Ionic liquids as solvents for in situ dispersive liquid–liquid microextraction of DNA

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.

Nanoconfinement of functionalized ionic liquid for enhanced adsorption and rapid sensitive detection of phenylurea herbicides in food and environmental samples

The novel ILs@CNTs was synthesized by encapsulating task-specific ionic liquids (ILs) within carbon nanotubes (CNTs) derived from ZIF-67. These hybrid materials served as multifunctional adsorbents enabling simultaneous sorptive removal, sensitive detection, molecular sieve selection, and magnetic separation. In contrast to pristine CNTs, ILs@CNTs demonstrate significantly enhanced adsorption of phenylurea herbicides (PUHs). The complex interactions between ILs@CNTs and PUHs were comprehensively analyzed using a combination of experimental results and theoretical calculations. Furthermore, a magnetic solid phase extraction-high performance liquid chromatography (MSPE-HPLC) method was developed for the determination of multiple trace PUHs in real samples. The method exhibited lower detection limits (0.02-0.03 μg L-1) and higher enrichment factors (131 < EFs < 185). Interestingly, a portable lab-in-a-syringe device was developed to facilitate rapid on-site extraction and enrichment of PUHs. Additionally, the developed methods successfully applied in river water, tea drinks, and cucumber samples, highlighting its substantial potential for rapid PUH detection.

Sequence-specific eDNA extraction using hydrophobic magnetic ionic liquids attached with oligonucleotide strand

Isolation of high-purity nucleic acids, especially sequence-specific DNA, from complex samples is critical to the downstream nucleic acid analysis. In this work, an oligonucleotide strand-attached magnetic ionic liquid (OSMIL) was designed and prepared for DNA extraction. The attached oligonucleotide strand has a sequence complementary to that of a specific DNA to be extracted. The OSMIL has good hydrophobicity and magnetic response properties. At the extraction temperature, OSMIL was in a liquid state, which was favorable for maximizing the adsorption of DNA; while at the separation temperature, OSMIL was in a solid state (with an average particle size of 897 nm) and could be attracted by an external magnet in 3s, which was favorable for the separation and recovery of DNA. The sequence-specific DNA extraction process with OSMIL is simple and fast. After extraction, the DNA-enriched OSMILs were quickly attracted and separated by an external magnetic field. The extracted DNA was evaluated by a NanoDrop (wavelength detection at 260-280 nm) and the OSMIL can be recycled and reused. The enrichment factor was 0.81. Through single-factor experimental analysis, the effects of OSMIL extraction volume, thermal excitation temperature, thermal excitation time, pH, and other factors on the DNA extraction process were systematically investigated. The RSD of repeatability experiment was 1.19% (n = 3), showing the method has good repeatability. The extraction method presented here has been shown to extract DNA with specific sequences from mixtures containing DNA of different sequences and from mixtures containing proteins, respectively. In addition, the OSMIL has been applied to extract target environmental DNA with specific sequences from different water environments with high extraction efficiency. In the long run, OSMIL has great potential for identifying existing organisms in environmental samples or exploring unknown organisms.

Hexafluoroisopropanol-based deep eutectic solvents for high-performance DNA extraction†

In this study, hexafluoroisopropanol (HFIP)-based deep eutectic solvents (DESs) were developed and used for DNA extraction from human whole blood samples for the first time. HFIP-based DESs were prepared using HFIP and choline chloride (ChCl)/tetrabutylammonium chloride/cetyltrimethylammonium bromide as the hydrogen bond donor and acceptor, respectively. The two-phase system formation was promoted with different inorganic salts as the phase-forming component. According to the strong phase separation capability and high DNA extraction efficiency, DESs consisting of HFIP/ChCl-(NH₄)₂SO₄, HFIP/ChCl-Na₂SO₄ and HFIP/ChCl-MgSO₄ were then selected for application in DNA extraction. The factors that could have impacted the DNA extraction process, including molar ratio of DES, DES addition, salt species and addition, and sample pH, were systematically investigated via single-factor experimental analysis. Furthermore, we selectively examined bovine serum albumin and RNA to assess the specificity of the HFIP-based DESs for DNA extraction. Conclusively, 93.9%, 96.7% and 99.8% DNA could be extracted using the HFIP/ChCl-(NH₄)₂SO₄, HFIP/ChCl-Na₂SO₄, and HFIP/ChCl-MgSO₄ systems, respectively. Moreover, the developed systems were successfully used to extract DNA from human whole blood with satisfactory results. The DNA secondary structure was stable after DES extraction with the electrostatic interaction between DES and DNA as the main force driving DNA adsorption by DES.

