Partition of plasmid DNA in polymer–salt aqueous two-phase systems

Partitioning behavior of short DNA fragments in polymer/salt aqueous two-phase systems

The development of liquid biopsy as a minimally invasive technique for tumor profiling has created a need for efficient biomarker extraction systems from body fluids. The analysis of circulating cell-free DNA (cfDNA) is especially promising, but the low amounts and high fragmentation of cfDNA found in plasma pose challenges to its isolation. While the potential of aqueous two-phase systems (ATPS) for the extraction and purification of various biomolecules has already been successfully established, there is limited literature on the applicability of these findings to short cfDNA-like fragments. This study presents the partitioning behavior of a 160 bp DNA fragment in polyethylene glycol (PEG)/salt ATPS at pH 7.4. The effect of PEG molecular weight, tie-line length, neutral salt additives, and phase volume ratio is evaluated to maximize DNA recovery. Selected ATPS containing a synthetic plasma solution spiked with human serum albumin and immunoglobulin G are tested to determine the separation of DNA fragments from the main plasma protein fraction. By adding 1.5% (w/w) NaCl to a 17.7% (w/w) PEG 400/17.3% (w/w) phosphate ATPS, 88% DNA recovery was achieved in the salt-rich bottom phase while over 99% of the protein was removed.

Water-in-water droplet microfluidics: A design manual

Droplet microfluidics is utilized in a wide range of applications in biomedicine and biology. Applications include rapid biochemical analysis, materials generation, biochemical assays, and point-of-care medicine. The integration of aqueous two-phase systems (ATPSs) into droplet microfluidic platforms has potential utility in oil-free biological and biomedical applications, namely, reducing cytotoxicity and preserving the native form and function of costly biomolecular reagents. In this review, we present a design manual for the chemist, biologist, and engineer to design experiments in the context of their biological applications using all-in-water droplet microfluidic systems. We describe the studies achievable using these systems and the corresponding fabrication and stabilization methods. With this information, readers may apply the fundamental principles and recent advancements in ATPS droplet microfluidics to their research. Finally, we propose a development roadmap of opportunities to utilize ATPS droplet microfluidics in applications that remain underexplored.

Attomolar Sensitivity in Single Biomarker Counting upon Aqueous Two-Phase Surface Enrichment

From longstanding techniques like enzyme-linked immunosorbent assay (ELISA) to modern next-generation sequencing, many of the most sensitive and specific biomarker detection assays require capture of the analyte at a surface. While surface-based assays provide advantages, including the ability to reduce background by washing away excess reagents and/or increase specificity through analyte-specific capture probes, the limited efficiency of capture from dilute solution often restricts assay sensitivity to the femtomolar-to-nanomolar range. Although assays for many nucleic acid analytes can decrease limits of detection (LODs) to the subfemtomolar range using polymerase chain reaction, such amplification may introduce biases, errors, and an increased risk of sample cross-contamination. Furthermore, many analytes cannot be amplified easily, including short nucleic acid fragments, epigenetic modifications, and proteins. To address the challenge of achieving subfemtomolar LODs in surface-based assays without amplification, we exploit an aqueous two-phase system (ATPS) to concentrate target molecules in a smaller-volume phase near the assay surface, thus increasing capture efficiency compared to passive diffusion from the original solution. We demonstrate the utility of ATPS-enhanced capture via single molecule recognition through equilibrium Poisson sampling (SiMREPS), a microscopy technique previously shown to possess >99.9999% detection specificity for DNA mutations but an LOD of only ∼1-5 fM. By combining ATPS-enhanced capture with a Förster resonance energy transfer (FRET)-based probe design for rapid data acquisition over many fields of view, we improve the LOD ∼ 300-fold to <10 aM for an EGFR exon 19 deletion mutation. We further validate this ATPS-assisted FRET-SiMREPS assay by detecting endogenous exon 19 deletion molecules in cancer patient blood plasma.

