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Conventional DNA sample preparation methods involve tedious sample handling steps that require numerous inhibitors of the polymerase chain reaction (PCR) and instrumentation to implement. These disadvantages limit the applicability of conventional cell lysis and DNA extraction methods in high-throughput applications, particularly in forensics and clinical laboratories. To overcome these drawbacks, a series of nine hydrophobic magnetic ionic liquids (MILs) previously shown to preconcentrate DNA were explored as cell lysis reagents. The MILs were found to lyse white blood cells from whole blood, 2-fold diluted blood, and dry blood samples while simultaneously extracting human genomic DNA. The identity of metal ion incorporated within the MIL appears to cause hemolysis while the cationic component further reduces the cell’s integrity. Over 500 pg of human genomic DNA was isolated from 50 μL of whole blood using the trioctylbenzylammonium tris(hexafluoroacetylaceto)nickelate(II) ([N8,8,8,Bz+][Ni(hfacac)3−]) MIL, and 800 pg DNA was isolated from a dry blood samples using the trihexyl(tetradecyl)phosphonium tris(phenyltrifluoroacetylaceto)nickelate(II) ([P6,6,6,14+][Ni(Phfacac)3−]) MIL following a 1-min vortex step. A rapid, one-step cell lysis and DNA extraction from blood is ideal for settings that seek high-throughput analysis while minimizing the potential for contamination.Graphical abstract

A novel microextraction method is introduced based on dispersive liquid-liquid microextraction (DLLME) in which an in situ metathesis reaction forms a water-immiscible ionic liquid (IL) that preconcentrates aromatic compounds from water followed by separation using high-performance liquid chromatography. The simultaneous extraction and metathesis reaction forming the IL-based extraction phase greatly decreases the extraction time as well as provides higher enrichment factors compared to traditional IL DLLME and direct immersion single-drop microextraction methods. The effects of various experimental parameters including type of extraction solvent, extraction and centrifugation times, volume of the sample solution, extraction IL and exchanging reagent, and addition of organic solvent and salt were investigated and optimized for the extraction of 13 aromatic compounds. The limits of detection for seven polycyclic aromatic hydrocarbons varied from 0.02 to 0.3 µg L⁻¹. The method reproducibility produced relative standard deviation values ranging from 3.7% to 6.9%. Four real water samples including tap water, well water, creek water, and river water were analyzed and yielded recoveries ranging from 84% to 115%. [graphic removed]

In this study, a series of magnetic ionic liquids (MILs) were investigated for the extraction and preconcentration of bacteria from aqueous samples. By dispersing small volumes (e.g., 15 μL) of MIL within an aqueous cell suspension, bacteria were rapidly extracted and isolated using a magnetic field. Of the seven hydrophobic MILs examined, the trihexyl(tetradecyl)phosphonium Ni(II) hexafluoroacetylacetonate ([P 66614 + ][Ni(hfacac) 3 − ]) MIL exhibited the greatest enrichment of viable Escherichia coli K12 when coupled with microbiological culture as the detection method. The MIL-based strategy was applied for the preconcentration of E. coli from aqueous samples to obtain enrichment factors ( E F ) as high as 44.6 in less than 10 min. The MIL extraction approach was also interfaced with polymerase chain reaction (PCR) amplification where the positive detection of E. coli was achieved with the [P 66614 + ][Co(hfacac) 3 − ], [P 66614 + ][Ni(hfacac) 3 − ], [P 66614 + ][Dy(hfacac) 4 − ], and [P 66614 + ][Nd(hfacac) 4 − ] MILs. While direct sampling of an aqueous cell suspension at a concentration of 1.68 × 10 4 colony-forming units (CFUs) mL −1 yielded no amplicon when subjected to PCR, extraction of the sample with the [P 66614 + ][Ni(hfacac) 3 − ] MIL under optimized conditions provided sufficient enrichment of E. coli for amplicon detection. Importantly, the enrichment of bacteria using the Ni(II)-, Co(II)-, and Dy(III)-based MILs was compatible with real-time quantitative PCR amplification to dramatically improve sample throughput and lower detection limits to 1.0 × 10 2 CFUs mL −1 . The MIL-based method is much faster than existing enrichment approaches that typically require 24-h cultivation times prior to detection and could potentially be applied for the preconcentration of a variety of Gram-negative bacteria from aqueous samples. Graphical abstract Magnetic ionic liquid solvents rapidly preconcentrate viable E. coli cells for unambiguous pathogen detection using microbiological culture and qPCR

