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

Versatile DNA extraction from diverse plant taxa using ionic liquids and magnetic ionic liquids: a methodological breakthrough for enhanced sample utility

BACKGROUND

There is a growing demand for fast and reliable plant biomolecular analyses. DNA extraction is the major bottleneck in plant nucleic acid-based applications especially due to the complexity of tissues in different plant species. Conventional methods for plant cell lysis and DNA extraction typically require extensive sample preparation processes and large quantities of sample and chemicals, elevated temperatures, and multiple sample transfer steps which pose challenges for high throughput applications.

RESULTS

In a prior investigation, an ionic liquid (IL)-based modified vortex-assisted matrix solid phase dispersion approach was developed using the model plant, Arabidopsis thaliana (L.) Heynh. Building upon this foundational study, the present study established a simple, rapid and efficient protocol for DNA extraction from milligram fragments of plant tissue representing a diverse range of taxa from the plant Tree of Life including 13 dicots and 4 monocots. Notably, the approach was successful in extracting DNA from a century old herbarium sample. The isolated DNA was of sufficient quality and quantity for sensitive molecular analyses such as qPCR. Two plant DNA barcoding markers, the plastid rbcL and nuclear ribosomal internal transcribed spacer (nrITS) regions were selected for DNA amplification and Sanger sequencing was conducted on PCR products of a representative dicot and monocot species. Successful qPCR amplification of the extracted DNA up to 3 weeks demonstrated that the DNA extracted using this approach remains stable at room temperature for an extended time period prior to downstream analysis.

CONCLUSIONS

The method presented here is a rapid and simple approach enabling cell lysis and DNA extraction from 1.5 mg of plant tissue across a broad range of plant taxa. Additional purification prior to DNA amplification is not required due to the compatibility of the extraction solvents with qPCR. The method has tremendous potential for applications in plant biology that require DNA, including barcoding methods for agriculture, conservation, ecology, evolution, and forensics.

Combined ionic liquid and supercritical carbon dioxide based dynamic extraction of six cannabinoids from Cannabis sativa L

The potential of supercritical CO2 and ionic liquids (ILs) as alternatives to traditional extraction of natural compounds from plant material is of increasing importance. Both techniques offer several advantages over conventional extraction methods. These two alternatives have been separately employed on numerous ocassions, however, until now, they have never been combined for the extraction of secondary metabolites from natural sources, despite properties that complement each other perfectly. Herein, we present the first application of an IL-based dynamic supercritical CO2 extraction of six cannabinoids (CBD, CBDA, Δ9-THC, THCA, CBG and CBGA) from industrial hemp (Cannabis sativa L.). Various process parameters were optimized, i.e., IL-based pre-treatment time and pre-treatment temperature, as well as pressure and temperature during supercritical fluid extraction. In addition, the impact of different ILs on cannabinoid extraction yield was evaluated, namely, 1-ethyl-3-methylimidazolium acetate, choline acetate and 1-ethyl-3-methylimidazolium dimethylphosphate. This novel technique exhibits a synergistic effect that allows the solvent-free acquisition of cannabinoids from industrial hemp, avoiding further processing steps and the additional use of resources. The newly developed IL-based supercritical CO2 extraction results in high yields of the investigated cannabinoids, thus, demonstrating an effective and reliable alternative to established extraction methods. Ultimately, the ILs can be recycled to reduce costs and to improve the sustainability of the developed extraction process.

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.

Simple lysis of bacterial cells for DNA-based diagnostics using hydrophilic ionic liquids

The extraction of nucleic acids from microorganisms for subsequent molecular diagnostic applications is still a tedious and time-consuming procedure. We developed a method for the rapid preparation of genomic DNA from bacteria based on hydrophilic ionic liquids (ILs). First, we tested eight ILs in different buffer systems for their inhibitory effects on quantitative PCR. The cell lysis potential of different IL/buffer combinations was assessed by application on Enterococcus faecalis as a model organism for Gram-positive bacteria. The two best ILs, choline hexanoate and 1-ethyl-3-methylimidazolium acetate, were compared with the reference enzymatic method and two commercial DNA extraction kits. All methods were evaluated on four Gram-positive and four Gram-negative bacterial species that are highly relevant for environmental, food, or clinical diagnostics. In comparison to the reference method, extraction yields of the IL-based procedure were within one order of magnitude for most of the strains. The final protocol for DNA extraction using the two ILs is very low-cost, avoids the use of hazardous chemicals and can be performed in five minutes on a simple heating block. This makes the method ideal for high sample throughput and offers the opportunity for DNA extraction from bacteria in resource-limited settings or even in the field.

