Plasmid DNA partitioning and separation using poly(ethylene glycol)/poly(acrylate)/salt aqueous two-phase systems

Aqueous two-phase systems - versatile and advanced (bio)process engineering tools

Aqueous two-phase systems (ATPS), also known as Aqueous Biphasic Systems (ABS), have been extensively studied as platforms for the separation and purification of biomolecules and other valuable compounds. These liquid-liquid extraction (LLE) systems have been a tool for biotechnology since its origin (Albertsson, 1950's), recently expanding to exciting fields such as health, biomedicine and material sciences. Due to their biocompatibility, amenability, flexibility, and versatility, ATPS have been applied across various research areas, addressing many challenges associated with conventional methodologies. In this feature article, we first discuss the fundamentals of ATPS and the molecular mechanisms that govern their formation and are crucial for their application. We then explore the most prominent and innovative applications of these systems in downstream processing. Additionally, we provide insights into the design of in situ upstream-downstream integrated platforms, and their use as pre-treatment and analytical tools. The latest advancements in ATPS applications within disruptive bioengineering and biotechnology fields are presented, along with their pioneering use in emerging scientific areas, such as the formation of all-aqueous (water-in-water) emulsions, microfluidic systems, and membrane-free batteries. Overall, this work underscores the transformative potential of ATPS in various branches of science, pinpointing directions for future research to fully explore and maximize ATPS capabilities, overcome existing hurdles, and drive innovation forward.

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.

Confinement of Suspension-Cultured Cells in Polyethylene Glycol/Polyethylene Oxide-Albumin Aqueous Two-Phase Systems

Aqueous two-phase systems (ATPSs) have numerous applications in separation science, and more recently, in bioassays enabled by the solution micropatterning of cells. The most frequently used ATPS in these applications is the polyethylene glycol (PEG)-dextran (Dex) system, as the polymers that form this ATPS have been extensively characterized in terms of their physicochemical properties. However, in addition to this well-known system, there exist many other ATPSs with properties that may be exploited to improve upon the PEG-dextran system for specific applications. One of these underexplored systems is the ATPS formed from PEG/polyethylene oxide (PEO) and albumin. In this article, we characterize the phase separation of PEG (35 kDa) and polyethylene oxide (PEO) (200, 900, and 4,000 kDa) with bovine serum albumin (BSA). We describe the microscopic emulsion behavior of these systems in the presence of NaCl and compounds (NaHCO3, NaH2PO4, and HEPES) commonly used in buffer solutions and cell culture media. We further demonstrate that PEG- and PEO-albumin systems can be used in place of the PEG-dextran system for confinement of suspension-cultured cells (Jurkat T cells and RPMI-8226 B cells). Cell viability and morphology are examined for various polymer formulations relative to the commonly used PEG 35 kDa-Dex 500 kDa system and polymer-free cell culture medium. In addition, we examine cell activation for various phase-separating medium components by measuring IL-2 and IL-6 secretion. We demonstrate that we can confine immune cells and cytokines in the PEG-BSA system, and that this system can be employed to screen immune responses by enzyme-linked immunospot (ELISpot) assay. This new system represents a promising ATPS formulation for applications where low levels of baseline cell activation are required, for instance, when culturing immune cells.

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.

Emerging Biotechnology Applications of Aqueous Two-Phase Systems

Liquid-liquid phase separation between aqueous solutions containing two incompatible polymers, a polymer and a salt, or a polymer and a surfactant, has been exploited for a wide variety of biotechnology applications throughout the years. While many applications for aqueous two-phase systems fall within the realm of separation science, the ability to partition many different materials within these systems, coupled with recent advances in materials science and liquid handling, has allowed bioengineers to imagine new applications. This progress report provides an overview of the history and key properties of aqueous two-phase systems to lend context to how these materials have progressed to modern applications such as cellular micropatterning and bioprinting, high-throughput 3D tissue assembly, microscale biomolecular assay development, facilitation of cell separation and microcapsule production using microfluidic devices, and synthetic biology. Future directions and present limitations and design considerations of this adaptable and promising toolkit for biomolecule and cellular manipulation are further evaluated.

In Aqua Veritas: The Indispensable yet Mostly Ignored Role of Water in Phase Separation and Membrane-less Organelles

Despite the common practice of presenting structures of biological molecules on an empty background and the assumption that interactions between biological macromolecules take place within the inert solvent, water represents an active component of various biological processes. This Perspective addresses indispensable, yet mostly ignored, roles of water in biological liquid-liquid phase transitions and in the biogenesis of various proteinaceous membrane-less organelles. We point out that changes in the structure of water reflected in the changes in its abilities to donate and/or accept hydrogen bonds and participate in dipole-dipole and dipole-induced dipole interactions in the presence of various solutes (ranging from small molecules to synthetic polymers and biological macromolecules) might represent a driving force for the liquid-liquid phase separation, define partitioning of various solutes in formed phases, and define the exceptional ability of intrinsically disordered proteins to be engaged in the formation of proteinaceous membrane-less organelles.

