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Shil, S.; Tsuruta, M.; Kawauchi, K.; Miyoshi, D. Biomolecular Liquid–Liquid Phase Separation for Biotechnology. Encyclopedia. Available online: https://encyclopedia.pub/entry/43183 (accessed on 14 December 2025).
Shil S, Tsuruta M, Kawauchi K, Miyoshi D. Biomolecular Liquid–Liquid Phase Separation for Biotechnology. Encyclopedia. Available at: https://encyclopedia.pub/entry/43183. Accessed December 14, 2025.
Shil, Sumit, Mitsuki Tsuruta, Keiko Kawauchi, Daisuke Miyoshi. "Biomolecular Liquid–Liquid Phase Separation for Biotechnology" Encyclopedia, https://encyclopedia.pub/entry/43183 (accessed December 14, 2025).
Shil, S., Tsuruta, M., Kawauchi, K., & Miyoshi, D. (2023, April 18). Biomolecular Liquid–Liquid Phase Separation for Biotechnology. In Encyclopedia. https://encyclopedia.pub/entry/43183
Shil, Sumit, et al. "Biomolecular Liquid–Liquid Phase Separation for Biotechnology." Encyclopedia. Web. 18 April, 2023.
Biomolecular Liquid–Liquid Phase Separation for Biotechnology
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This entry is adapted from the peer-reviewed paper 10.3390/biotech12020026

The liquid–liquid phase separation (LLPS) of biomolecules induces condensed assemblies called liquid droplets or membrane-less organelles. In contrast to organelles with lipid membrane barriers, the liquid droplets induced by LLPS do not have distinct barriers (lipid bilayer). Biomolecular LLPS in cells has attracted considerable attention in broad research fields from cellular biology to soft matter physics. The number of biomolecular droplets produced via LLPS is rapidly growing, and their biological functions have been identified.

liquid–liquid phase separation biomolecules biotechnology DNA RNA droplets

1. Droplets in Cytoplasm

Biomolecular droplets which are present in the cytoplasm have been identified. Stress granules are a typical example and are the most extensively studied in the cytoplasmic droplets. Stress granules are membrane-less organelles, ranging in size from 0.1 to 2 μm [1]. The essential components for stress granule formation are T-cell-restricted intracellular antigen-1 (TIA-1) and Ras-GTPase-activating protein SH3-domain-binding protein 1 (G3BP1) and RNAs. The primary function of stress granules is to promote cell survival by condensing translationally stalled mRNAs, ribosomal components, translation initiation factors, and RNA-binding proteins (RBPs). On the other hand, certain transcripts such as heat shock protein 70 are excluded from stress granules which are selectively translated under the stress conditions [2]. Therefore, stress granules can control protein expression (translation) through the inclusion and exclusion of certain mRNAs in response to unfavorable conditions for cells. Stress granules are formed under acute stress conditions such as hypoxia, oxidative stress, osmotic stress, and temperature change [3]. The timescale of the disassembly of stress granules varies depending on the stress factors. For example, cold-shock-induced stress granules disassemble within minutes after returning to normal temperature [4]. On the other hand, recovery after arsenate stress, H2O2 treatment, osmotic stress, or heat shock occurs between 60 and 120 min [5]. In addition to the recovery time varies, this range of time is much shorter than the gene expression response. Therefore, LLPS including the assembly of stress granules is critical for promptly controlling cellular functions to protect cells from death under adverse conditions. Moreover, stress granules under stress conditions alter nuclear events, providing a linkage between the nuclear and the cytoplasmic processes [4]. Stress granules also respond to diseases such as viral infections and cancer [6]. Stress granules are further recognized as potential precursors of pathological aggregates in neurodegenerative diseases [7]. The position, function, chemical composition, and detection technique of cytoplasmic droplets are briefly listed in Table 1 [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26].
Table 1. Components, roles, and observation procedures of droplets in cytoplasm.
Droplet Main Component Role Observation Ref.
Stress granule Proteins and RNAs Translational regulation mRNA storage CM (1), smFISH (2) [5][6]
Centrosome Pericentriolar material Formation of mitotic spindles during mitosis CM (1) [7][8]
U body Uridine-rich small nuclear ribonucleoproteins Storage and assembly of snRNPs CM (1) [9][10]
G body Lipid and protein Controlling the rate of glycolysis CM (1) [11][12]
P body Translationally repressed mRNAs and proteins related to mRNA decay mRNA decay and silencing CM (1) [13][14]
Balbiani body (germ cells) Endoplasmic reticulum/Golgi-like vesicles, mitochondria, and specific RNAs transporter. Storage and facilitating the organization of the oocyte into a polarized cell CM (1), EM (3) [15][16][17][18]
Germ granules (germ cells) Proteins and RNAs Storage of proteins and RNAs that are required for germ cell development EM (3) [19][20][21]
RNA transport granule (neuronal cell) mRNAs and proteins Storage and transport of mRNAs CM (1) [22][23]
(1) CM, confocal microscopy; (2) smFISH, single molecular fluorescence in situ hybridization; (3) EM, electron microscopy.

