Ionic liquid-based aqueous biphasic system as an alternative tool for enhanced bacterial DNA extraction

BACKGROUND

Developing an alternative and benign method for DNA extraction is imperative due to the high cost and potential harms associated with conventional techniques. Investigation of Ionic liquid (IL) as a solvent for DNA storage and stability revealed the ability of IL to assist DNA processes. IL-based aqueous biphasic system emerges as a comprehensive extraction platform capitalizing on the task-specificity of ILs and the wide applicability of ABS for biomolecule extractions. Therefore, it is beneficial to optimize an IL-based ABS specifically for DNA extraction, taking into account the fundamental interactions between the IL and DNA.

RESULTS

The primary objective was to design ABS consisting of Ammonium based ILs, and Potassium phosphate buffer as the salting-out agent for the partitioning of salmon sperm DNA. The analysis focused on optimizing biocompatible anions for the extraction. Moreover, the stability of the DNA in the IL rich phases was analysed to validate the method. The proposed process was then employed for extracting plasmid DNA from bacteria, demonstrating results comparable to those obtained with a commercially available kit. Further validation using agarose gel electrophoresis and transformation of the extracted DNA into E.coli were conducted, producing promising outcomes. Although there is room for improvement in terms of recovery of DNA and reusability of ABS, the described approach is comparable with the conventional one while being cost-effective, and showcases a noticeable and convincing link to eco-friendly processes.

SIGNIFICANCE

There is limited literature on IL-based ABS for DNA extraction, and the existing studies predominantly concentrate on systems derived from Cholinium ILs. However, their high hydrophilicity limits the choice of the second-phase forming component to polymers for the formation of ABS. Ammonium ILs efficiently form biphasic systems with various available salting-out agents, and biocompatible anions are introduced to mitigate the toxicity of the ILs.

Environmental impact assessment of dicationic ionic liquids with ammonium-phosphonium cations and amino acid anions

Progress in the development of biodegradable or biobased ionic liquids (ILs) has led to the design of green compounds for several applications. Herein, four biocompatible dicationic ionic liquids (DILs) with ammonium-phosphonium cations and amino acid anions were synthesized and investigated their environmental impact. The structures of the DILs were confirmed by spectral analyses (1H, 13C and 31P NMR). Furthermore, physicochemical properties such as density, viscosity and refractive index were determined. Water content, bromide content and solubility were thereafter determined as the parameters needed for further studies. Subsequently, their antifeedant activity towards economically important pests of grain in storage warehouses: the granary weevil, the confused flour beetle, and the khapra beetle was examined, showing the dependence on structure. Moreover, selected DILs were investigated for toxicity towards white mustard, Daphnia magna, and Artemia franciscana to specify the environmental impact. These studies were complemented by understand the biodegradation of DILs by bacterial communities derived from soil at the agricultural land. The result was DILs with limited environmental footprints that have great potential for further application studies.

Ionic Liquids in Metal, Photo-, Electro-, and (Bio) Catalysis

Ionic liquids (ILs) have unique physicochemical properties that make them advantageous for catalysis, such as low vapor pressure, non-flammability, high thermal and chemical stabilities, and the ability to enhance the activity and stability of (bio)catalysts. ILs can improve the efficiency, selectivity, and sustainability of bio(transformations) by acting as activators of enzymes, selectively dissolving substrates and products, and reducing toxicity. They can also be recycled and reused multiple times without losing their effectiveness. ILs based on imidazolium cation are preferred for structural organization aspects, with a semiorganized layer surrounding the catalyst. ILs act as a container, providing a confined space that allows modulation of electronic and geometric effects, miscibility of reactants and products, and residence time of species. ILs can stabilize ionic and radical species and control the catalytic activity of dynamic processes. Supported IL phase (SILP) derivatives and polymeric ILs (PILs) are good options for molecular engineering of greener catalytic processes. The major factors governing metal, photo-, electro-, and biocatalysts in ILs are discussed in detail based on the vast literature available over the past two and a half decades. Catalytic reactions, ranging from hydrogenation and cross-coupling to oxidations, promoted by homogeneous and heterogeneous catalysts in both single and multiphase conditions, are extensively reviewed and discussed considering the knowledge accumulated until now.