In a novel approach, hexafluoroisopropanol-based deep eutectic solvents were synthesized and utilized as an efficient alternative for extracting DNA from human whole blood.

Phenylpropyl Guanidinium Magnetic Ionic Liquid for Green and Selective Extraction of RNA

A phenylpropyl guanidinium magnetic ionic liquid (PGMIL) was designed and prepared to extract RNA from complex samples. The properties of PGMIL were characterized by a vibrating sample magnetometer, Fourier transform infrared spectrometer, thermogravimetric analyzer, transmission electron microscope, and scanning electron microscope. Through single-factor analysis, the factors affecting the RNA extraction process, such as PGMIL volume, temperature, extraction time, and pH, were systematically investigated. The ability of PGMIL to selectively extract RNA was investigated by a NanoDrop. Under the optimized conditions, the extraction efficiency of RNA can reach 81.9 ± 1.9%. The proposed extraction method has been demonstrated with the extraction of RNA from a series of complex sample matrices, including a metal ion mixture and medicinal yeast. After extraction, the retained RNA could be readily recovered by simply using Tris-HCl buffer, with a recovery rate of 68.11 ± 2.45%. Regeneration studies have shown that the extraction efficiency of PGMIL did not change significantly after using 4 times. This study provides a green, rapid, and environmental friendly extraction method for the selective extraction of RNA.

Modulation of DNAzyme Activity via Butanol Dehydration

Understanding the activity of biomolecules in cosolvent systems is important for catalysis, separation and developing biosensors. The majority of previously studied solvents are either phase separated with water or miscible with water. Butanol was recently used to extract water for the conjugation of DNA to gold nanoparticles. In this work, the effect of butanol on the activity of a few RNA-cleaving DNAzymes was studied. A 130-fold improvement in sensitivity for the Na⁺ -specific EtNa DNAzyme was observed, and butanol also improved the activity of another Na⁺ -specific DNAzyme, NaA43T by a few folds. However, when divalent metal ions were used for both EtNa and 17E DNAzymes, the activity was inhibited. A main driven force for enhanced DNAzyme activity is the concentration effect due to butanol dehydration. This study provides insights into the interplay between DNA, metal ions and organic solvents, and such an understanding might be useful for developing sensitive biosensors.

Guanidinium Hydrophobic Magnetic Ionic Liquid-Based Dispersive Droplet Extraction for the Selective Extraction of DNA

Six hydrophobic magnetic guanidinium ionic liquids (HMILs) were designed and prepared for the extraction of DNA. The physical and thermal properties of the HMILs were characterized using vibrating sample magnetometry, density meter, rotational rheometer, Karl Fischer moisture, Fourier transform infrared spectrometry, and thermogravimetric analysis. Single-stranded DNA and duplex DNA extracted by HMILs can be rapidly collected by a magnet. Three assisted extraction methods, including vortex extraction, mechanical shaking extraction, and ultrasonic extraction, were introduced to extract DNA with HMILs and the extraction efficiencies were evaluated using NanoDrop. Influencing factors of the DNA extraction were comprehensively evaluated, involving the HMIL volume, extraction time, pH, and extraction temperature. The HMIL-based extraction method can well extract DNA from complex matrices and Escherichia coli cell lysates.

Sugar-Based Ionic Liquids: Multifaceted Challenges and Intriguing Potential

Carbohydrates represent a promising option in transitioning from oil-based chemical resources to renewable ones, with the goal of developing chemistries for a sustainable future. Cellulose, hemicellulose, and largely available monosaccharides already provide useful chemical building blocks, so-called platform chemicals, such as levulinic acid and hydroxymethyl furfural, as well as solvents like cyrene or gamma-valerolactone. Therefore, there is great anticipation for novel applications involving materials and chemicals derived from sugars. In the field of ionic liquids (ILs), sugar-based ILs have been overlooked for a long time, mainly on account of their multistep demanding preparation. However, exploring new strategies for accessing sugar-based ILs, their study, and their exploitation, are attracting increasing interest. This is due to the growing concerns about the negative (eco)toxicity profile of most ILs in conjunction with their non-sustainable nature. In the present review, a literature survey concerning the development of sugar-based ILs since 2011 is presented. Their preparation strategies and thermal behavior analyses, sorted by sugar type, make up the first two sections with the intention to provide the reader with a useful guide. A final overview of the potential applications of sugar-based ILs and their future perspectives complement the present analysis.

