suitable for transfer to non-specialized laboratories, a microfluidic online fluorescence anisotropy immunoassay was developed. A single islet was housed inside a microfluidic chamber and stimulated with varying glucose levels from a gravity-based perfusion system. The total effluent of the islet chamber containing the islet secretions was mixed with gravity-driven solutions of insulin antibody and Cy5-labeled insulin. After mixing was complete, a linearly polarized 635 nm laser was used to excite the immunoassay mixture and the emission was split into parallel and perpendicular components for determination of anisotropy. Key factors for reproducible anisotropy measurements, including temperature homogeneity and flow rate stability were optimized, which resulted in a 4 nM limit of detection for insulin with <1% RSD of anisotropy values. The capability of this system for measuring insulin secretion from single islets was shown by stimulating an islet with varying glucose levels. As the entire analysis is performed optically, this system should be readily transferable to other laboratories.

Quantitative Affinity Determination by Fluorescence Anisotropy Measurements of Individual Nanoliter Droplets

Fluorescence anisotropy measurements of reagents compartmentalized into individual nanoliter droplets are shown to yield high-resolution binding curves from which precise dissociation constants (K_d) for protein-peptide interactions can be inferred. With the current platform, four titrations can be obtained per minute (based on ∼100 data points each), with stoichiometries spanning more than 2 orders of magnitude and requiring only tens of microliters of reagents. In addition to affinity measurements with purified components, K_d values for unpurified proteins in crude cell lysates can be obtained without prior knowledge of the concentration of the expressed protein, so that protein purification can be avoided. Finally, we show how a competition assay can be set up to perform focused library screens, so that compound labeling is not required anymore. These data demonstrate the utility of droplet compartments for the quantitative characterization of biomolecular interactions and establish fluorescence anisotropy imaging as a quantitative technique in a miniaturized droplet format, which is shown to be as reliable as its macroscopic test tube equivalent.

Multiplexing Fluorescence Anisotropy Using Frequency Encoding

In this report, a method to multiplex fluorescence anisotropy measurements is described using frequency encoding. As a demonstration of the method, simultaneous competitive immunoassays for insulin and glucagon were performed by measuring the ratio of bound and free Cy5-insulin and FITC-glucagon in the presence of their respective antibodies. A vertically polarized 635 nm laser was pulsed at 73 Hz and used to excite Cy5-insulin, while a vertically polarized 488 nm laser pulsed at 137 Hz excited FITC-glucagon. The total emission was split into parallel and perpendicular polarizations and collected onto separate photomultiplier tubes. The signals from each channel were demodulated using a fast Fourier transform, resolving the contributions from each fluorophore. Anisotropy calculations were carried out using the magnitude of the peaks in the frequency domain. The method produced the expected shape of the calibration curves with limits of detection of 0.6 and 5 nM for insulin and glucagon, respectively. This methodology could readily be expanded to other biological systems and further multiplexed to monitor increased numbers of analytes.

Fluorescence polarization measurement system using a liquid crystal layer and an image sensor

The detection system which enables simultaneous fluorescence polarization (FP) measurement of multiple samples was proposed and proven by a proof-of-concept experiment on the viscosity dependence of FP of fluorescein sample in water-ethylene glycol solution and another experiment on the FP immunoassay of prostaglandin E2 sample. The measurement principle of FP is based on the synchronization between the orientation of the liquid crystal molecules and the sampling frequency of a CCD. This report is the first description of the simultaneous FP measurement of multiple samples. This system has a great potential for equipment miniaturization and price reduction as well as providing simultaneous FP measurement of multiple samples.

Enzyme engineering in biomimetic compartments

The success of a directed evolution approach to creating custom-made enzymes relies in no small part on screening as many clones as possible. The miniaturisation of assays into pico to femtoliter compartments (emulsion droplets, vesicles or gel-shell beads) makes directed evolution campaigns practically more straightforward than current large scale industrial screening that requires liquid handling equipment and much manpower. Several recent experimental formats have established protocols to screen more than 10 million compartments per day, representing unprecedented throughput at low cost. This review introduces the emerging approaches towards making biomimetic man-made compartments that are poised to be adapted by a wider circle of researchers. In addition to cost and time saving, control of selection pressures and conditions, the quantitative readout that reports on every library members and the ability to develop strategies based on these data will increase the degrees of freedom in designing and testing strategies for directed evolution experiments.

Analytical strategies used to identify the readers of histone modifications: A review

The so-called "readers" of histone post-translational modifications (HPTMs) refer to proteins or complexes that are recruited to HPTMs thus eventually regulate gene transcription. To identify these "readers", mass spectrometry plays an essential role following various enriching strategies. These enriching methods include the use of modified histone peptides/proteins or chemically synthesized histones/nucleosomes containing desired HPTMs to enrich the readers of HPTMs. Despite the peptide- or protein-based assay is straightforward and easy to perform for most labs, this strategy has limited applications for those weak or combinational interactions among various HPTMs and false-positive results are a potential big problem. While the results derived from synthesized histone proteins/nucleosomes is more reliable as it mimics the real chromatic conditions thus is able to analyze the binders of those cross-talked HPTMs, usually the synthesis is so difficult that their applications are impeded for high throughput analysis. In this review, an overview of these analytical techniques is provided and their advantages and disadvantages are discussed.

Hybridization-induced Ag(i) dissociation from an immobilization-free and label-free hairpin DNA: toward a novel electronic monitoring platform

A novel silver ion-assisted hairpin DNA through C–Ag⁺–C coordination chemistry was designed for homogeneous electronic monitoring of HIV DNA on a negatively charged electrode, based on hybridization-induced Ag⁺ dissociation from hairpin DNA.