Selective extraction of genomic DNA from leopard cat (Prionailurus bengalensis), hairy-crowned deer (Elaphodus cephalophus) and muntjac (Muntiacus reevesi) using hydrophobic magnetic deep eutectic solvents.

Wild animals, as a vital component of our natural world, serve a crucial role in preserving ecological equilibrium and biodiversity. By delving into the genetic constitution of wild animal populations, the evolutionary history, genetic diversity, and adaptation mechanisms could be explored, thereby informing conservation strategies and safeguarding the future of these species. In order to study the genetic information of wild animals, it is necessary to extract high purity and high concentration of wild animal genomic DNA. In this work, a hydrophobic magnetic deep eutectic solvent (HMDES) based vortexed extraction was developed for the extraction of genomic DNA from leopard cat (Prionailurus bengalensis), hairy-crowned deer (Elaphodus cephalophus) and muntjac (Muntiacus reevesi) muscle tissue, respectively. Extraction conditions like the pH value, extraction time, temperature and the amount of HMDES used were optimized by single-factor experiments. Under the optimized condition, genomic DNA could be selectively extracted from the three animal tissues. The limits of detection (LOD) and limits of quantification (LOQ) of the proposed method were 2.86 ng/µL and 8.66 ng/µL, respectively. Meanwhile, the relative standard deviation (RSD) of the method precision and repeatability were 1.64 % and 5.57 % at 20 ng/µL, showing the method has good precision and repeatability. After extraction, the DNA extracted into the HMDES droplets can be quickly recovered and the HMDES can be recycled and reused. The method proposed is a fast, environmental-friendly and high efficient extraction strategy for purification and enrichment of genomic DNA from leopard cat, hairy-crowned deer and muntjac tissues.

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.

Hydrophobic magnetic deep eutectic solvent: Synthesis, properties, and application in DNA separation.

Isolating high-purity nucleic acids from complex biological samples is critical to nucleic acid analysis. In the current work, four hydrophobic magnetic deep eutectic solvents (HMDESs) were firstly designed and prepared for the extraction of DNA. The conformations of the HMDESs were simulated and H-bonding interactions in the HMDESs were investigated by density functional theory (DFT) calculation. Characterization of HMDESs' physical (magnetism, density, viscosity and hydrophobicity), and thermal (melting point and decomposition temperature) properties were conducted. Single stranded DNA (ssDNA), double stranded DNA (dsDNA) and DNA sodium salts (stDNA) that were extracted by HMDESs could be quickly collected by an external magnet. Three auxiliary extraction methods, including vortex auxiliary extraction, mechanical shaking auxiliary extraction and ultrasonic auxiliary extraction, were introduced to extract DNA with HMDESs and the extraction efficiencies were evaluated using NanoDrop. Factors that could impact the DNA extraction process, such as HMDESs volume, temperature, time, and pH, were systematically investigated via single-factor experimental analysis. The proposed extraction method can successfully extract DNA from complex matrices and E. coli cell lysate. The DNA extracted by using HMDESs are well suitable for PCR amplifications. The interaction and corresponding binding sites between HMDESs and DNA were investigated by FT-IR and DFT calculation. The extraction mechanisms were discussed: hydrophobic interaction and electrostatic interaction are two main forces driving DNA extraction by HMDESs.

Synthesis of low-viscosity hydrophobic magnetic deep eutectic solvent: Selective extraction of DNA.