2. Droplets in Nucleus

The interior of a cell nucleus is a complex environment: a crowded mixture of biomolecules, including very long DNA strands in the form of chromatin with histone proteins, mRNAs that are newly transcribed, other RNAs for controlling gene expressions, and proteins for transcription and other processes. A wide variety of droplets are required to proceed biologically critical reactions under the complex environment.
One of the most well-known cellular droplets is the nucleolus, which, in the 1830s, was the first membrane-less component to be identified [27]. The number (usually 2–5 per cell) and size of the nucleoli depend on the cell type, cell cycle phase, and metabolic conditions. The nucleolus provides a site for the transcription of ribosomal RNA from ribosomal DNA and ribosome assembly for ribosome biogenesis. The nucleolus also serves other processes, such as maintaining cell homeostasis [28]. Recently, new roles of the nucleoli have attracted attention: as stress granules, the nucleoli act as sensors and regulators for cellular stresses such as RNA polymerase I inhibitors, prevalent cytotoxic agents, viral proteins, UV radiation, heat shock, and DNA damage, apoptosis, and senescence [29].
A nucleolus contains several functional modules, each constituting three sub-compartments or layers. From the inner to the periphery, the three layers are the fibrillar center, the dense fibrillar component, and the granular component, responsible for different steps of ribosomal biogenesis. The nucleolus is composed of hundreds of copies of ribosomal genes, newly synthesized ribosomal RNA (rRNA), ribosomal proteins, and ribonucleoproteins. Other droplets found in the nucleus are listed in Table 2 [30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50][51][52][53][54][55][56][57].
Table 2. Components, roles, and observation procedures of droplets in the nucleus.
Droplet Main Component Role Observation Ref.
Nucleolus Proteins and canonical nucleic acids, non-coding RNA Ribosome biogenesis FM 1 [26][28][30]
Histone locus body NPAT 10, SLBP 11, the U7 spliceosomal snRNP-specific components, such as Sm proteins, LSm10 and LSm11, and the U7 spliceosomal snRNA, FLASH 12 Histone mRNA biogenesis BFM 2 [29][31]
Heterochromatin HP1 13, nucleosomal DNA Promote the formation of heterochromatin CM 3 [32][33][34][35][36][37]
Nuclear pore central transport channel and nuclear pore complex Nups 14, FG 15 Chromosomal translocations, change in protein expression levels.
Fuse with oncoproteins, nuclear import/export		 HS-AFM 4, FM 1 [38][39][40][41]
Nuclear speckles RNAs and proteins mRNA splicing CM 3 [42][43]
DNA damage foci Rad52 DNA repair proteins DNA damage repair Live-cell CM 5 [44][45]
Gem SMN complex, ZPR1, GEMIN2–8 16. Storage aid histone, mRNA processing CM 3 [46][47][48]
PcG body   Transcriptional repression IM 6, EM 7 [49][50]
Paraspeckle NONO 17, PSP1 17, PSP2 17, SFPQ 18, CFIm68 19, CFIm, hnRNPs 20 NEAT1 21 RNA processing CM 3 [51][52][53]
OPT domain The RNA polymerases and the general transcription factors Transcriptional regulation FM 1, EM 7 [54][55][56]
Cajal body Coilin, CB-specific RNAs Assembly and/or modification of splicing machinery BFM 2 [31][57][58]
Perinuclear compartment RNA-binding proteins and pol III RNA Associated with malignancy EM 7, IM 6 [57]
Cleavage body snRNPs 22, p80-coilin protein, RNA polymerases, transcriptional factors, nucleolar constituents mRNA processing IL 8 [59]
Nuclear bodies (NBs) Protein and non-protein components, heat shock transcription factors, HSF1 23 and HSF2 24, SAF-B 25, Sam68 26, SRSF1 27, SRSF7 27 and SRSF9 27. RNA Pol II. Regulation of genome function IM 6, SRM 9 [31][60]
PML body DAXX, SUMO 28 Transcriptional regulation; apoptosis signaling; antiviral defense EM 7 [47][61]
1 FM, fluorescence microscopy; 2 BFM: bright-field microscopy; 3 CM, confocal microscopy; 4 HS-AFM, high-speed atomic force microscopy; 5 live-cell CM; 6 IM, immunofluorescence microscopy; 7 EM, electron microscopy; 8 IL, immunofluorescence labelling; 9 SRM, super-resolution microscopy; 10 NPAT, factors required for processing histone pre-mRNAs, nuclear protein, ataxia–telangiectasia locus; 11 SLBP, stem-loop binding protein; 12 FLASH, FLICE-associated huge protein; 13 HP1, heterochromatin protein; 14 Nups, nucleoporins; 15 FG, phenylalanine–glycine; 16 GEMIN2–8, gem-associated proteins 2–8; 17 NONO, PSP1, PSP2, paraspeckle component proteins; 18 SFPQ, splicing factor proline/glutamine-rich; 19 CFIm68, mammalian cleavage factor I 68; 20 hnRNPs, Heterogeneous nuclear ribonucleoproteins; 21 NEAT1, long ncRNA nuclear-enriched abundant transcript 1; 22 snRNPs, small nuclear ribonucleoproteins; 23 HSF1, heat shock factor 1; 24 HSF2, heat shock factor 2; 25 SAF-B, scaffold attachment factor B; 26 Sam68: Src-associated mitosis 68 kDa protein; 27 SRSF1, SRSF7, SRSF9, SRSF family members; 28 SUMO, a potent repressor of transcription and modulator of apoptosis, ubiquitin-like protein.