Arabidopsis thaliana ITS sequence-specific DNA extraction by ion-tagged oligonucleotides coupled with a magnetic ionic liquid

This study reports a follow-up investigation on the capture of specific DNA sequences using ion-tagged oligonucleotides (ITOs) and magnetic ionic liquids (MIL). Five allylimidazolium salts bearing octyl substituents ([AOIM⁺]-ITOs) were used for the selective extraction of the internal transcribed spacer region (ITS) from Arabidopsis thaliana. In this work, the ability of the [AOIM⁺]-ITOs to enhance the extraction of longer target sequences (~ 700 bp) of plant origin was shown. Moreover, the independence of the probe binding position and the importance of complementarity to the target region for the extraction performance were demonstrated. To test the specificity of the ITOs, the same experiments were performed using the ITS region from another plant species, with a lower target capture for the probes which were specific for the A. thaliana sequence. Finally, extraction in the presence of interferences (heterogenous DNA, primary and secondary metabolites, proteins) provided interesting and insightful results. This work illustrates the feasibility and versatility of these probes when coupled to MILs for rapid, cost-effective, and environmentally sensitive sample preparation in the extraction of specific target sequences from different origins. Graphical abstract.

Development of an innovative and sustainable one-step method for rapid plant DNA isolation for targeted PCR using magnetic ionic liquids

BACKGROUND

Nowadays, there is an increasing demand for fast and reliable plant biomolecular analyses. Conventional methods for the isolation of nucleic acids are time-consuming and require multiple and often non-automatable steps to remove cellular interferences, with consequence that sample preparation is the major bottleneck in the bioanalytical workflow. New opportunities have been created by the use of magnetic ionic liquids (MILs) thanks to their affinity for nucleic acids.

RESULTS

In the present study, a MIL-based magnet-assisted dispersive liquid-liquid microextraction (maDLLME) method was optimized for the extraction of genomic DNA from Arabidopsis thaliana (L.) Heynh leaves. MILs containing different metal centers were tested and the extraction method was optimized in terms of MIL volume and extraction time for purified DNA and crude lysates. The proposed approach yielded good extraction efficiency and is compatible with both quantitative analysis through fluorimetric-based detection and qualitative analysis as PCR amplification of multi and single locus genes. The protocol was successfully applied to a set of plant species and tissues.

CONCLUSIONS

The developed MIL-based maDLLME approach exhibits good enrichment of nucleic acids for extraction of template suitable for targeted PCR; it is very fast, sustainable and potentially automatable thereby representing a powerful tool for screening plants rapidly using DNA-based methods.

Challenges and perspectives in the application of isothermal DNA amplification methods for food and water analysis

Molecular diagnostic tools in the field of food and water quality analysis are becoming increasingly widespread. Usually, based on DNA amplification techniques such as polymerase chain reaction (PCR), these methods are highly sensitive and versatile but require well-equipped laboratories and trained personnel. To reduce analysis time and avoid expensive equipment, isothermal DNA amplification methods for detecting various target organisms have been developed. However, to make molecular diagnostics suitable for low-resource settings and in-field applications, it is crucial to continuously adapt the working steps associated with DNA amplification, namely sample preparation, DNA extraction, and visualization of the results. Many novel approaches have been evaluated in recent years to tackle these challenges, e.g., the use of ionic liquids for the rapid isolation of nucleic acids from organisms relevant for food and water analysis or the integration of entire analytical workflows on microfluidic chips. In any event, the future of applications in the field of isothermal amplification will probably lie in ready-to-use cartridges combined with affordable handheld devices for on-site analysis. This trend article aims to make prospective users more familiar with this technology and its potential for moving molecular diagnostics from the laboratory to the field. Graphical abstract ᅟ.

New dimensions in salt-solvent mixtures: a 4th evolution of ionic liquids

In the field of ionic liquids (ILs) it has long been of fundamental interest to examine the transition from salt-in-solvent behaviour to pure liquid-salt behaviour, in terms of structures and properties. At the same time, a variety of applications have beneficially employed IL-solvent mixtures as media that offer an optimal set of properties. Their properties in many cases can be other than as expected on the basis of simple mixing concepts. Instead, they can reflect the distinct structural and interaction changes that occur as the mixture passes through the various stages from pure coulombic medium, to "plasticised" coulombic medium, into a meso-region where distinct molecular and ionic domains can co-exist. Such domains can persist to quite a high dilution into the salt-in-solvent regime and their presence manifests itself in a number of important synergistic interaction effects in diverse areas such as membrane transport and corrosion protection. Similarly, the use of ionic liquids in synthetic processes where there is a significant volume fraction of molecular species present can produce a variety of distinct and unexpected effects. The range of these salt-solvent mixtures is considerably broader than just those based on ionic liquids, since there is only minor value in the pure salt being a liquid at the outset. In other words, the extensive families of organic and metal salts become candidates for study and use. Our perspective then is of an evolution of ionic liquids into a broader field of fundamental phenomena and applications. This can draw on an even larger family of tuneable salts that exhibit an exciting combination of properties when mixed with molecular liquids.