Encapsulated Nanodroplets for Enhanced Fluorescence Detection by Nano-Extraction

Enhancement of the detection signal of fluorescence microscopy in highly diluted solutions is of great importance in chemical analysis, sensing, and bioassay applications. Surface nanodroplets with atto- to femto-liter volumes are promising tools for sensitive online detection by integrating their extremely efficient nano-extraction and optical advantages. In this paper, the development of novel basic units of nanodroplets-in-a-microdroplet by simple solvent exchange is reported. The encapsulated nanodroplets are applied for ultrasensitive and online detection in fluorescence imaging. The biphasic nature of the droplet composite enables simultaneous extraction and enrichment of both hydrophobic and hydrophilic compounds. Furthermore, the desirable lensing effect of the curved surface of the nanodroplets enhances the collection of light emitted from the fluorophore extracted in the droplets by ≈60-fold, allowing sensitive and quantitative analysis of the fluorophore using fluorescence microscopy. The results highlight the potential of encapsulated nanodroplets as a simple and innovative method of signal enhancement in chemical analysis. By integrating selective concentration, extraction, and sensitive detection, the encapsulated nanodroplets reported here may have broad applications in many chemical and biological matrices.

Allelic discrimination between circulating tumor DNA fragments enabled by a multiplex-qPCR assay containing DNA-enriched magnetic ionic liquids

Multiplex amplification of DNA can be highly valuable in circulating tumor DNA (ctDNA) analysis due to the sheer number of potential mutations. However, commercial ctDNA extraction methods struggle to preconcentrate low concentrations of DNA and require multiple sample handling steps. Recently, magnetic ionic liquids (MILs) have been used to extract DNA and were integrated with a quantitative polymerase chain reaction (qPCR). However, in previous studies, DNA could not be preconcentrated from plasma and only one fragment could be amplified per reaction. In this study, MILs were utilized as DNA extraction solvents and directly integrated into a multiplex-qPCR buffer to simultaneously amplify wild-type KRAS, G12S KRAS, and wild-type BRAF, three clinically-relevant genes whose mutation status can affect the success of anti-EGFR therapy. DNA was desorbed from the MIL solvent during a multiplex-PCR without having a significant effect on the amplification efficiency, and allelic discrimination of single-nucleotide polymorphisms could still be achieved. Enrichment factors over 35 for all three sequences were achieved from Tris buffer using the [N_8,8,8,Bz⁺][Ni(hfacac)₃^-]) and [P_6,6,6,14⁺][Ni(Phtfacac)₃^-] MILs. DNA could still be preconcentrated from 2-fold diluted human plasma using the [N_8,8,8,Bz⁺][Ni(hfacac)₃^-] MIL. Extractions from undiluted plasma were reproducible with the [P_6,6,6,14⁺][Ni(Phtfacac)₃^-] MIL although DNA was not preconcentrated with enrichment factors around 0.6 for all three fragments. Compared to commercial DNA extraction methods (i.e., silica-based spin columns and magnetic beads), the MIL-based extraction achieved higher enrichment factors in Tris buffer and plasma. The ability of the MIL-based dispersive liquid-liquid microextraction (DLLME) direct-multiplex-qPCR method to simultaneously achieve high enrichment factors of multiple DNA fragments from human plasma is highly promising in the field of ctDNA detection.

Extraction of DNA with magnetic ionic liquids using in situ dispersive liquid-liquid microextraction