Stereoselective Reduction of Steroidal 4-Ene-3-ketones in the Presence of Biomass-Derived Ionic Liquids Leading to Biologically Important 5β-Steroids

The stereoselective reduction of the steroidal 4-ene-3-ketone moiety (enone) affords the 5β-steroid backbone that is a key structural element of biologically important neuroactive steroids. Neurosteroids have been currently studied as novel and potent central nervous system drug-like compounds for the treatment of, e.g., postpartum depression. As a green methodology, we studied the palladium-catalyzed hydrogenation of steroidal 4-ene-3-ketones in the presence of ionic liquids derived from natural carboxylic acids. The hydrogenation proceeds with improved 5β-selectivity in the presence of tetrabutylammonium carboxylates as additives compared to the exclusive use of an organic solvent. Under optimal conditions, using tetrabutylammonium d-mandelate, the reduction of testosterone led to 5β-dihydrotestosterone in high yield and stereoselectivity and no byproduct formation was observed. Moreover, the catalyst could be recycled. The presence of additional substituents on the steroid backbone showed a significant effect on the 5β-selectivity.

Evaluation of new L-amino acids triethanolammonium salts usability for controlling protease activity

Twenty new triethanolammonium amino acid salts (TEA AA) have been prepared from triethanolammonium hydroxide and L-amino acids. The physicochemical properties of TEA AA depended on the applied amino acid. Five of the synthesised salts, i.e. mono- and bis-salts of L-glutamic acid, L-aspartic acid, and TEA salt of l-glutamine were solids with melting points between 127.32 °C to 171.51 °C. The other TEA AA exhibited glass transition temperatures from -68.45 °C for TEA Ser to -6.27 °C for TEA Trp and were assigned as amino acid ionic liquids (AAILs). The TEA His was characterised by the highest thermal stability, with an average temperature of 5 % weight loss at 186.4 °C, whereas the lowest stability was determined for TEA Asp (107.5 °C). The developed salts were tested as reaction medium additives for proteolytic enzymes (papain, subtilisin, bromelain). Most AAILs showed an inhibitory effect on tested proteases but with different mechanisms related to the enzyme substrate specificity and structural diversity. The TEA Ser was the most effective competitive inhibitor (K_i = 0.24 10^-4 mol/L) for bromelain, while TEA Val uncompetitive inhibitor for papain (K_i = 0.25 10^-4 mol/L). The developed TEA AA salts exhibit potential as enzyme-controlling agents for use in industrial processes.

Thermal, chemical, electrochemical, radiolytic and biological stability of ionic liquids and deep eutectic solvents

Ionic liquids (ILs) and deep eutectic solvents (DESs) are regarded as two kinds of novel solvents with high tunability and they exist in liquid-state for a wide range of temperature....

Toward the Proactive Design of Sustainable Chemicals: Ionic Liquids as a Prime Example

The tailorable and often unique properties of ionic liquids (ILs) drive their implementation into a broad variety of seminal technologies. The modular design of ILs allows in this context a proactive selection of structures that favor environmental sustainability─ideally without compromising their technological performance. To achieve this objective, the whole life cycle must be taken into account and various aspects considered simultaneously. In this review, we discuss how the structural design of ILs affects their environmental impacts throughout all stages of their life cycles and scrutinize the available data in order to point out knowledge gaps that need further research activities. The design of more sustainable ILs starts with the selection of the most beneficial precursors and synthesis routes, takes their technical properties and application specific performance into due account, and considers its environmental fate particularly in terms of their (eco)toxicity, biotic and abiotic degradability, mobility, and bioaccumulation potential. Special emphasis is placed on reported structure-activity relationships and suggested mechanisms on a molecular level that might rationalize the empirically found design criteria.

Towards the Prediction of Antimicrobial Efficacy for Hydrogen Bonded, Self-Associating Amphiphiles

Herein we report 50 structurally related supramolecular self-associating amphiphilic (SSA) salts and related compounds. These SSAs are shown to act as antimicrobial agents, active against model Gram-positive (methicillin-resistant Staphylococcus aureus) and/or Gram-negative (Escherichia coli) bacteria of clinical interest. Through a combination of solution-state, gas-phase, solid-state and in silico measurements, we determine 14 different physicochemical parameters for each of these 50 structurally related compounds. These parameter sets are then used to identify molecular structure-physicochemical property-antimicrobial activity relationships for our model Gram-negative and Gram-positive bacteria, while simultaneously providing insight towards the elucidation of SSA mode of antimicrobial action.