The solvent side of proteinaceous membrane-less organelles in light of aqueous two-phase systems

Water represents a common denominator for liquid-liquid phase transitions leading to the formation of the polymer-based aqueous two-phase systems (ATPSs) and a set of the proteinaceous membrane-less organelles (PMLOs). ATPSs have a broad range of biotechnological applications, whereas PMLOs play a number of crucial roles in cellular compartmentalization and often represent a cellular response to the stress. Since ATPSs and PMLOs contain high concentrations of polymers (such as polyethylene glycol (PEG), polypropylene glycol (PPG), Ucon, and polyvinylpyrrolidone (PVP), Dextran, or Ficoll) or biopolymers (peptides, proteins and nucleic acids), it is expected that the separated phases of these systems are characterized by the noticeable changes in the solvent properties of water. These changes in solvent properties can drive partitioning of various compounds (proteins, nucleic acids, organic low-molecular weight molecules, metal ions, etc.) between the phases of ATPSs or between the PMLOs and their surroundings. Although there is a sizable literature on the properties of the ATPS phases, much less is currently known about PMLOs. In this perspective article, we first represent liquid-liquid phase transitions in water, discuss different types of biphasic (or multiphasic) systems in water, and introduce various PMLOs and some of their properties. Then, some basic characteristics of polymer-based ATPSs are presented, with the major focus being on the current understanding of various properties of ATPS phases and solvent properties of water inside them. Finally, similarities and differences between the polymer-based ATPSs and biological PMLOs are discussed.

Aqueous two-phase system (ATPS): an overview and advances in its applications

Aqueous two-phase system (ATPS) is a liquid-liquid fractionation technique and has gained an interest because of great potential for the extraction, separation, purification and enrichment of proteins, membranes, viruses, enzymes, nucleic acids and other biomolecules both in industry and academia. Although, the partition behavior involved in the method is complex and difficult to predict. Current research shows that it has also been successfully used in the detection of veterinary drug residues in food, separation of precious metals, sewage treatment and a variety of other purposes. The ATPS is able to give high recovery yield and is easily to scale up. It is also very economic and environment friendly method. The aim of this review is to overview the basics of ATPS, optimization and its applications.

Affinity Partitioning-Induced Self-Assembly in Aqueous Two-Phase Systems: Templating for Polyelectrolyte Microcapsules

Affinity partitioning refers to the preferential dissolution of solute molecules in a particular liquid phase of an immiscible liquid-liquid mixture, such as an aqueous two-phase system (ATPS). Affinity partitioning in ATPS is widely used to achieve extraction and purification of biomolecules. However, the potential of applying it to direct the self-assembly of solutes into controlled structures has been largely overlooked. Here we introduce the affinity partitioning of polyelectrolytes in ATPS to induce their self-assembly into polyelectrolyte microcapsules. The approach is purely based on the preferential solubility of different polyelectrolytes in different aqueous phases; therefore it has wide applicability and exhibits excellent compatibility with bioactives. The release of encapsulated components can be triggered by changing the pH value or ionic strength of the surrounding environment. The proposed method represents an important advance in fabricating multifunctional materials and inspires new ways to engineer sophisticated structures with hydrophilic macromolecules.

A novel aqueous micellar two-phase system composed of surfactant and sorbitol for purification of pectinase enzyme from Psidium guajava and recycling phase components

A novel aqueous two-phase system composed of a surfactant and sorbitol was employed for the first time to purify pectinase from Psidium guajava. The influences of different parameters, including the type and concentration of the surfactant and the concentration and composition of the surfactant/sorbitol ratio, on the partitioning behavior and recovery of pectinase were investigated. Moreover, the effects of system pH and the crude load on purification fold and the yield of purified pectinase were studied. The experimental results indicated that the pectinase was partitioned into surfactant-rich top phase, and the impurities were partitioned into the sorbitol-rich bottom phase with the novel method involving an ATPS composed of 26% (w/w) Triton X-100 and 23% (w/w) sorbitol at 54.2% of the TLL crude load of 20% (w/w) at pH 6.0. The enzyme was successfully recovered by this method with a high purification factor of 15.2 and a yield of 98.3%, whereas the phase components were also recovered and recycled at rates above 96%. This study demonstrated that this novel ATPS method can be used as an efficient and economical alternative to the traditional ATPS for the purification and recovery of the valuable enzyme.

A novel aqueous two phase system composed of a thermo-separating polymer and an organic solvent for purification of thermo-acidic amylase enzyme from red pitaya (Hylocereus polyrhizus) peel

The purification of thermo-acidic amylase enzyme from red pitaya (Hylocereus polyrhizus) peel for the first time was investigated using a novel aqueous two-phase system (ATPS) consisting of a thermo-separating copolymer and an organic solvent. The effectiveness of different parameters such as molecular weight of the thermo-separating ethylene oxide-propylene oxide (EOPO) copolymer and type and concentration of organic solvent on the partitioning behavior of amylase was investigated. In addition, the effects of phase components, volume ratio (VR), pH and crude load of purification factor and yield of amylase were evaluated to achieve the optimum partition conditions of the enzyme. In the novel ATPS method, the enzyme was satisfactorily partitioned into the polymer-rich top phase in the system composed of 30% (w/w) EOPO 2500 and 15% (w/w) 2-propanol, at a volume ratio of 1.94 and with a crude load scale of 25% (w/w) at pH 5.0. Recovery and recycling of components was also measured in each successive step of the ATPS process. The enzyme was successfully recovered by the method with a high purification factor of 14.3 and yield of 96.6% and copolymer was also recovered and recycled at a rate above 97%, making the method was more economical than the traditional ATPS method.