A new class of magnetic ionic liquids (MILs) with metal-containing cations was applied in in situ dispersive liquid-liquid microextraction (DLLME) for the extraction of long and short double-stranded DNA. For developing the method, MILs comprised of N-substituted imidazole ligands (with butyl-, benzyl-, or octyl-groups as substituents) coordinated to different metal centers (Ni²⁺, Mn²⁺, or Co²⁺) as cations, and chloride anions were investigated. These water-soluble MILs were reacted with the bis[(trifluoromethyl)sulfonyl]imide anion during the extraction to generate a water-immiscible MIL capable of preconcentrating DNA. The feasibility of combining the extraction methodology with anion-exchange high-performance liquid chromatography with diode array detection (HPLC-DAD) or fluorescence spectroscopy was studied. The method with the Ni²⁺- and Co²⁺-based MILs was easily combined with fluorescence spectroscopy and provided a faster and more sensitive method than HPLC-DAD for the determination of DNA. In addition, the method was compared to conventional DLLME using analogous water-immiscible MILs. The developed in situ MIL-DLLME method required only 3 min for DNA extraction and yielded 1.1-1.5 times higher extraction efficiency (EFs) than the conventional MIL-DLLME method. The in situ MIL-DLLME method was also compared to the trihexyl(tetradecyl)phosphonium tris(hexafluorocetylaceto)nickelate(II) MIL, which has been used in previous DNA extraction studies. EFs of 42-99% were obtained using the new generation of MILs, whereas EFs of only 20-38% were achieved with the phosphonium MIL. This new class of MILs is simple and inexpensive to prepare. In addition, the MILs present operational advantages such as easier manipulation in comparison to hydrophobic MILs, which can have high viscosities. These MILs are a promising new class of DNA extraction solvents that can be manipulated using an external magnetic field. Graphical abstract Magnetic ionic liquids with metal-containing cations are applied in in situ dispersive liquid-liquid microextraction for the extraction of long and short double-stranded DNA.

Analysis of circulating non-coding RNAs in a non-invasive and cost-effective manner

Non-coding RNAs (ncRNAs) participate in regulation of gene expression, and are highly relevant to pathological development. They are found to be stably present in diverse body fluids, including those in the circulatory system, which can be sampled non-invasively for clinical tests. Thus, circulating ncRNAs have great potential to be disease biomarkers. However, tremendous efforts are desired to discover and utilize ncRNAs as biomarkers in clinical diagnosis, calling for technological advancement in analysis of circulating ncRNAs in biospecimens. Hence, this review summarizes the recent developments in this area, highlighting the works devoted to cancer diagnosis and prognosis. Three main directions are focused: 1) Extraction and purification of ncRNAs from body fluids; 2) Quantification of the purified circulating ncRNAs; and 3) Microfluidic platforms for integration of both steps to enable point-of-care diagnostics. These technologies have laid a solid foundation to move forward the applications of circulating ncRNAs in disease diagnosis and cure.

State-of-the-art on the technique of dispersive liquid-liquid microextraction

Dispersive liquid-liquid microextraction is a new sample pretreatment technology based on traditional liquid liquid extraction. In this paper, the application of low-toxicity extractants such as low-density extractants, auxiliary extractants, stripping agents and ionic liquids in this technology and the extraction modes such as solvent de-emulsification, suspension extractant curing, auxiliary extraction, back extraction, and ionic liquid-dispersion liquid microextraction, are summarized. In addition, the synergism of this technique with other sample preparation techniques, such as liquid-liquid extraction, solid-phase extraction, solid-phase microextraction, dispersive solid phase extraction, matrix solid-phase dispersion extraction, supercritical fluid extraction and ultrasound-assisted dispersive liquid-liquid microextraction is discussed.

In situ generation of hydrophobic magnetic ionic liquids in stir bar dispersive liquid-liquid microextraction coupled with headspace gas chromatography

For the first time, an in situ stir bar dispersive liquid-liquid microextraction approach has been developed and coupled with headspace gas chromatography-mass spectrometry for the determination of a group of organic pollutants. The method exploits a new generation of magnetic ionic liquids (MILs) that contain paramagnetic cations based on Ni²⁺ or Co²⁺ metal centers coordinated with either N-butylimidazole or N-octylimidazole ligands and chloride anions. The reactants are added to an aqueous solution containing a high field neodymium rod magnet, followed by the addition of the bis[(trifluoromethyl)sulfonyl]imide anion that promotes a metathesis reaction for the in situ generation of a hydrophobic MIL. Concurrently, a high stirring rate is maintained to exceed the magnetic field of the rod magnet and disperse the generated MIL in the sample solution. When stirring is stopped, the MIL coats the rod magnet due to its paramagnetic nature, facilitating the MIL transfer and subsequent desorption and analysis. Under optimum conditions, the method required a 2.5-18% (w/v) aqueous solution of sodium chloride, 10 mL of sample, 20 or 30 mg of MIL, the addition of a small volume of dispersive solvent, and stirring for 5-7.5 min, depending on the MIL. The method provided limits of detection (LODs) down to 10 μg L^-1, adequate reproducibility (with relative standard deviation values lower than 10% for a spiked level of 80 μg L^-1), and relative recoveries between 72.5% and 102%. Furthermore, the method was successfully applied in the analysis of tap and mineral water.

