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[Methods in Enzymology] || Fluorescence Depolarization Kinetics to Study the Conformational Preference, Structural Plasticity, Binding, and Assembly of Intrinsically Disordered Proteins
摘要： Fluorescence depolarization kinetics measured by the time-resolved fluorescence anisotropy decay serves as a sensitive and powerful methodology to study the conformational dynamics of macromolecules. This methodology allows us to delineate the different modes of biomolecular motional dynamics including the local, segmental, and global rotational dynamics on the timescale ranging from picoseconds to nanoseconds. In this chapter, we describe the principles and applications of this methodology to obtain unique molecular insights into the intrinsically disordered proteins (IDPs). Fluorescence depolarization kinetics, when performed in a site-specific manner, can offer a reliable tool to monitor the intrinsic backbone torsional dynamics of expanded IDPs and is capable of discerning the conformational preference of IDPs. Additionally, the time-resolved fluorescence anisotropy measurements allow us to investigate the mechanism of binding and assembly of a wide range of IDPs that are involved in crucial function and disease.
关键词： Fluorescence depolarization kinetics,conformational dynamics,time-resolved fluorescence anisotropy decay,biomolecular interactions,intrinsically disordered proteins
更新于2025-09-23 15:21:01
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Plasmonic biosensors fabricated by galvanic displacement reactions for monitoring biomolecular interactions in real time
摘要： Optical sensors are prepared by reduction of gold ions using freshly etched hydride-terminated porous silicon, and their ability to specifically detect binding between protein A/rabbit IgG and asialofetuin/Erythrina cristagalli lectin is studied. The fabrication process is simple, fast, and reproducible, and does not require complicated lab equipment. The resulting nanostructured gold layer on silicon shows an optical response in the visible range based on the excitation of localized surface plasmon resonance. Variations in the refractive index of the surrounding medium result in a color change of the sensor which can be observed by the naked eye. By monitoring the spectral position of the localized surface plasmon resonance using reflectance spectroscopy, a bulk sensitivity of 296 nm ± 3 nm/RIU is determined. Furthermore, selectivity to target analytes is conferred to the sensor through functionalization of its surface with appropriate capture probes. For this purpose, biomolecules are deposited either by physical adsorption or by covalent coupling. Both strategies are successfully tested, i.e., the optical response of the sensor is dependent on the concentration of respective target analyte in the solution facilitating the determination of equilibrium dissociation constants for protein A/rabbit IgG as well as asialofetuin/Erythrina cristagalli lectin which are in accordance with reported values in literature. These results demonstrate the potential of the developed optical sensor for cost-efficient biosensor applications.
关键词： Surface functionalization,Optical sensor,Lectin,Localized surface plasmon resonance,Biomolecular interactions,Gold nanostructure
更新于2025-09-23 15:19:57
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High-throughput, non-equilibrium studies of single biomolecules using glass-made nanofluidic devices
摘要： Single-molecule detection schemes offer powerful means to overcome static and dynamic heterogeneity inherent to complex samples. However, probing biomolecular interactions and reactions with high throughput and time resolution remains challenging, often requiring surface-immobilized entities. Here, we introduce glass-made nanofluidic devices for the high-throughput detection of freely-diffusing single biomolecules by camera-based fluorescence microscopy. Nanochannels of 200 nm height and a width of several micrometers confine the movement of biomolecules. Using pressure-driven flow through an array of parallel nanochannels and by tracking the movement of fluorescently labelled DNA oligonucleotides, we observe conformational changes with high throughput. In a device geometry featuring a T-shaped junction of nanochannels, we drive steady-state non-equilibrium conditions by continuously mixing reactants and triggering chemical reactions. We use the device to probe the conformational equilibrium of a DNA hairpin as well as to continuously observe DNA synthesis in real time. Our platform offers a straightforward and robust method for studying reaction kinetics at the single-molecule level.
关键词： fluorescence microscopy,DNA,nanofluidic devices,single-molecule detection,biomolecular interactions
更新于2025-09-04 15:30:14