3. Droplets in Membranes

Although they do not occur via LLPS, in cell membranes, biomolecular droplets are also produced, such as membrane clusters, as listed in Table 3 [58][59][60][61][62][63][64][65][66][67][68][69][70][71][72]. A membrane cluster is a lipid droplet consisting of triacylglycerols, phospholipids, sphingolipids, cholesterol, and proteins [73]. These clusters play important roles in various cellular processes, including signaling, and the transport of cell take and cell release material such as lipids, amino acids, ions water, and hormones, amines, and peptides [58]. The membrane cluster has a significant role not only in the uptake of lipids, but also in the distribution and storage of lipids. A representative example of a membrane cluster is the photosystem II (PSII) complex, which is involved in the light-dependent reactions of photosynthesis in plants, algae, and some bacteria [74]. PSII is a large and complex protein complex that contains over 20 different subunits, most of which are membrane-bound. It consists of a core antenna complex that captures light energy, a reaction center that uses this energy to split water into oxygen, and electron carriers that transfer the electrons to other components of the photosynthetic system [75]. The formation of PSII clusters is essential for their proper functioning. PSII clusters help to organize the various components and to create a favorable environment for the transport of electrons [76].
Table 3. Components, roles, and observation procedures of droplets in membranes.
Droplet Main Component Role Observation Ref.
Membrane cluster Triacylglycerols, phospholipid, protein Lipid uptake, distribution, storage, and use in the cell. - [65]
Synaptic densities Actin’s cytoskeleton, kinases, phosphatases, and regulators, GTPases, subunits of AMPA and NMDA receptors, Catenin, N-Cadherin Neurotransmission AEM 1 [66][67]
Focal adhesions p130Cas (‘Cas’) and FAK 7 Cell adhesion/migration SDCM 2 [68][69]
Nephrin clusters Cytoplasmic adaptor protein Nck, the nephrin–Nck–N-WASp complex Glomerular filtration barrier SRSIM 5 [62][63][70]
TCR clusters LAT 8 Immune synapse TIRF 3 [71][72][73]
Podosomes F-actin and its regulatory molecules, structural proteins Cell adhesion/migration PCM 4 [74][75]
Actin patches Actin-associated proteins, upstream signaling molecules Endocytosis EM 6 [76][77]
1 AEM, advanced electron microscopy; 2 SDCM, spinning disk confocal microscopy; 3 TIRF, total internal reflection fluorescence microscopy; 4 PCM, phase-contrast microscopy; 5 SRSIM, super-resolution structured illumination microscopy; 6 EM, electron microscopy; 7 FAK, focal adhesion kinase; 8 LAT, linker protein for activation of T cells.