In situ formation of hydrophobic magnetic ionic liquids for dispersive liquid-liquid microextraction

A new class of magnetic ionic liquid (MIL) containing paramagnetic cations has been applied for in situ dispersive liquid-liquid microextraction in the determination of both polar and non-polar pollutants, including ultraviolet filters, polycyclic aromatic hydrocarbons, alkylphenols, a plasticizer and a preservative in aqueous samples. The MILs were based on cations containing Ni(II) metal centers coordinated with four N-alkylimidazole ligands and chloride anions. The MILs were capable of undergoing in situ metathesis reaction with the bis[(trifluoromethyl)sulfonyl]imide ([NTf₂^-]) anion during the microextraction procedure, generating a water-immiscible extraction solvent containing the preconcentrated analytes. The MIL was then isolated by magnetic separation, followed by direct analysis using reversed-phase high performance liquid chromatography with diode array detection. Among all of the studied MILs, those containing the N-butylimidazole and N-benzylimidazole ligands ([Ni(C₄IM)₄²⁺]2[Cl^-] and [Ni(BeIM)₄²⁺]2[Cl^-], respectively) exhibited the best extraction performance. The method under optimum conditions required 5 mL of sample at pH 3, 20 mg of [Ni(C₄IM)₄²⁺]2[Cl^-] or 30 mg of [Ni(BeIM)₄²⁺]2[Cl^-], 300 μL of acetone or acetonitrile as dispersive solvent (depending on the MIL), a 1:2 M ratio of MIL to [NTf₂^-], and 3 min of vortex. The developed method achieved higher extraction efficiency compared to the conventional MIL-dispersive liquid-liquid microextraction mode, with extraction efficiencies of 46.8-88.6% and 65.4-97.0% for the [Ni(C₄IM)₄²⁺]2[Cl^-] and the [Ni(BeIM)₄²⁺]2[Cl^-] MILs (at a spiked level of 81 μg L^-1), respectively, limits of detection down to 5.2 μg L^-1, and inter-day relative standard deviation lower than 16%.

Exploiting Fluorescence Spectroscopy To Identify Magnetic Ionic Liquids Suitable for the Isolation of Oligonucleotides

Magnetic ionic liquids (MILs), which incorporate paramagnetic ions, promise to minimize manual user intervention, decrease extraction times, and facilitate rapid recovery of the analyte-enriched extraction solvent. If, however, fluorescence is employed in the downstream analysis of an analyte tagged with a fluorophore, the paramagnetic ion may quench fluorescence by introducing new nonradiative processes. Thus, it is necessary to employ a paramagnetic ion that offers a compromise between possessing a high magnetic moment and not introducing new nonradiative channels. Mn(II), Fe(III), Co(II), and Ni(II) are considered in combination with phosphonium cations and anionic ligands based upon halides or hexafluoroacetylacetonate. Among the possibilities examined, MILs containing Mn(II) provide the best alternative for a model system involving DNA.

Microgels and apparatus for PAGE of nucleic acids in one or two dimensions

We describe a system for horizontal 1D or 2D PAGE comprising an apparatus and microgels. There is no buffer outside the gel, making handling and sample loading easy. Specially designed electrodes on all four sides allow 2D electrophoresis without gel rotation. Electrophoresis is completed within 20 min and sensitivity is in the subnanogram range. The system is temperature controlled for speed, denaturation of nucleic acid molecules and maintaining molecules single-stranded. The system allows characterization of structure, conformation and damage in complex nucleic acid preparations. Besides quick 1D PAGE, 2D applications include characterization of efficiency of complex molecular procedures, checking quality of biosamples and detecting DNA damage in cells and body fluids. The system should also run protein gels.

Aqueous ionic liquids in comparison with standard co-solutes : Differences and common principles in their interaction with protein and DNA structures

Ionic liquids (ILs) are versatile solvents for a broad range of biotechnological applications. Recent experimental and simulation results highlight the potential benefits of dilute ILs in aqueous solution (aqueous ILs) in order to modify protein and DNA structures systematically. In contrast to a limited number of standard co-solutes like urea, ectoine, trimethylamine-N-oxide (TMAO), or guanidinium chloride, the large amount of possible cation and anion combinations in aqueous ILs can be used to develop tailor-made stabilizers or destabilizers for specific purposes. In this review article, we highlight common principles and differences between aqueous ILs and standard co-solutes with a specific focus on their underlying macromolecular stabilization or destabilization behavior. In combination with statistical thermodynamics theories, we present an efficient framework, which is used to classify structure modification effects consistently. The crucial importance of enthalpic and entropic contributions to the free energy change upon IL-assisted macromolecular unfolding in combination with a complex destabilization mechanism is described in detail. A special focus is also set on aqueous IL-DNA interactions, for which experimental and simulation outcomes are summarized and discussed in the context of previous findings.