Ionic liquids are a class of solvents and materials that hold great promise in bioanalytical chemistry. Task-specific ionic liquids have recently been designed for the selective extraction, separation, and detection of proteins, peptides, nucleic acids, and other physiologically relevant analytes from complex biological samples. To facilitate rapid bioanalysis, ionic liquids have been integrated in miniaturized and automated procedures. Bioanalytical separations have also benefited from the modification of nonspecific magnetic materials with ionic liquids or the implementation of ionic liquids with inherent magnetic properties. Furthermore, the direct detection of the extracted molecules in the analytical instrument has been demonstrated with structurally tuned ionic liquids and magnetic ionic liquids, providing a significant advantage in the analysis of low-abundance analytes. This article gives an overview of these advances that involve the application of ionic liquids and derivatives in bioanalysis.

Background Modern plant breeding strategies rely on the intensive use of advanced genomic tools to expedite the development of improved crop varieties. Genomic DNA extraction from crop seeds eliminates the need to grow plants in contrast to fresh leaf tissue; however, it can still be a bottleneck due to the presence of stored compounds and the complexity of the matrix. The interaction of environmentally benign choline-based ionic liquids (ILs) with DNA offers an innovative approach to enhance the quality of extracted DNA from seeds. While prior IL-based plant DNA extraction workflows have primarily supported polymerase chain reaction (PCR) and quantitative PCR-based applications, their suitability for high-throughput sequencing (HTS) remained largely unexplored. This study explores the efficacy of IL-assisted method for genomic DNA extraction from soybean ( Glycine max ) seeds, addressing the limited application of ILs in HTS. Results The optimized DNA extraction method, utilizing 25% (w/v) choline formate, enabled the recovery of high-purity DNA with abundant fragment sizes > 20 kb, suitable for downstream applications including PCR, whole genome amplification (WGA), simple sequence repeat (SSR) amplification, and high-throughput Illumina sequencing. The IL-method was benchmarked against a silica-binding method using cetyltrimethylammonium bromide (CTAB) and sodium dodecyl sulfate (SDS) as lysis agents using a commercial plant DNA extraction kit in terms of DNA yield, purity, abundant DNA fragment size distribution, and integrity. In addition, DNA isolated from this method demonstrated successful PCR amplification of markers from both the nuclear and plastid genomes and yielded > 99% whole genome coverage with Illumina (PE150) sequencing reads. Conclusions This is the first known instance of a whole genome sequence generated from DNA extracted with ILs. These findings mark a significant milestone in establishing ILs as promising alternatives to conventional methods for seed DNA extraction, with potential utility in third generation (long-read) sequencing experiments.

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.

Background Plant DNA isolation and purification is a time-consuming and laborious process relative to epithelial and viral DNA sample preparation due to the cell wall. The lysis of plant cells to free intracellular DNA normally requires high temperatures, chemical surfactants, and mechanical separation of plant tissue prior to a DNA purification step. Traditional DNA purification methods also do not aid themselves towards fieldwork due to the numerous chemical and bulky equipment requirements. Results In this study, intact plant tissue was coated by hydrophobic magnetic ionic liquids (MILs) and ionic liquids (ILs) and allowed to incubate under static conditions or dispersed in a suspension buffer to facilitate cell disruption and DNA extraction. The DNA-enriched MIL or IL was successfully integrated into the qPCR buffer without inhibiting the reaction. The two aforementioned advantages of ILs and MILs allow plant DNA sample preparation to occur in one minute or less without the aid of elevated temperatures or chemical surfactants that typically inhibit enzymatic amplification methods. MIL or IL-coated plant tissue could be successfully integrated into a qPCR assay without the need for custom enzymes or manual DNA isolation/purification steps that are required for conventional methods. Conclusions The limited amount of equipment, chemicals, and time required to disrupt plant cells while simultaneously extracting DNA using MILs makes the described procedure ideal for fieldwork and lab work in low resource environments.

