Nanofluidic Fluorescence Microscopy (NFM) for real-time monitoring of protein binding kinetics and affinity studies

Residence time prediction in magnetically controlled biomolecular local rebinding-dissociation kinetics

The residence time of drug-target conjugates is a critical factor in drug screening and efficacy prediction. The local rebinding-dissociation kinetics gives insights into in-vivo drug-target interactions. A magnetic torque system (MTS) is designed to observe rebinding-dissociation kinetics for predicting residence time. The system utilizes an alternating magnetic field (AMF) to manipulate the magnetization motion of magnetically labeled biomolecules and the forces acting upon biomolecular bonds. The motion, sensed by a quartz crystal microbalance (QCM), reflects biomolecular interactions occurring at the particle surface. Meanwhile, the motion facilitates the separation of dissociated molecules from the surface, thereby obviating the necessity for fixed and mobile phases in common kinetics observations. The constant and static solution environment minimizes reagent consumption. The MTS was utilized to observe the local rebinding-dissociation of antibodies (PAB and MAB) to magnetic beads (MB) and to HER2 receptors. The residence times recorded by the MTS were larger than the results obtained via SPR method, due to the occurrences of rebinding-dissociation kinetics. Interaction behaviours can be meticulously regulated for varying affinities by modulating the intensity of magnetic field. A high intensity field (400 Oe) was applied for strong binding between antibody-MB (biotin-streptavidin), and a low intensity field (300 Oe) was applied for weak antigen-antibody interactions. An increase in AMF strength enhanced dissociation, with a shift from 300 Oe to 400 Oe resulting in a 1 ∼ 4-fold reduction in residence time. Overall, the MTS provides an interactive and customizable perspective on kinetics observations.

Assessing Aptamer-Analyte Binding Kinetics by Microfluidic Fluorescence Microscopy

Kinetic measurement plays a crucial role in understanding aptamer binding mechanisms and identifying appropriate aptamers for clinical and research applications. Current techniques, while well established, generally require large sample volumes, bulky and expensive instruments operated by trained personnel, and are hence not readily accessible to resource-limited research laboratories. This paper presents a fluorescence microscopy-based microfluidic assay for measuring aptamer-analyte binding kinetics in a simple and cost-effective manner. Kinetic measurements are achieved by monitoring time-course fluorescence of fluorescently labeled aptamers as they bind to the targets trapped in a microfluidic chip. Fluorescence measurements are performed on a standard fluorescence microscope and are accessible to laboratories with only modest resources. Moreover, microfluidic technology allows efficient and cost-effective immobilization of small amounts of target molecules or live cells as well as flow-based manipulation of aptamers for the measurements. Kinetic measurements of aptamer binding to immunoglobulin E protein and CCRF-CEM cells have yielded results consistent with those obtained from established methods, demonstrating the potential utility of our method for exploring aptamer-target interactions and identifying aptamers that best suit specific given biomedical applications.

Real-time kinetics and affinity analysis of the interaction between protein A and immunoglobulins G derived from different species on silica colloidal crystal films

Kinetic and affinity analysis of protein interactions reveals information on their related activities in biological processes. Herein, we established a system for evaluating the kinetics and affinity of the interaction between protein A and various IgG species on the surface of silica spheres of silica colloidal crystal (SCC) films by the extraordinary optical interference capabilities of 190 nm silica spheres after self-assembly. The equilibrium association constant (KA) was calculated by the equilibrium Langmuir model and nonlinear least-squares analysis of time-dependent data. The relative protein A/IgG binding affinity is human > rabbit >cow >goat. In addition, the competitive interaction of distinct species of IgG with protein A at the interface of SCC films was studied and performed. These findings may help with the use of protein A and other recognition components in a number of sensor types. Furthermore, this research might offer a novel approach to determining the kinetics and affinity of proteins on the surface of spheres particles, which may contribute to the development of the application of spheres particles in pharmaceutical science, biomedical engineering, and other techniques.