Beneficial Contribution of Biosourced Ionic Liquids and Microwaves in the Michael Reaction

We developed a synthesis of chiral ionic liquids from proline and one of its derivatives. Nine chiral ionic liquids were synthesized with yields from 78% to 95%. These synthesized ionic liquids played two roles in Michael reactions, as solvents, and as basic catalysts, where the ionic phase could also be reused at least five times without loss of activity. The yields up to 99% were improved by increasing the amount of dimethylmalonate from 1.2 equivalents to 3 or 4 equivalents. Furthermore, the reaction time could be reduced from 24 h to 45 min through microwaves activation.

Controllable hydrogen bonded self-association for the formation of multifunctional antimicrobial materials

SSAs are a class of supramolecular self-associating amphiphilic salt, the anionic component of which contains a covalently bound hydrogen bond donor-acceptor motif. This results in a monomeric unit which can adopt multiple hydrogen bonding modes simultaneously. Previous investigations have shown examples of SSAs to act as antimicrobial agents against clinically relevant methicillin-resistant Staphylococcus aureus (MRSA). Herein, we report an intrinsically fluorescent SSA which can self-associate producing dimers, spherical aggregates and hydrogels dependent on solvent environment, while retaining antimicrobial activity against both model Gram-positive (MRSA) and Gram-negative (Escherichia coli) bacteria. Finally, we demonstrate the SSA supramolecular hydrogel to tolerate the inclusion of the antibiotic ampicillin, leading to the enhanced inhibition of growth with both model bacteria, and derive initial molecular structure-physicochemical property-antimicrobial activity relationships.

Protein-Rich Biomass Waste as a Resource for Future Biorefineries: State of the Art, Challenges, and Opportunities

Protein-rich biomass provides a valuable feedstock for the chemical industry. This Review describes every process step in the value chain from protein waste to chemicals. The first part deals with the physicochemical extraction of proteins from biomass, hydrolytic degradation to peptides and amino acids, and separation of amino acid mixtures. The second part provides an overview of physical and (bio)chemical technologies for the production of polymers, commodity chemicals, pharmaceuticals, and other fine chemicals. This can be achieved by incorporation of oligopeptides into polymers, or by modification and defunctionalization of amino acids, for example, their reduction to amino alcohols, decarboxylation to amines, (cyclic) amides and nitriles, deamination to (di)carboxylic acids, and synthesis of fine chemicals and ionic liquids. Bio- and chemocatalytic approaches are compared in terms of scope, efficiency, and sustainability.

Microwave-Assisted Synthesis of Some Potential Bioactive Imidazolium-Based Room-Temperature Ionic Liquids

An environmentally-friendly and easy synthesis of a series of novel functionalized imidazolium-based ionic liquids (ILs) is described under both the conventional procedure and microwave irradiation. The structures of newly synthesized room-temperature ionic liquids (RTILs) were established by different spectral analyses. All ILs (1–14) were screened for their in vitro antimicrobial activity against a panel of clinically isolated bacteria. The results of the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) showed that some of the tested ILs are very promising anti-bacterial agents especially those containing an alkyl chain with a phenyl group (most notably 1, 2, 12, and 13).

Biodiversity of soil bacteria exposed to sub-lethal concentrations of phosphonium-based ionic liquids: Effects of toxicity and biodegradation

Little is known about the effect of ionic liquids (ILs) on the structure of soil microbial communities and resulting biodiversity. Therefore, we studied the influence of six trihexyl(tetradecyl)phosphonium ILs (with either bromide or various organic anions) at sublethal concentrations on the structure of microbial community present in an urban park soil in 100-day microcosm experiments. The biodiversity decreased in all samples (Shannon's index decreased from 1.75 down to 0.74 and OTU's number decreased from 1399 down to 965) with the largest decrease observed in the microcosms spiked with ILs where biodegradation extent was higher than 80%. (i.e. [P₆₆₆₁₄][Br] and [P₆₆₆₁₄][2,4,4]). Despite this general decrease in biodiversity, which can be explained by ecotoxic effect of the ILs, the microbial community in the microcosms was enriched with Gram-negative hydrocarbon-degrading genera e.g. Sphingomonas. It is hypothesized that, in addition to toxicity, the observed decrease in biodiversity and change in the microbial community structure may be explained by the primary biodegradation of the ILs or their metabolites by the mentioned genera, which outcompeted other microorganisms unable to degrade ILs or their metabolites. Thus, the introduction of phosphonium-based ILs into soils at sub-lethal concentrations may result not only in a decrease in biodiversity due to toxic effects, but also in enrichment with ILs-degrading bacteria.

