scholarly journals CRISPR-based DNA and RNA detection with liquid-liquid phase separation

2018 ◽  
Author(s):  
Willem Kasper Spoelstra ◽  
Jeroen M. Jacques ◽  
Franklin L. Nobrega ◽  
Anna C. Haagsma ◽  
Marileen Dogterom ◽  
...  
Keyword(s):  
Phase Separation ◽  
Nucleic Acid ◽  
Liquid Phase ◽  
Clinical Diagnostics ◽  
Liquid Phase Separation ◽  
Molecular Diagnostic ◽  
Target Sequence ◽  
Dna And Rna ◽  
Wide Range ◽  
Liquid Liquid Phase Separation

AbstractThe ability to detect specific nucleic acid sequences allows for a wide range of applications including identification of pathogens, clinical diagnostics, and genotyping. CRISPR-Cas proteins Cas12a and Cas13a are RNA-guided endonucleases that bind and cleave specific DNA and RNA sequences, respectively. After recognition of a target sequence both enzymes activate a unique, indiscriminate nucleic acid cleavage activity, which has been exploited for detection of sequence specific nucleotides using labelled reporter molecules. We here present a label-free detection approach that uses a readout based on solution turbidity caused by liquid-liquid phase separation (LLPS). Turbidity arises from coacervates of positively charged polyelectrolytes with long poly(dT) or poly(U) oligonucleotides. In the presence of a target sequence, long oligonucleotides are progressively shortened, changing the solution from turbid to transparent. We explain how oligonucleotide cleavage resolves LLPS by using a mathematical model which we validate with poly(dT) phase separation experiments. The deployment of LLPS complements CRISPR-based molecular diagnostic applications and facilitates easy and low-cost nucleotide sequence detection.

scholarly journals Liquid-liquid phase separation and viscosity within secondary organic aerosol generated from diesel fuel vapors

2019 ◽  
Author(s):  
Mijung Song ◽  
Adrian M. Maclean ◽  
Yuanzhou Huang ◽  
Natalie R. Smith ◽  
Sandra L. Blair ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Diesel Fuel ◽  
Diffusion Coefficients ◽  
Secondary Organic Aerosol ◽  
Organic Aerosol ◽  
Liquid Phase Separation ◽  
Small Diffusion ◽  
Wide Range ◽  
Liquid Liquid Phase Separation

Abstract. Information on liquid-liquid phase separation (LLPS) and viscosity (or diffusion) within secondary organic aerosol (SOA) is needed to improve predictions of particle size, mass, reactivity, and cloud nucleating properties in the atmosphere. Here we report on LLPS and viscosities within SOA generated by the photooxidation of diesel fuel vapors. Diesel fuel contains a wide range of volatile organic compounds, and SOA generated by the photooxidation of diesel fuel vapors may be a good proxy for SOA from anthropogenic emissions. In our experiments, LLPS occurred over the relative humidity (RH) range of ~ 70 % to ~ 100 %, resulting in an organic-rich outer phase and a water-rich inner phase. These results may have implications for predicting the cloud nucleating properties of anthropogenic SOA since the organic-rich outer phase can lower the kinetic barrier for activation to a cloud droplet. At ≤ 10 % RH, the viscosity was in the range of ≥ 1 × 108 Pa s, which corresponds to roughly the viscosity of tar pitch. At 38–50 % RH the viscosity was in the range of 1 × 108–3 × 105 Pa s. These measured viscosities are consistent with predictions based on oxygen to carbon elemental ratio (O : C) and molar mass as well as predictions based on the number of carbon, hydrogen, and oxygen atoms. Based on the measured viscosities and the Stokes–Einstein relation, at ≤ 10 % RH diffusion coefficients of organics within diesel fuel SOA is ≤ 5.4 × 10−17cm2 s−1 and the mixing time of organics within 200 nm diesel fuel SOA particles (τmixing) is ≳ 50 h. These small diffusion coefficients and large mixing times may be important in laboratory experiments, where SOA is often generated and studied using low RH conditions and on time scales of minutes to hours. At 38–50 % RH, the calculated organic diffusion coefficients are in the range of 5.4 × 10−17 to 1.8 × 10−13 cm2 s−1 and calculated τmixing values are in the range of ~ 0.01 h to ~ 50 h. These values provide important constraints for the physicochemical properties of anthropogenic SOA.

scholarly journals Liquid–liquid phase separation and viscosity within secondary organic aerosol generated from diesel fuel vapors