Valorization of olive tree leaves: Extraction of oleanolic acid using aqueous solutions of surface-active ionic liquids

The global olive oil industry annually generates approximately 750,000-1,500,000 tons of Olea europaea leaves as waste that are typically burned for energy production. Yet, this agricultural by-product is a rich source of oleanolic acid, a high value triterpenic acid with outstanding pharmaceutical and nutraceutical activities. The present study focuses on the extraction of oleanolic acid from dried O. europaea leaves using aqueous solutions of surface-active ionic liquids as alternative solvents. A number of imidazolium-based ionic liquids with variable chain length, different anions and optional side-chain functionalization was synthesized and employed in the extraction of oleanolic acid. Ionic liquids with long alkyl chains remarkably enhance the solubility of oleanolic acid in water, thus being able to compete with the solubilities afforded by molecular organic solvents, such as chloroform. Consequently, they are suitable alternatives for the solid-liquid extraction of triterpenic acids from natural matrices and provide improved extraction yields of up to 2.5 wt% oleanolic acid extracted from olive tree leaves.

A Complementary Isothermal Amplification Method to the U.S. EPA Quantitative Polymerase Chain Reaction Approach for the Detection of Enterococci in Environmental Waters

We report a novel molecular assay, based on helicase-dependent amplification (HDA), for the detection of enterococci as markers for fecal pollution in water. This isothermal assay targets the same Enterococcus 23S rRNA gene region as the existing quantitative polymerase chain reaction (qPCR) assays of U.S. Environmental Protection Agency Methods 1611 and 1609 but can be entirely performed on a simple heating block. The developed Enterococcus HDA assay successfully discriminated 15 enterococcal from 15 non-enterococcal reference strains and reliably detected 48 environmental isolates of enterococci. The limit of detection was 25 target copies per reaction, only 3 times higher than that of qPCR. The applicability of the assay was tested on 30 environmental water sample DNA extracts, simulating a gradient of fecal pollution. Despite the isothermal nature of the reaction, the HDA results were consistent with those of the qPCR reference. Given this performance, we conclude that the developed Enterococcus HDA assay has great potential as a qualitative molecular screening method for resource-limited settings when combined with compatible up- and downstream processes. This amplification strategy can pave the way for developing a new generation of rapid, low-cost, and field-deployable molecular diagnostic tools for water quality monitoring.

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.

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.

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.

Charging and aggregation of latex particles in aqueous solutions of ionic liquids: towards an extended Hofmeister series

Ion specific effects govern the aggregation of latex particles in aqueous solutions of ionic liquids.

Stability studies of ionic liquid [EMIm][NTf2] under short-term thermal exposure

Mass spectrometer coupled TG analysis was used to identify decomposition products of thermally highly stressed ionic liquids.

Dimethyl adipimidate/Thin film Sample processing (DTS); A simple, low-cost, and versatile nucleic acid extraction assay for downstream analysis

Sample processing, especially that involving nucleic acid extraction, is a prerequisite step for the isolation of high quantities of relatively pure DNA for downstream analyses in many life science and biomedical engineering studies. However, existing methods still have major problems, including labor-intensive time-consuming methods and high costs, as well as requirements for a centrifuge and the complex fabrication of filters and membranes. Here, we first report a versatile Dimethyl adipimidate/Thin film based Sample processing (DTS) procedure without the limitations of existing methods. This procedure is useful for the extraction of DNA from a variety of sources, including 6 eukaryotic cells, 6 bacteria cells, and 2 body fluids in a single step. Specifically, the DTS procedure does not require a centrifuge and has improved time efficiency (30 min), affordability, and sensitivity in downstream analysis. We validated the DTS procedure for the extraction of DNA from human body fluids, as well as confirmed that the quality and quantity of the extracted DNA were sufficient to allow robust detection of genetic and epigenetic biomarkers in downstream analysis.

Fast and efficient extraction of DNA from meat and meat derived products using aqueous ionic liquid buffer systems

We present a fast and efficient strategy for DNA extraction from meat based on aqueous-ionic liquid systems that could extract DNA in significantly higher yields compared to the pure phosphate buffer.