Fast extraction of high-purity nucleic acid from complex biological sample is the key to downstream nucleic acid analysis. In this work, two low-viscosity hydrophobic magnetic deep eutectic solvents (HMDESs) were synthesized for the selective extraction of DNA. The conformation of the HMDES was simulated by density functional theory (DFT) calculation. Characterization of HMDESs' physical (magnetism, density, viscosity, and hydrophobicity) properties and thermal (melting point and decomposition temperature) properties were conducted. Based on the HMDESs, a vortex-assisted liquid-liquid micro-extraction (VALLME) DNA method was developed. Single stranded DNA that was extracted by HMDESs could be quickly collected by an external magnet. Factors that could impact the DNA extraction process, such as HMDESs volume, temperature, extraction time, and pH were systematically investigated via single-factor experimental analysis. Under the optimized condition, the proposed extraction method has been demonstrated with the extraction of DNA from a series of complex sample matrices, including metal mixture, protein mixture and E. coli cell lysate. The DNA extracted by using HMDES-based VALLME method was well suitable for PCR amplifications. After extraction, the retained DNAs could be readily recovered by simply using Britton-Robison (BR) buffer. In addition, the interaction and corresponding binding sites between HMDESs and DNA were investigated by FT-IR and DFT calculation. This work provides a new green magnetic solvent and a rapid and environmental-friendly extraction method for the enrichment of DNA and other biological macromolecules.

Restricted access supramolecular solvent based magnetic solvent bar liquid-phase microextraction for determination of non-steroidal anti-inflammatory drugs in human serum coupled with high performance liquid chromatography-tandem mass spectrometry.

A hexafluroisopropanol (HFIP)-alkanol supramolecular solvent (SUPRAS) based magnetic solvent bar (MSB) liquid-phase microextraction (LPME) method was proposed for extraction of non-steroidal anti-inflammatory drugs (NSAIDs, including ketoprofen, naproxen, indomethacin and diclofenac) in human serum. The restricted access HFIP-alkanol SUPRAS was prepared by injecting a mixture of HFIP and alkanol into water. A stainless-steel needle was inserted into a piece of hollow fiber to prepare a magnetic bar. Then the magnetic bar was dipped in SUPRAS to impregnate the wall pores of the hollow fiber, followed by placing it into the serum sample for extraction. Only 4 µL of SUPRAS was consumed per bar. The MSB not only functioned for stirring, but also played the role of extraction and magnetic separation. Under the optimal extraction conditions (seven MSBs, extraction time 33 min and stirring rate 730 rpm), which was obtained by one variable-at-a-time and response surface methodology, the novel MSB-LPME was coupled with high performance liquid chromatography-tandem mass spectrometry to determine NSAIDs in human serum. The method showed a good linear relationship (correlation coefficients ≥ 0.9939). Method limits of detection and method limits of quantitation were in the range of 0.25-0.95 µg L-1 and 0.83-3.16 µg L-1, respectively. The recoveries for the spiked human serum samples ranged from 86.8% to 125.1% with intra- and inter-day relative standard deviations less than 9.2% and 18.1%, respectively. Moreover, the method did not require a protein precipitation step, and matrix effects of 72.8%-117.7% showed little interference with mass spectrometry detection, which was due to the double cleanup provided by the restricted access property of SUPRAS and the filtration capacity of hollow fiber. The HFIP-alkanol SUPRAS-based MSB-LPME method proved to be simple, highly efficient and environment-friendly for the pretreatment of serum/plasma.

Application of magnetic solvent bar liquid-phase microextraction for determination of organophosphorus pesticides in fruit juice samples by gas chromatography mass spectrometry.

A simple, rapid and sensitive sample pretreatment technique, magnetic solvent bar liquid-phase microextraction (MSB-LPME) was developed for extracting organophosphorus pesticides from fruit juice. The analytes were extracted from the sample to the organic solvent immobilized in the fiber. The magnetic solvent bar not only can be used to stir the samples but also extract the analytes. After extraction, the analyte-adsorbed magnetic solvent bar can be readily isolated from the sample solution by a magnet, which could greatly simplify the operation and reduce the whole pretreatment time. The bar was eluted with methanol. The elute was evaporated to dryness and residue was dissolved in hexane. Several experimental parameters were investigated and optimized, including type of extraction solvent, number of magnetic solvent bar, extraction temperature, extraction time, salt concentration, stirring speed, pH and desorption conditions. The recoveries were in the range of 81.3-104.6%, and good reproducibilities were obtained with relative standard deviation below 6.1%.