4. Enzymes and Transcription Factors Undergoing LLPS

Recent studies suggest that some enzymes show different activity inside droplets. For example, Saini et al. recently discovered that macromolecular crowding induces LLPS, which leads to an increase in the intrinsic catalytic efficiencies of horseradish peroxidase (HRP) and glucose oxidase (GOx) [77]. Transcription factors (TFs) and RNAs also induce the formation of transcriptional condensates via LLPS, which contain clusters of multiple enhancers (super-enhancers) [78]. This phenomenon is supported by the dynamic interaction of TFs with RNA polymerase II (Pol II) clusters [79]. To form transcriptional condensates, TFs bind to various cis-regulatory DNA elements (e.g., promoters and enhancers) and stimulate the transcription of active genes in proximity, facilitating the precise control of gene expression [80]. Other examples of enzymes and transcription factors which undergo LLPS are listed in Table 4 [77][81][82][83][84][85][86][87][88][89][90][91][92][93][94][95][96][97][98][99][100][101][102][103][104][105].
Table 4. Components, roles, and observation procedures of droplet enzymes.
Enzyme Role Observation Ref.
Horseradish peroxidase (HRP) Catalyst (horseradish peroxidase (HRP) CM 1 [82]
Glucose oxidase (GOx) Catalyst (oxidation of β-d-glucose to d-glucono-δ-lactone) CM 1 [86]
Hexokinase Catalyst, catalyzing the phosphorylation of keto- and aldohexoses OM 2 [87]
Lipase Fat breakdown CM 1 [88][89]
Hammerhead ribozyme Cleavage and ligation of RNA molecule FRET 6, CD 4, CM 1 [90][91]
Pfk2, Eno1, Eno2, Fba1 Glycolysis FM 3 [92]
GIT1 GTPase activator FRAP 5, CM 1 [93]
HSF1 Transcription factor FM 3 [94][95]
NELFE Transcriptional regulation FM 3 [96]
p53 Transcription factor FM 3 [97][98][99][100][101][102]
PLK4 Serine/threonine-protein kinase CM 1 [103][104]
SOX-2 Transcription factor FM 3 [105]
TFE3 Transcription factor FM 3 [106]
TFEB Transcription factor FRAP 5 [107]
USP42 Deubiquitinating enzyme FM 3 [108]
YAP Transcription factor FM 3 [109][110]
1 CM, confocal microscopy; 2 OM, optical microscopy; 3 FM, fluorescence microscopy; 4 CD, circular dichroism; 5 FRAP, fluorescence recovery after photobleaching; 6 FRET, fluorescence resonance energy transfer microscopy.

