Measurement of Protein and Nucleic Acid Diffusion Coefficients Within Biomolecular Condensates Using In-Droplet Fluorescence Correlation Spectroscopy. 2023

Ibraheem Alshareedah, and Priya R Banerjee
Department of Physics, University at Buffalo SUNY, Buffalo, NY, USA.

Liquid-liquid phase separation of protein and RNA complexes into biomolecular condensates has emerged as a ubiquitous phenomenon in living systems. These protein-RNA condensates are thought to be involved in many biological functions in all forms of life. One of the most sought-after properties of these condensates is their dynamical properties, as they are a major determinant of condensate physiological function and disease processes. Measurement of the diffusion dynamics of individual components in a multicomponent biomolecular condensate is therefore routinely performed. Here, we outline the experimental procedure for performing in-droplet fluorescence correlation spectroscopy (FCS) measurements to extract the diffusion coefficient of individual molecules within a biomolecular condensate in vitro. Unlike more common experiments such as fluorescence recovery after photobleaching (FRAP), where data interpretation is not straightforward and strictly model dependent, FCS offers a robust and more accurate way to quantify biomolecular diffusion rates in the dense phase. The small observation volume allows FCS experiments to report on the local diffusion coefficient within a spatial resolution of <1 μm, making it ideal for probing spatial inhomogeneities within condensates as well as variable dynamics within subcompartments of multiphasic condensates.

UI MeSH Term Description Entries
D009696 Nucleic Acids High molecular weight polymers containing a mixture of purine and pyrimidine nucleotides chained together by ribose or deoxyribose linkages. Nucleic Acid,Acid, Nucleic,Acids, Nucleic
D000091582 Biomolecular Condensates Membraneless intracellular compartments formed through liquid-liquid phase separation from the surrounding CYTOPLASM or nucleoplasm or by the concentration of proteins and nucleic acids into droplets as they aggregate on static cellular structures such as CELL MEMBRANES. Examples include CELL NUCLEOLI; STRESS GRANULES; PARASPECKLES; HISTONE LOCUS BODIES; and POSTSYNAPTIC DENSITIES. Membraneless Organelles,Biomolecular Condensate,Condensate, Biomolecular,Condensates, Biomolecular,Membraneless Organelle,Organelle, Membraneless,Organelles, Membraneless
D012313 RNA A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed) RNA, Non-Polyadenylated,Ribonucleic Acid,Gene Products, RNA,Non-Polyadenylated RNA,Acid, Ribonucleic,Non Polyadenylated RNA,RNA Gene Products,RNA, Non Polyadenylated
D013057 Spectrum Analysis The measurement of the amplitude of the components of a complex waveform throughout the frequency range of the waveform. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Spectroscopy,Analysis, Spectrum,Spectrometry
D036681 Fluorescence Recovery After Photobleaching A method used to study the lateral movement of MEMBRANE PROTEINS and LIPIDS. A small area of a cell membrane is bleached by laser light and the amount of time necessary for unbleached fluorescent marker-tagged proteins to diffuse back into the bleached site is a measurement of the cell membrane's fluidity. The diffusion coefficient of a protein or lipid in the membrane can be calculated from the data. (From Segen, Current Med Talk, 1995). Fluorescence Photobleaching Recovery,FRAP (Fluorescence Recovery After Photobleaching),FRAPs (Fluorescence Recovery After Photobleaching)

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