Fetal hemoglobin is much less prone to DNA cleavage compared to the adult protein

Hemoglobin (Hb) is well protected inside the red blood cells (RBCs). Upon hemolysis and when free in circulation, Hb can be involved in a range of radical generating reactions and may thereby attack several different biomolecules. In this study, we have examined the potential damaging effects of cell-free Hb on plasmid DNA (pDNA). Hb induced cleavage of supercoiled pDNA (sc pDNA) which was proportional to the concentration of Hb applied. Almost 70% of sc pDNA was converted to open circular or linear DNA using 10 µM of Hb in 12 h. Hb can be present in several different forms. The oxy (HbO₂) and met forms are most reactive, while the carboxy-protein shows only low hydrolytic activity. Hemoglobin A (HbA) could easily induce complete pDNA cleavage while fetal hemoglobin (HbF) was three-fold less reactive. By inserting, a redox active cysteine residue on the surface of the alpha chain of HbF by site-directed mutagenesis, the DNA cleavage reaction was enhanced by 82%. Reactive oxygen species were not directly involved in the reaction since addition of superoxide dismutase and catalase did not prevent pDNA cleavage. The reactivity of Hb with pDNA can rather be associated with the formation of protein based radicals.

•

Hemoglobin induced plasmid DNA cleavage in the absence of hydrogen peroxide.

•

Fetal hemoglobin was three-fold less reactive compared to the adult protein on plasmid DNA.

•

Insertion of a cysteine residue in the alpha chain enhanced the DNA cleavage reaction by 82%.

•

Protein based radicals are associated with the DNA cleavage activity of hemoglobin.

Miniaturization of aqueous two-phase extraction for biological applications: From micro-tubes to microchannels

Aqueous two-phase extraction (ATPE) is a biocompatible liquid-liquid (L-L) separation technique that has been under research for several decades towards the purification of biomolecules, ranging from small metabolites to large animal cells. More recently, with the emergence of rapid-prototyping techniques for fabrication of microfluidic structures with intricate designs, ATPE gained an expanded range of applications utilizing physical phenomena occurring exclusively at the microscale. Today, research is being carried simultaneously in two different volume ranges, mL-scale (microtubes) and nL-scale (microchannels). The objective of this review is to give insight into the state of the art at both microtube and microchannel-scale and to analyze whether miniaturization is currently a competing or divergent technology in a field of applications including bioseparation, bioanalytics, enhanced fermentation processes, catalysis, high-throughput screening and physical/chemical compartmentalization. From our perspective, both approaches are worthy of investigation and, depending on the application, it is likely that either (i) one of the approaches will eventually become obsolete in particular research areas such as purification at the preparative scale or high-throughput screening applications; or (ii) both approaches will function as complementing techniques within the bioanalytics field.

Partitioning in aqueous two-phase systems: Analysis of strengths, weaknesses, opportunities and threats

For half a century aqueous two-phase systems (ATPSs) have been applied for the extraction and purification of biomolecules. In spite of their simplicity, selectivity, and relatively low cost they have not been significantly employed for industrial scale bioprocessing. Recently their ability to be readily scaled and interface easily in single-use, flexible biomanufacturing has led to industrial re-evaluation of ATPSs. The purpose of this review is to perform a SWOT analysis that includes a discussion of: (i) strengths of ATPS partitioning as an effective and simple platform for biomolecule purification; (ii) weaknesses of ATPS partitioning in regard to intrinsic problems and possible solutions; (iii) opportunities related to biotechnological challenges that ATPS partitioning may solve; and (iv) threats related to alternative techniques that may compete with ATPS in performance, economic benefits, scale up and reliability. This approach provides insight into the current status of ATPS as a bioprocessing technique and it can be concluded that most of the perceived weakness towards industrial implementation have now been largely overcome, thus paving the way for opportunities in fermentation feed clarification, integration in multi-stage operations and in single-step purification processes.

Efficient Packaging of Plasmid DNA Using a pH Sensitive Cationic Lipid for Delivery to Hepatocytes

Plasmid DNA (pDNA) is expected to be a new class of medicine for treating currently incurable diseases. To deliver these nucleic acids, we developed a liposomal delivery system we have called a multifunctional envelope-type nano device (MEND). In this report, we demonstrate that a MEND containing a pH-sensitive cationic lipid, YSK05 (YSK-MEND), efficiently delivered pDNA via systemic injection, and that its expression was highly dependent on the encapsulation state of the pDNA. In the preparation, the pH, ionic strength, and sodium chloride (NaCl) concentration of the lipid/pDNA mixture strongly affected the encapsulation efficiency of pDNA. Additionally, the transgene expression of luciferase in the liver by the injected YSK-MEND was dependent on the encapsulation state of pDNA rather than the nature of the YSK-MEND. Confocal laser scanning microscopy findings revealed that injection of the YSK-MEND led to homogenous gene expression in the liver compared to injection via the hydrodynamic tail vein (HTV). Concerning the safety of the YSK-MEND, a transient increase in the activity of liver enzymes was observed. However, no significant adverse events were observed. Taken together, the YSK-MEND represents a potentially attractive therapy for the treatment of various hepatic diseases.