2019 ◽  
Vol 19 (19) ◽  
pp. 12515-12529 ◽  
Author(s):  
Mijung Song ◽  
Adrian M. Maclean ◽  
Yuanzhou Huang ◽  
Natalie R. Smith ◽  
Sandra L. Blair ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Diesel Fuel ◽  
Diffusion Coefficients ◽  
Secondary Organic Aerosol ◽  
Organic Aerosol ◽  
Liquid Phase Separation ◽  
Small Diffusion ◽  
Wide Range ◽  
Liquid Liquid Phase Separation

Abstract. Information on liquid–liquid phase separation (LLPS) and viscosity (or diffusion) within secondary organic aerosol (SOA) is needed to improve predictions of particle size, mass, reactivity, and cloud nucleating properties in the atmosphere. Here we report on LLPS and viscosities within SOA generated by the photooxidation of diesel fuel vapors. Diesel fuel contains a wide range of volatile organic compounds, and SOA generated by the photooxidation of diesel fuel vapors may be a good proxy for SOA from anthropogenic emissions. In our experiments, LLPS occurred over the relative humidity (RH) range of ∼70 % to ∼100 %, resulting in an organic-rich outer phase and a water-rich inner phase. These results may have implications for predicting the cloud nucleating properties of anthropogenic SOA since the presence of an organic-rich outer phase at high-RH values can lower the supersaturation with respect to water required for cloud droplet formation. At ≤10 % RH, the viscosity was ≥1×108 Pa s, which corresponds to roughly the viscosity of tar pitch. At 38 %–50 % RH, the viscosity was in the range of 1×108 to 3×105 Pa s. These measured viscosities are consistent with predictions based on oxygen to carbon elemental ratio (O:C) and molar mass as well as predictions based on the number of carbon, hydrogen, and oxygen atoms. Based on the measured viscosities and the Stokes–Einstein relation, at ≤10 % RH diffusion coefficients of organics within diesel fuel SOA is ≤5.4×10-17 cm2 s−1 and the mixing time of organics within 200 nm diesel fuel SOA particles (τmixing) is 50 h. These small diffusion coefficients and large mixing times may be important in laboratory experiments, where SOA is often generated and studied using low-RH conditions and on timescales of minutes to hours. At 38 %–50 % RH, the calculated organic diffusion coefficients are in the range of 5.4×10-17 to 1.8×10-13 cm2 s−1 and calculated τmixing values are in the range of ∼0.01 h to ∼50 h. These values provide important constraints for the physicochemical properties of anthropogenic SOA.

scholarly journals Three archetypical classes of macromolecular regulators of protein liquid–liquid phase separation

2019 ◽  
Vol 116 (39) ◽  
pp. 19474-19483 ◽  
Author(s):  
Archishman Ghosh ◽  
Konstantinos Mazarakos ◽  
Huan-Xiang Zhou
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Computational Study ◽  
Quantitative Measure ◽  
Liquid Phase Separation ◽  
Wide Range ◽  
Regulatory Effects ◽  
High Concentrations ◽  
Droplet Phase ◽  
Liquid Liquid Phase Separation

Membraneless organelles, corresponding to the droplet phase upon liquid–liquid phase separation (LLPS) of protein or protein–RNA mixtures, mediate myriad cellular functions. Cells use a variety of biochemical signals such as expression level and posttranslational modification to regulate droplet formation and dissolution, but the physical basis of the regulatory mechanisms remains ill-defined and quantitative assessment of the effects is largely lacking. Our computational study predicted that the strength of attraction by droplet-forming proteins dictates whether and how macromolecular regulators promote or suppress LLPS. We experimentally tested this prediction, using the pentamers of SH3 domains and proline-rich motifs (SH35 and PRM5) as droplet-forming proteins. Determination of the changes in phase boundary and the partition coefficients in the droplet phase over a wide range of regulator concentrations yielded both a quantitative measure and a mechanistic understanding of the regulatory effects. Three archetypical classes of regulatory effects were observed. Ficoll 70 at high concentrations indirectly promoted SH35–PRM5 LLPS, by taking up volume in the bulk phase and thereby displacing SH35 and PRM5 into the droplet phase. Lysozyme had a moderate partition coefficient and suppressed LLPS by substituting weaker attraction with SH35 for the stronger SH35–PRM5 attraction in the droplet phase. By forming even stronger attraction with PRM5, heparin at low concentrations partitioned heavily into the droplet phase and promoted LLPS. These characteristics were recapitulated by computational results of patchy particle models, validating the identification of the 3 classes of macromolecular regulators as volume-exclusion promotors, weak-attraction suppressors, and strong-attraction promotors.