Fluorescence based miniaturized microfluidic and nanofluidic systems for biomedical applications

Over the last two decades miniaturized microfluidic and nanofluidic systems with fluorescence setup emerged as a powerful technological platform for diverse biomedical applications. Bio-macromolecules such as nucleic acids and proteins are the core cellular components, their single molecule analysis allow us to understand biological processes, disease creation and progression, and development of novel treatment policies. Design and development of foolproof treatment methods requires rigorously analysis of nucleic acids and proteins such as length quantifications, sequence profiling, sequence mapping, analysis of conformational changes, analysis and recognition of epigenetic changes, and their interactions with other biomolecules. Miniaturized microfluidic and nanofluidic systems with fluorescence spectroscopy enable worldwide researchers to perform nucleic acids and proteins extractions and single molecule analysis from the trace amount of biological samples. In the present chapter we mostly highlighted over one decade applications of microfluidic and nanofluidic systems for single cell micro ribonucleic acid (miRNA) isolation and detection, deoxyribonucleic acid (DNA) mapping, DNA barcoding, identification of epigenetic mark on single DNA molecule, DNA-protein interactions study, protein sensing, protein sequencing, protein binding kinetics and many other applications. We also presented the recently reported microfluidic platform for the preparation of reproducible unisize aggregation induced emission (AIE) active nanomaterials and their biological applications.

Integrated multichannel all-fiber optofluidic biosensing platform for sensitive and simultaneous detection of trace analytes

An integrated multichannel all-fiber optofluidic biosensing platform (M-AOB) has been developed for a sensitive, rapid, and simultaneous detection of up to three trace analytes. The M-AOB platform employs a 1 × 3 fiber optical switch and three single-multimode fiber optic couplers for the transmission of excitation light and fluorescence and one photodiode detector for the simultaneous detection of fluorescence signals of multiple channels based on the time-resolve effect of the fiber optical switch. This design greatly simplified the entire system structure and improved light transmission efficiency. Through an indirect competitive immunoassay mechanism, we detected two highly regulated small molecules, namely, atrazine and 2,4-D, to demonstrate the value of M-AOB to the simultaneous measurement of trace analytes in water samples. The limits of detection of 0.03 μg/L and 0.04 μg/L were obtained for atrazine and 2,4-D, respectively, and were highly comparable with those of other analytical techniques. The high sensitivity of M-AOB benefited from the high light collective efficiency and low light loss of the excellent all-fiber optical structures and from the advantages of the evanescent wave technique. The regeneration of the biosensor surface, 200 assay cycles, were performed without any significant activity loss. Each assay cycle was less than 15 min. The immunoassay performance of the M-AOB, evaluated in several spiked water samples, showed good recovery, accuracy, and precision, indicating that the M-AOB was less susceptible to matrix effects of water samples. All these results illustrated that M-AOB can be readily extended toward the simultaneous and rapid detection of other trace small molecules using different biosensors modified by other analyte conjugates and their respective fluorescence-labeled antibodies.

Spatial Analysis of Nanofluidic-Embedded Biosensors for Wash-Free Single-Nucleotide Difference Discrimination

In this work, we demonstrate that the analysis of spatially resolved nanofluidic-embedded biosensors permits the fast and direct discrimination of single-nucleotide difference (SND) within oligonucleotide sequences in a single step interaction. We design a sensor with a linear dimension much larger than the channel depth in order to ensure that the reaction over the whole sensor is limited by the convection rate. Thus, the targets are fully collected, inducing a nonuniform spatial hybridization profile. We also use the nanoscale height of the channel, which enables us to minimize the amount of labeled molecules flowing over the sensor and hence to reduce the fluorescence background, to carry out real-time hybridization detection by fluorescence microscopy. Taken together, these design rules allow us to show that the spatial hybridization profile depends on the duplex affinity, and we speculate that the on and off-rate constants can be inferred during target injection, which is not possible in local analysis where the dissociation step through rinsing must be conducted. We finally manage to discriminate a GT mismatch on a microRNA sequence by optimizing the interaction temperature and the probe design after a few minutes of interaction in a single step protocol. This work may be applied to any biosensing transduction scheme with spatial resolution, e.g., surface plasmon resonance imaging, integrated into nanofluidic channels for applications where high oligonucleotide sequence selectivity and short analysis times are required.

An electricity-fluorescence double-checking biosensor based on graphene for detection of binding kinetics of DNA hybridization

In this paper, an electricity-fluorescence double-checking biosensor based on graphene materials has been presented for detection of DNA hybridization kinetics.

Microcontact printing with aminosilanes: creating biomolecule micro- and nanoarrays for multiplexed microfluidic bioassays

Aqueous based microcontact printing (μCP) to create micro- and nanoarrays of (3-aminopropyl)triethoxysilane (APTES) on glass substrates of microfluidic devices for covalent immobilization of DNA aptamers and antibodies.