New dendritic ionic liquids (DILs) for the extraction of metallic species from water

Four dendritic ionic liquids (DILs) have been easily synthesized from 3rd generation PAMAM and PPI: PAMAM G3 NH₃⁺ Tf₂N⁻ (1), PPI G3 NH₃⁺ Tf₂N⁻ (2), PPI G3 NH₂ Me⁺ BF₄⁻ (3) and PAMAM G3 NH₂ Me⁺ BF₄⁻ (4).

Environmental Impact of Ionic Liquids: Recent Advances in (Eco)toxicology and (Bio)degradability

This Review aims to integrate the most recent and pertinent data available on the (bio)degradability and toxicity of ionic liquids for global and critical analysis and on the conscious use of these compounds on a large scale thereafter. The integrated data will enable focus on the recognition of toxicophores and on the way the community has been dealing with them, with the aim to obtain greener and safer ionic liquids. Also, an update of the most recent biotic and abiotic methods developed to overcome some of these challenging issues will be presented. The review structure aims to present a potential sequence of events that can occur upon discharging ionic liquids into the environment and the potential long-term consequences.

Using chiral ionic liquid additives to enhance asymmetric induction in a Diels–Alder reaction

A bis-oxazoline ligand has been complexed using Cu(ii) and Zn(ii) trifluoromethanesulfonate and a range of chiral ionic liquid (CIL) additives based on natural products were used as a co-catalyst for a Diels–Alder reaction.

Mandelic acid derived ionic liquids: synthesis, toxicity and biodegradability

Novel ionic liquids have been synthesised directly from the renewable resource mandelic acid and evaluated for their antimicrobial activity and biodegradability.

New biobased tetrabutylphosphonium ionic liquids: synthesis, characterization and use as a solvent or co-solvent for mild and greener Pd-catalyzed hydrogenation processes

Phosphonium-based ionic liquids with natural organic derived anions were easily prepared and showed good performance and recyclability in Pd-catalyzed hydrogenation processes at room temperature under atmospheric H₂ pressure.

Synthesis, characterization and properties of amino acid ionic liquids derived from the triaminocyclopropenium cation

Amino acid ionic liquids based on the triaminocyclopropenium cation form a variety of structural types depending on the amino acid. Dications were obtained with Lys, His, Arg, and Cys.

Coordinating Chiral Ionic Liquids: Design, Synthesis, and Application in Asymmetric Transfer Hydrogenation under Aqueous Conditions

Hydrophilic coordinating chiral ionic liquids with an amino alcohol substructure were developed and efficiently applied to the asymmetric reduction of ketones. Their careful design and adaptability to the desired reaction conditions allow for these chiral ionic liquids to be used as the sole source of chirality in a ruthenium-catalyzed transfer hydrogenation reaction of aromatic ketones. When used in this reaction system, these chiral ionic liquids afforded excellent yields and high enantioselectivities.

Biodegradation of ionic liquids – a critical review

The importance of biodegradation data as part of the design of safer chemicals is presented using ionic liquids (ILs) as a model study.

Tetrakis-imidazolium and benzimidazolium ionic liquids: a new class of biodegradable surfactants

Novel tetrakis-imidazolium and benzimidazolium ILs containing tetra-ester groups with incorporated quadruple side chains were synthesized successfully as degradable surfactants of expected medical and industrial applications.

An unexpected increase of toxicity of amino acid-containing ionic liquids

The influence of the structure of cations and anions on the biological activity of ionic liquids is addressed.

Dual functionalized task specific ionic liquid promoted in situ generation of palladium nanoparticles in water: synergic catalytic system for Suzuki–Miyaura cross coupling

A new task specific ionic liquid with hydroxyl and prolinate functionalities acts as a reducing agent and serves as a ligand and stabilizer for in situ formed palladium nanoparticles. This system displays high catalytic activity for Suzuki–Miyaura cross-coupling in water.