Pesticide removal from aqueous solutions by adding salting out agents

Phase segregation in aqueous biphasic systems (ABS) composed of four hydrophilic ionic liquids (ILs): 1-butyl-3-methylimidazolium methylsulfate and 1-ethyl-3-methylimidazolium methylsulfate (C(n)C₁im C₁SO₄, n = 2 and 4), tributylmethyl phosphonium methylsulfate (P₄₄₄₁ C₁SO₄) and methylpyridinium methylsulfate (C₁Py C₁SO₄) and two high charge density potassium inorganic salts (K₂CO₃ and K₂HPO₄) were determined by the cloud point method at 298.15 K. The influence of the addition of the selected inorganic salts to aqueous mixtures of ILs was discussed in the light of the Hofmeister series and in terms of molar Gibbs free energy of hydration. The effect of the alkyl chain length of the cation on the methylsulfate-based ILs has been investigated. All the solubility data were satisfactorily correlated to several empirical equations. A pesticide (pentachlorophenol, PCP) extraction process based on the inorganic salt providing a greater salting out effect was tackled. The viability of the proposed process was analyzed in terms of partition coefficients and extraction efficiencies.

Novel physico-biological treatment for the remediation of textile dyes-containing industrial effluents

In this work, a novel remediation strategy consisting of a sequential biological and physical process is proposed to remove dyes from a textile polluted effluent. The decolorization ability of Anoxybacillus flavithermus in an aqueous effluent containing two representative textile finishing dyes (Reactive Black 5 and Acid Black 48, as di-azo and antraquinone class, respectively) was proved. The decolorization efficiency for a mixture of both dyes reached almost 60% in less than 12h, which points out the suitability of the selected microorganism. In a sequential stage, an aqueous biphasic system consisting of non-ionic surfactants and a potassium-based organic salt, acting as the salting out agent, was investigated. The phase segregation potential of the selected salts was evaluated in the light of different thermodynamic models, and remediation levels higher than 99% were reached.

Liquid-Liquid Equilibrium Data for the Ionic Liquid N-Ethyl-Pyridinium Bromide with Several Sodium Salts and Potassium Salts

The liquid-liquid equilibrium (LLE) data for systems containing N-ethyl-pyridinium bromide ([EPy]Br), salt (Na2HPO4,K2HPO4,K2SO4,C4O6H4KNa), and water have been measured experimentally atT=298.15 K and the formations of these four aqueous two-phase systems (ATPSs) have been discussed. Also, the effective excluded volume (EEV) values obtained from the binodal models for the four systems were determined and the salting-out abilities of different salts follow the order ofK2SO4>K2HPO4>Na2HPO4>C4O6H4KNa. The solubility data were correlated by the Merchuk and other equations while the tie-line data by the Othmer-Tobias, Bancroft, two-parameter, and Setschenow-type equations. The correlation coefficients evidenced that experimental data fitted well to all these equations. These four salts were proved successfully to form ATPSs with N-ethyl-pyridinium bromide, making a significant contribution to the further study of this kind of ATPS.

Microfluidics with aqueous two-phase systems

An overview is given about research activities in which aqueous two phase systems (ATPSs) are utilized in microfluidic setups. ATPSs consist of two immiscible aqueous phases and have traditionally been used for the separation and purification of biological material such as proteins or cells. Microfluidic implementations of such schemes are usually based on a number of co-flowing streams of immiscible phases in a microchannel, thereby replacing the standard batch by flow-through processes. Some aspects of the stability of such flow patterns and the recovery of the phases at the channel exit are reviewed. Furthermore, the diffusive mass transfer and sample partitioning between the phases are discussed, and corresponding applications are highlighted. When diffusion is superposed by an applied electric field normal to the liquid/liquid interface, the transport processes are accelerated, and under specific conditions the interface acts as a size-selective filter for molecules. Finally, the activities involving droplet microflows of ATPSs are reviewed. By either forming ATPS droplets in an organic phase or a droplet of one aqueous phase inside the other, a range of applications has been demonstrated, extending from separation/purification schemes to the patterning of surfaces covered with cells.