Ionic-Liquid-Mediated Extraction and Separation Processes for Bioactive Compounds: Past, Present, and Future Trends

Ionic liquids (ILs) have been proposed as promising media for the extraction and separation of bioactive compounds from the most diverse origins. This critical review offers a compilation on the main results achieved by the use of ionic-liquid-based processes in the extraction and separation/purification of a large range of bioactive compounds (including small organic extractable compounds from biomass, lipids, and other hydrophobic compounds, proteins, amino acids, nucleic acids, and pharmaceuticals). ILs have been studied as solvents, cosolvents, cosurfactants, electrolytes, and adjuvants, as well as used in the creation of IL-supported materials for separation purposes. The IL-based processes hitherto reported, such as IL-based solid-liquid extractions, IL-based liquid-liquid extractions, IL-modified materials, and IL-based crystallization approaches, are here reviewed and compared in terms of extraction and separation performance. The key accomplishments and future challenges to the field are discussed, with particular emphasis on the major lacunas found within the IL community dedicated to separation processes and by suggesting some steps to overcome the current limitations.

Hydrophobic ionic liquids for quantitative bacterial cell lysis with subsequent DNA quantification

DNA is one of the most frequently analyzed molecules in the life sciences. In this article we describe a simple and fast protocol for quantitative DNA isolation from bacteria based on hydrophobic ionic liquid supported cell lysis at elevated temperatures (120-150 °C) for subsequent PCR-based analysis. From a set of five hydrophobic ionic liquids, 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide was identified as the most suitable for quantitative cell lysis and DNA extraction because of limited quantitative PCR inhibition by the aqueous eluate as well as no detectable DNA uptake. The newly developed method was able to efficiently lyse Gram-negative bacterial cells, whereas Gram-positive cells were protected by their thick cell wall. The performance of the final protocol resulted in quantitative DNA extraction efficiencies for Gram-negative bacteria similar to those obtained with a commercial kit, whereas the number of handling steps, and especially the time required, was dramatically reduced. Graphical Abstract After careful evaluation of five hydrophobic ionic liquids, 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([BMPyr + ][Ntf 2- ]) was identified as the most suitable ionic liquid for quantitative cell lysis and DNA extraction. When used for Gram-negative bacteria, the protocol presented is simple and very fast and achieves DNA extraction efficiencies similar to those obtained with a commercial kit. ddH 2 O double-distilled water, qPCR quantitative PCR.

Sample Preparation for Bioanalytical and Pharmaceutical Analysis

Biological and pharmaceutical samples represent formidable challenges in sample preparation that hold important consequences for bioanalysis and genotoxic impurity quantification. This Feature will emphasize significant advances toward the development of rapid, sensitive, and selective sample preparation methods.

Extraction and Purification of DNA from Complex Biological Sample Matrices Using Solid-Phase Microextraction Coupled with Real-Time PCR

The determination of extremely small quantities of DNA from complex biological sample matrices represents a significant bottleneck in nucleic acid analysis. In this study, polymeric ionic liquid (PIL)-based solid-phase microextraction (SPME) was applied for the extraction and purification of DNA from crude bacterial cell lysate with subsequent quantification by real-time PCR (qPCR) analysis. Using an on-fiber ultraviolet initiated polymerization technique, eight different PIL sorbent coatings were generated and their DNA extraction performance evaluated using qPCR. The PIL sorbent coating featuring halide anions and carboxylic acid groups in the cationic portion exhibited superior DNA extraction capabilities when compared to the other studied PILs and a commercial polyacrylate SPME fiber. Electrostatic interactions as well as an ion-exchange mechanism were identified as the driving forces in DNA extraction by the PIL sorbents. The selectivity of the PIL sorbent coating for DNA was demonstrated in the presence of PCR inhibitors at high concentration, where a quantifiable amount of template DNA was extracted from aqueous samples containing CaCl2 and FeCl3. Furthermore, the PIL-based SPME method was successfully applied for the extraction of DNA from crude bacterial cell lysate spiked with 1 pg mL(-1) template DNA without requiring the use of organic solvents or centrifugation steps. Following PIL-based SPME of DNA from a dilute cell lysate, the qPCR amplification efficiency was determined to be 100.3%, demonstrating the feasibility of the developed method to extract high purity DNA from complex sample matrices.