scholarly journals Water uptake of subpollen aerosol particles: hygroscopic growth, CCN activation, and liquid-liquid phase separation

2020 ◽  
Author(s):  
Eugene F. Mikhailov ◽  
Mira L. Pöhlker ◽  
Kathrin Reinmuth-Selzle ◽  
Sergey S. Vlasenko ◽  
Ovid O. Krüger ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Water Uptake ◽  
Chemical Reactivity ◽  
Fine Fraction ◽  
Liquid Phase Separation ◽  
Hygroscopic Growth ◽  
Model Calculations ◽  
Wide Range ◽  
Liquid Liquid Phase Separation

Abstract. Pollen grains emitted from vegetation can release subpollen particles (SPP) that contribute to the fine fraction of atmospheric aerosols and may act as cloud condensation nuclei (CCN), ice nuclei (IN), or aeroallergens. Here, we investigate and characterize the hygroscopic growth and CCN activation of birch, pine, and rapeseed SPP. A high humidity tandem differential mobility analyzer (HHTDMA) was used to measure particle restructuring and water uptake over a wide range of relative humidity (RH) from 2 % to 99.5 %, and a continuous flow CCN counter was used for size-resolved measurements of CCN activation at supersaturations (S) in the range of 0.2 % to 1.2 %. For both, subsaturated and supersaturated conditions, effective hygroscopicity parameters κ, were obtained by Köhler model calculations. Gravimetric and chemical analyses, electron microscopy, and dynamic light scattering measurements were performed to characterize further properties of SPP from aqueous pollen extracts such as chemical composition (starch, proteins, DNA, and inorganic ions) and the hydrodynamic size distribution of water-insoluble material. All investigated SPP samples exhibited sharp increases of water uptake and κ above ~95 % RH, suggesting a liquid-liquid phase separation (LLPS). The HHTDMA measurements at RH > 95 % enable closure between the CCN activation at water vapor supersaturation and hygroscopic growth at subsaturated conditions, which is often not achieved when HTDMA measurements are performed at lower RH where the water uptake and effective hygroscopicity may be limited by the effects of LLPS. Such effects may be important not only for closure between hygroscopic growth and CCN activation but also for the chemical reactivity, allergenic potential, and related health effects of SPP.

scholarly journals Tandem RNA binding sites induce self-association of the stress granule marker protein TIA-1

2021 ◽  
Author(s):  
Fionna E Loughlin ◽  
Danella L West ◽  
Menachem J Gunzburg ◽  
Saboora Waris ◽  
Simon A Crawford ◽  
...  
Keyword(s):  
Phase Separation ◽  
Nucleic Acid ◽  
Liquid Phase ◽  
Binding Sites ◽  
Rna Binding ◽  
Liquid Phase Separation ◽  
Stress Granule ◽  
Granule Formation ◽  
Self Association ◽  
Liquid Liquid Phase Separation

Abstract TIA-1 is an RNA-binding protein that sequesters target RNA into stress granules under conditions of cellular stress. Promotion of stress granule formation by TIA-1 depends upon self-association of its prion-like domain that facilitates liquid-liquid phase separation and is thought to be enhanced via RNA binding. However, the mechanisms underlying the influence of RNA on TIA-1 self-association have not been previously demonstrated. Here we have investigated the self-associating properties of full-length TIA-1 in the presence of designed and native TIA-1 nucleic acid binding sites in vitro, monitoring phase separation, fibril formation and shape. We show that single stranded RNA and DNA induce liquid-liquid phase separation of TIA-1 in a multisite, sequence-specific manner and also efficiently promote formation of amyloid-like fibrils. Although RNA binding to a single site induces a small conformational change in TIA-1, this alone does not enhance phase separation of TIA-1. Tandem binding sites are required to enhance phase separation of TIA-1 and this is finely tuned by the protein:binding site stoichiometry rather than nucleic acid length. Native tandem TIA-1 binding sites within the 3′ UTR of p53 mRNA also efficiently enhance phase separation of TIA-1 and thus may potentially act as potent nucleation sites for stress granule assembly.

scholarly journals Structure of biomolecular condensates from dissipative particle dynamics simulations

2019 ◽  
Author(s):  
Julian C. Shillcock ◽  
Maelick Brochut ◽  
Etienne Chénais ◽  
John H. Ipsen
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Intrinsically Disordered Proteins ◽  
Liquid Phase Separation ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Wide Range ◽  
End Caps ◽  
Liquid Liquid Phase Separation