5. Droplets Discovered in Various Biological Processes

The list of biomolecular condensates is increasing rapidly. For example, rubisco (pyrenoids) plays a crucial role in photosynthesis acceleration and in carbon fixation [106][107][108]. Another interesting droplet recently found is the Wnt droplet [109]. The Wnt droplet consists of proteins such as kinase that regulate β-catenin stability. Wnt droplets play a vital role in stem cell differentiation. These findings demonstrate that LLPS is pivotal and versatile not only in controlling the central dogma, but also in various biological processes. Therefore, it is considerable that LLPS is one of the fundamental characteristics of biomolecules. The location, name, component, biological role, and observation procedure of droplets discovered in various biological processes are listed in Table 5 [106][107][108][109][110][111][112][113].
Table 5. Location, components, roles, and observation procedures of droplets discovered in various biological processes.
Droplet Location Role Main Component Observation Ref.
Pyrenoids (Rubisco), carboxysomes Chloroplast Photosynthesis, metabolism (Carbon fixation) Carboxysomal linker proteins CsoS2 and CcmM, Rubisco large subunit Microscopy and sedimentation assay [111][112][113]
Wnt droplet Cell cytoplasm Stem cell differentiation, controlling Wnt pathway Scaffold proteins and kinases that regulate β-catenin stability CRISPR-engineered fluorescent tags, optogenetic tools [114]
YTHDC droplet (nuclear bodies) Nucleus AML cell survival, differentiation state, leukemogenesis YTHDC1 protein, m6 A-containing RNA IF 1, SEM 2. [115]
LDAM 3 Hippocampus Promotion of pathogenesis, neuroinflammation Lipid CARS 4 [116]
Lipid droplets Cell cytoplasm (Stem cell) Skeletal muscle satellite cell fate determination Lipid TEM 5 [117]
Plant lipid droplets: LD-Erm LD-Peroxisomes Plant cell Unknown Triacylglycerols (TAGs), sterol esters (SEs) FM 6, CM 7 [118]
1 IF, immunofluorescent imaging; 2 SEM, scanning electron microscopy; 3 LDAM, hippocampus lipid droplet accumulating microglia; 4 CARS, coherent anti-Stokes Raman scattering microscopy; 5 TEM, transmission electron microscopy; 6 FM, fluorescence microscope; 7 CM, confocal microscopy.

6. Artificial Droplet System

Artificial and model droplet systems are gaining popularity. Artificial and model droplet systems have various uses because of their controllable size, concentration inside the droplet, and the component of the droplet. Researchers are focusing on the development of new artificial droplets as well as artificial systems. Artificial cells are simplified models of living cells for investigations of the molecular basis of life. Artificial cells are generally constructed using a water-in-oil (W/O) microdroplet. Water in an oil microdroplet is a micrometer-sized water droplet dispersed in an immiscible oil phase [114]. Another artificial droplet system that gains immense popularity is the droplet reactor system. Droplet reactor systems have considerable biochemical applications such as single-cell analysis, kinetic study, and controlled drug release [115]. Another interesting example of an artificial droplet system is DNA nanostructures. DNA nanostructures were employed by Sato and Takinoue to induce LLPS [116]. The DNA nanostructures localize at the oil–water interface when they are added to the oil–water system. Different two-dimensional phase separation patterns could be induced depending on the DNA sequences. Hydrogels were created as a result of the DNA nanostructures’ phase separation [116].
Recently, a novel class of short peptide derivatives that undergo LLPS has been created [117]. The peptide is made up of phenylalanine dipeptides joined by hydrophilic spacers (cystamine moiety). Disulfide bonds formed among spacers enable redox-chemistry-based dynamic regulation of the assembly. Additionally, researchers might functionalize the coacervates to act as a catalyst in the aldol and hydrazone production reaction [117]. Other examples of model droplet systems are given in Table 6 [118][119][120][121][122].
Table 6. Components, application, and observation procedures of artificial droplets.
Droplet Component Observation Application Ref.
Adiposomes (artificial lipid droplets (ALDs)) Phospholipids and neutral lipids such as TAG LM 1, EM 2 Potential usage in drug delivery. [123]
Cell-sized aqueous/aqueous microdroplets (CAMDs) PEG 3 and DEX 4, actin FM 5 Provide cell-like crowded microenvironments [124]
Microfluidic platform in a defined pattern Hexadecane/squalene with dissolved lipids   Broad range of applications in the field of artificial cells, bioreactors, and pharmacological studies. [125]
Lipase-stabilized tributyrin microcompartment and amylose-polymer-stabilized 2-ethyl-1-hexanol microcompartment Amy-PNIPAAm 6, BSA-PNIPAAm 7, Lipase OM 8 Synthetic biology, bottom-up reaction [126]
G-quadruplex-forming oligonucleotides and R-rich oligopeptides FMR1 RNA, C9orf72 RNA, peptide derived from FMRP CM 9 Droplet redissolution in a sequence-specific manner [127]
1 LM, light microscopy; 2 EM, electron microscopy; 3 PEG, poly (ethylene glycol); 4 DEX, dextran; 5 FM, fluorescence microscopy; 6 Amy-PNIPAAm, Poly(N-isopropylacrylamide; 7 BSA-PNIPAAm, bovine serum albumin-Poly(N-isopropylacrylamide; 8 OM, optical microscopy; 9 CM, confocal microscopy.

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