Recent advances in exploiting ionic liquids for biomolecules: Solubility, stability and applications

The technological utility of biomolecules (e.g. proteins, enzymes and DNA) can be significantly enhanced by combining them with ionic liquids (ILs) - potentially attractive "green" and "designer" solvents - rather than using in conventional organic solvents or water. In recent years, ILs have been used as solvents, cosolvents, and reagents for biocatalysis, biotransformation, protein preservation and stabilization, DNA solubilization and stabilization, and other biomolecule-based applications. Using ILs can dramatically enhance the structural and chemical stability of proteins, DNA, and enzymes. This article reviews the recent technological developments of ILs in protein-, enzyme-, and DNA-based applications. We discuss the different routes to increase biomolecule stability and activity in ILs, and the design of biomolecule-friendly ILs that can dissolve biomolecules with minimum alteration to their structure. This information will be helpful to design IL-based processes in biotechnology and the biological sciences that can serve as novel and selective processes for enzymatic reactions, protein and DNA stability, and other biomolecule-based applications.

Separation of curcuminoids using ionic liquid based aqueous two-phase system coupled with in situ dispersive liquid-liquid microextraction

An aqueous two-phase extraction system (ATPS) combined with an in situ dispersive liquid-liquid microextraction (DLLME) method using imidazolium ionic liquids (ILs) for the separation of curcuminoids is developed. The influence of structure of IL, the type of metathesis reagents, and the back extraction agents on the extraction efficiency is investigated. 2.0mg of curcuminoids are extracted by an IL ATPS composed of 0.4g 1,3-diethylimidazolium iodine (EeimI), 0.6g potassium hydrogen phosphate, 1.0g water. Then the bis[(trifluoromethyl)sulfonyl]imide lithium (LiNTf2) aqueous solution is added to the EeimI-rich phase of the ATPS. The water-immiscible ionic liquids, 1,3-diethylimidazole bis[(trifluoromethyl)sulfonyl]imide (EeimNTf2), forms by the metathesis reaction. The in situ DLLME is triggered simultaneously and further purifies the curcuminoids. 92% of EeimI transforms into EeimNTf2 and thus the Eeim(+) cation is used for twice in this method. Finally, 0.1mol/L NaOH aqueous solution is used as the back extraction reagent. The curcuminoids precipitate is achieved with 93% of recovery when the aqueous solution is adjusted to pH 3.0. This ATPS-DLLME method is successfully applied to the separation of curcuminoids from Curcuma Longa (0.96±0.02% of extraction yield, a purity of >51% with respect to the total dry mass of the product).

Extraction of DNA by magnetic ionic liquids: tunable solvents for rapid and selective DNA analysis

DNA extraction represents a significant bottleneck in nucleic acid analysis. In this study, hydrophobic magnetic ionic liquids (MILs) were synthesized and employed as solvents for the rapid and efficient extraction of DNA from aqueous solution. The DNA-enriched microdroplets were manipulated by application of a magnetic field. The three MILs examined in this study exhibited unique DNA extraction capabilities when applied toward a variety of DNA samples and matrices. High extraction efficiencies were obtained for smaller single-stranded and double-stranded DNA using the benzyltrioctylammonium bromotrichloroferrate(III) ([(C8)3BnN(+)][FeCl3Br(-)]) MIL, while the dicationic 1,12-di(3-hexadecylbenzimidazolium)dodecane bis[(trifluoromethyl)sulfonyl]imide bromotrichloroferrate(III) ([(C16BnIM)2C12(2+)][NTf2(-), FeCl3Br(-)]) MIL produced higher extraction efficiencies for larger DNA molecules. The MIL-based method was also employed for the extraction of DNA from a complex matrix containing albumin, revealing a competitive extraction behavior for the trihexyl(tetradecyl)phosphonium tetrachloroferrate(III) ([P6,6,6,14(+)][FeCl4(-)]) MIL in contrast to the [(C8)3BnN(+)][FeCl3Br(-)] MIL, which resulted in significantly less coextraction of albumin. The MIL-DNA method was employed for the extraction of plasmid DNA from bacterial cell lysate. DNA of sufficient quality and quantity for polymerase chain reaction (PCR) amplification was recovered from the MIL extraction phase, demonstrating the feasibility of MIL-based DNA sample preparation prior to downstream analysis.