ABSTRACTPhase separation of immiscible fluids is a common phenomenon in polymer chemistry, and is recognized as an important mechanism by which cells compartmentalize their biochemical reactions. Biomolecular condensates are condensed fluid droplets in cells that form by liquid-liquid phase separation of intrinsically-disordered proteins. They have a wide range of functions and are associated with chronic neurodegenerative diseases in which they become pathologically rigid. Intrinsically-disordered proteins are conformationally flexible and possess multiple, distributed binding sites for each other or for RNA. However, it remains unclear how their material properties depend on the molecular structure of the proteins. Here we use coarse-grained simulations to explore the phase behavior and structure of a model biomolecular condensate composed of semi-flexible polymers with attractive end-caps in a good solvent. Although highly simplified, the model contains the minimal molecular features that are sufficient to observe liquid-liquid phase separation of soluble polymers. The polymers condense into a porous, three-dimensional network in which their end-caps reversibly bind at junctions. The spatial separation of connected junctions scales with the polymer backbone length as a self-avoiding random walk over a wide range of concentration with a weak affinity-dependent prefactor. By contrast, the average number of polymers that meet at the junctions depends strongly on the end-cap affinity but only weakly on the polymer length. The regularity and porosity of the condensed network suggests a mechanism for cells to regulate biomolecular condensates. Interaction sites along a protein may be turned on or off to modulate the condensate’s porosity and tune the diffusion and interaction of additional proteins.

scholarly journals Self-limited uptake of α-pinene-oxide to acidic aerosol: the effects of liquid-liquid phase separation and implications for the formation of secondary organic aerosol and organosulfates from epoxides

2013 ◽  
Vol 13 (3) ◽  
pp. 7151-7174
Author(s):  
G. T. Drozd ◽  
J. L. Woo ◽  
V. F. McNeill
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Partition Coefficients ◽  
Secondary Organic Aerosol ◽  
Organic Aerosol ◽  
Organic Content ◽  
Liquid Phase Separation ◽  
Wide Range ◽  
Acidic Sulfate ◽  
Liquid Liquid Phase Separation

Abstract. The reactive uptake of α-pinene oxide (αPO) to acidic sulfate aerosol was studied under humid conditions in order to gain insight into the effects of liquid-liquid phase separation on aerosol heterogeneous chemistry and further elucidate the formation of secondary organic aerosol and organosulfates from epoxides. A continuous flow environmental chamber was used to monitor changes in diameter of monodisperse, deliquesced, acidic sulfate particles exposed to αPO at 30 and 50% RH. In order to induce phase separation and probe potential limits to particle growth from acidic uptake, αPO was introduced over a wide range of concentrations, from 200 ppb to 5 ppm. Uptake was observed to be highly dependent on initial aerosol pH. Significant uptake of αPO to aerosol was observed with initial pH < 0. When exposed to 200 ppb αPO, aerosol with pH = −1 doubled in volume, and 6% volume growth was observed at pH = 0. Aerosol with pH = 1 showed no growth. The extreme acidity required for efficient αPO uptake suggests that this chemistry is typically not a major route to formation of aerosol mass or organosulfates in the atmosphere. Partition coefficients (Kp) ranged from 0.2–1.6 × 10−4 m3 μg−1 and were correlated to initial particle acidity and particle organic content; particles with higher organic content had lower partition coefficients. Effective uptake coefficients (γ) ranged from 0.4 to 4.7 × 10−5 and are much lower than recently reported for uptake to bulk solutions. In experiments in which αPO was added to bulk H2SO4 solutions, phase separation was observed for mass loadings similar to those observed with particles, and product distributions were dependent on acid concentration. Liquid-liquid phase separation in bulk experiments, along with our observations of decreased uptake to particles with the largest growth factors, suggest an organic coating forms upon uptake to particles, limiting reactive uptake.

scholarly journals Self-limited uptake of α-pinene oxide to acidic aerosol: the effects of liquid–liquid phase separation and implications for the formation of secondary organic aerosol and organosulfates from epoxides

2013 ◽  
Vol 13 (16) ◽  
pp. 8255-8263 ◽  
Author(s):  
G. T. Drozd ◽  
J. L. Woo ◽  
V. F. McNeill
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Partition Coefficients ◽  
Secondary Organic Aerosol ◽  
Organic Aerosol ◽  
Organic Content ◽  
Liquid Phase Separation ◽  
Wide Range ◽  
Acidic Sulfate ◽  
Liquid Liquid Phase Separation