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.

Four different crosslinked polymeric ionic liquid (PIL)-based sorbent coatings were evaluated in an automated direct-immersion solid-phase microextraction method (automated DI-SPME) in combination with gas chromatography (GC). The crosslinked PIL coatings were based on vinyl-alkylimidazolium- (ViC n Im-) or vinylbenzyl-alkylimidazolium- (ViBzC n Im-) IL monomers, and di-(vinylimidazolium)dodecane ((ViIm) 2 C 12 -) or di-(vinylbenzylimidazolium)dodecane ((ViBzIm) 2 C 12 -) dicationic IL crosslinkers. In addition, a PIL-based hybrid coating containing multi-walled carbon nanotubes (MWCNTs) was also studied. The studied PIL coatings were covalently attached to derivatized nitinol wires and mounted onto the Supelco assembly to ensure automation when acting as SPME coatings. Their behavior was evaluated in the determination of a group of water pollutants, after proper optimization. A comparison was carried out with three common commercial SPME fibers. It was observed that those PILs containing a benzyl group in their structures, either in the IL monomer and crosslinker (PIL–1–1) or only in the crosslinker (PIL–0–1), were the most efficient sorbents for the selected analytes. The validation of the overall automated DI-SPME-GC-flame ionization detector (FID) method gave limits of detection down to 135 μg · L −1 for p -cresol when using the PIL–1–1 and down to 270 μg · L −1 when using the PIL–0–1; despite their coating thickness: ~2 and ~5 μm, respectively. Average relative recoveries with waters were of 85 ± 14 % and 87 ± 15 % for PIL–1–1 and PIL–0–1, respectively. Precision values as relative standard deviation were always lower than 4.9 and 7.6 % (spiked level between 10 and 750 μg · L −1 , as intra-day precision). Graphical Abstract Automated DI–SPME–GC–FID using crosslinked–PILs sorbent coatings for the determination of waterpollutants

In this study, a rapid and straightforward approach based on magnetic ionic liquids (MIL) as extraction phases and dispersive liquid-liquid microextraction (DLLME) was developed to analyze the hormones estriol, 17-β-estradiol, 17-α-ethynylestradiol, and estrone in human urine samples. This is the first report of an application of manganese-based MILs compatible with HPLC to extract compounds of biological interest from urine samples. The hydrophobic MILs trihexyltetradecylphosphonium tetrachloromanganate (II) ([P6,6,6,14+]2[MnCl42−]) and aliquat tetrachloromanganate (II) ([Aliquat+]2[MnCl42−]) were employed and the optimized extraction conditions were comprised of 5 mg of MIL ([P6,6,6,14+]2[MnCl42−]), 5 μL of methanol (MeOH) as disperser solvent, and an extraction time of 90 s at sample pH 6. The analytical parameters of merit were determined under optimized conditions and very satisfactory results were achieved, with LODs of 2 ng mL−1 for all analytes, determination coefficients (R2) ranging from 0.9949 for 17-β-estradiol to 0.9998 for estrone. In addition, good results of method precision were achieved with the intraday (n = 3) varying from 4.7% for 17-β-estradiol to 19.5% for estriol (both at 5 ng mL−1) and interday precision (evaluated at 100 ng mL−1) ranging from 11.4% for estrone to 17.7% for 17-α-ethynylestradiol and analyte relative recovery evaluated in three real samples ranged from 67.5 to 115.6%. The proposed DLLME/MIL-based approach allowed for a reliable, environmentally friendly and high-throughput methodology with no need for a centrifugation step.