Active biopolymers in green non-conventional media: a sustainable tool for developing clean chemical processes

By understanding structure–function relationships of active biopolymers (e.g. enzymes and nucleic acids) in green non-conventional media, sustainable chemical processes may be developed.

Ionic liquid poly(3-n-dodecyl-1-vinylimidazolium) bromide as an adsorbent for the sorption of hemoglobin

A novel polymeric ionic liquid, poly(1-vinylimidazolium-3-n-dodecyl) bromide, exhibits selective adsorption of hemoglobin from human whole blood.

Direct extraction of genomic DNA from maize with aqueous ionic liquid buffer systems for applications in genetically modified organisms analysis

To date, the extraction of genomic DNA is considered a bottleneck in the process of genetically modified organisms (GMOs) detection. Conventional DNA isolation methods are associated with long extraction times and multiple pipetting and centrifugation steps, which makes the entire procedure not only tedious and complicated but also prone to sample cross-contamination. In recent times, ionic liquids have emerged as innovative solvents for biomass processing, due to their outstanding properties for dissolution of biomass and biopolymers. In this study, a novel, easily applicable, and time-efficient method for the direct extraction of genomic DNA from biomass based on aqueous-ionic liquid solutions was developed. The straightforward protocol relies on extraction of maize in a 10 % solution of ionic liquids in aqueous phosphate buffer for 5 min at room temperature, followed by a denaturation step at 95 °C for 10 min and a simple filtration to remove residual biopolymers. A set of 22 ionic liquids was tested in a buffer system and 1-ethyl-3-methylimidazolium dimethylphosphate, as well as the environmentally benign choline formate, were identified as ideal candidates. With this strategy, the quality of the genomic DNA extracted was significantly improved and the extraction protocol was notably simplified compared with a well-established method.

Dispersive micro-solid-phase extraction using mesoporous hybrid materials for simultaneous determination of semivolatile compounds from plant tea by ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry

This report described the use of mesoporous hybrid materials (MHM) in a dispersive micro-solid-phase extraction procedure to extract semivolatile compounds from plant tea that were then analyzed by ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry. Dihydrotanshinone I, tanshinone I, cryptotanshinone, and tanshinone IIA were selected as the model compounds, and the extraction parameters, including mesoporous concentration, extraction time, sample agitation and desorption solvents, were optimized. The interaction with the analytes and the large surface area of the MHM facilitated the adsorption of analytes. The method showed good linearity, with correlation coefficients >0.9980 in the range 0.25-100 ng/mL, and low limits of detection (0.012-0.046 pg). Finally, the recovery values were 91-103% for Danshen tea, 89-102% for Danshen, and 88-96% for tanshinone capsules. The results showed that the proposed method was suitable for the extraction and determination of tanshinones in complex samples.

A novel surface-confined glucaminium-based ionic liquid stationary phase for hydrophilic interaction/anion-exchange mixed-mode chromatography

Glucaminium-based ionic liquids are a new class of recently developed ionic liquids and prepared by functionalizing the amine group of N-methyl-d-glucamine, which renders them good hydrophilicity due to the presence of the glucose structure and charged quaternary ammonium group. In the present study, a glucaminium-based ionic liquid N,N-diallyl-N-methyl-d-glucaminium bromide was synthesized and subsequently bonded to the surface of 3-mercaptopropyl modified silica materials through "thiol-ene" click chemistry. The obtained stationary phase was characterized by elemental analysis and infrared spectroscopy, and then packed as a HPLC column. A mixture of five nucleosides was used to characterize the separation performance of the obtained column under HILIC mode and the column efficiency was determined with cytidine as the test solute, reaching 80,000plates/m. Then, the retention behavior was evaluated by investigating the effect of various chromatographic factors on retention of different types of solutes, and the results revealed that the developed surface-confined glucaminium-based ionic liquid stationary phase exhibited a hydrophilic interaction/anion-exchange mixed-mode retention mechanism. Finally, two mixtures of nucleotides and flavonoids were separated on the glucaminium-based ionic liquid column, respectively under hydrophilic interaction and hydrophilic interaction/anion-exchange mixed-mode chromatography. In conclusion, the multimodal retention capabilities of the glucaminium-based ionic liquid column could offer a wider range of retention behavior and flexible selectivity toward polar and hydrophilic compounds.