Abstract. The reactive uptake of α-pinene oxide (αPO) to acidic sulfate aerosol was studied under humid conditions in order to gain insight into the effects of liquid–liquid phase separation on aerosol heterogeneous chemistry and to elucidate further the formation of secondary organic aerosol and organosulfates from epoxides. A continuous flow environmental chamber was used to monitor changes in diameter of monodisperse, deliquesced, acidic sulfate particles exposed to αPO at 25% and 50% RH (relative humidity). In order to induce phase separation and probe potential limits to particle growth from acidic uptake, αPO was introduced over a wide range of concentrations, from 200 ppb to 5 ppm. Uptake was observed to be highly dependent on initial aerosol pH. Significant uptake of αPO to aerosol was observed with initial pH < 0. When exposed to 200 ppb αPO, aerosol with pH = -0.5 showed 23% growth, and 6% volume growth was observed at pH = 0. Aerosol with pH = 1 showed no growth. The extreme acidity required for efficient αPO uptake suggests that this chemistry is typically not a major route to formation of aerosol mass or organosulfates in the atmosphere. Effective partition coefficients (Kp, eff) were in the range of (0.1–2) x 10-4 m3μg-1 and were correlated to initial particle acidity and particle organic content; particles with higher organic content had lower partition coefficients. Effective uptake coefficients (γeff) ranged from 0.1 to 1.1 x 10-4 and are much lower than recently reported for uptake to bulk solutions. In experiments in which αPO was added to bulk H2SO4 solutions, phase separation was observed for mass loadings similar to those observed with particles, and product distributions were dependent on acid concentration. Liquid–liquid phase separation in bulk experiments, along with our observations of decreased uptake to particles with the largest growth factors, suggests an organic coating forms upon uptake to particles, limiting reactive uptake.

Water uptake of subpollen aerosol particles: hygroscopic growth, CCN activation, and liquid-liquid phase separation

2021 ◽  
Author(s):  
Eugene Mikhailov ◽  
Mira Pöhlker ◽  
Kathrin Reinmuth-Selzle ◽  
Sergey Vlasenko ◽  
Christopher Pöhlker ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Water Uptake ◽  
Chemical Reactivity ◽  
Fine Fraction ◽  
Liquid Phase Separation ◽  
Hygroscopic Growth ◽  
Model Calculations ◽  
Wide Range ◽  
Liquid Liquid Phase Separation

&lt;p&gt;Pollen grains emitted from vegetation can release subpollen particles (SPP) that contribute to the fine fraction of atmospheric aerosols and may act as cloud condensation nuclei (CCN), ice nuclei (IN), or aeroallergens. Here, we investigate and characterize the hygroscopic growth and CCN activation of birch, pine, and rapeseed SPP. A high humidity tandem differential mobility analyzer (HHTDMA) was used to measure particle restructuring and water uptake over a wide range of relative humidity (RH) from 2 % to 99.5 %, and a continuous flow CCN counter was used for size-resolved measurements of CCN activation at supersaturations (S) in the range of 0.2 % to 1.2 %. For both subsaturated and supersaturated conditions, effective hygroscopicity parameters &amp;#1082; , were obtained by K&amp;#246;hler model calculations. Gravimetric and chemical analyses, electron microscopy, and dynamic light scattering measurements were performed to characterize further properties of SPP from aqueous pollen extracts such as chemical composition (starch, proteins, DNA, and inorganic ions) and the hydrodynamic size distribution of water-insoluble material. All investigated SPP samples exhibited a sharp increase of water uptake and k above ~95 % RH, suggesting a liquid-liquid phase separation (LLPS). The HHTDMA measurements at RH&gt; 95% enable closure between the CCN activation at water vapor supersaturation and hygroscopic growth at subsaturated conditions, which is often not achieved when HTDMA measurements are performed at lower RH where the water uptake and effective hygroscopicity may be limited by the effects of LLPS. Such effects may be important not only for closure between hygroscopic growth and CCN activation but also for the chemical reactivity, allergenic potential, and related health effects of SPP.&lt;/p&gt;&lt;p&gt;This research has been supported by the Russian Science Foundation (grant no. 18-10 17-00076) and Max Planck Society.&lt;/p&gt;

CRISPR-based DNA and RNA detection with liquid-liquid phase separation

2021 ◽  
Vol 120 (7) ◽  
pp. 1198-1209 ◽  
Author(s):  
Willem Kasper Spoelstra ◽  
Jeroen M. Jacques ◽  
Rodrigo Gonzalez-Linares ◽  
Franklin L. Nobrega ◽  
Anna C. Haagsma ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Liquid Phase Separation ◽  
Rna Detection ◽  
Dna And Rna ◽  
Liquid Liquid Phase Separation
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