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Sequence-specific eDNA extraction using hydrophobic magnetic ionic liquids attached with oligonucleotide strand. Anal Chim Acta 2023; 1239:340612. [PMID: 36628697 DOI: 10.1016/j.aca.2022.340612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/09/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
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.
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González-Martín R, Lodoso-Ruiz E, Trujillo-Rodríguez MJ, Pino V. Magnetic Ionic Liquids in Analytical Microextraction: A Tutorial Review. J Chromatogr A 2022; 1685:463577. [DOI: 10.1016/j.chroma.2022.463577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 11/27/2022]
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Rapid Determination of RNA Modifications in Consensus Motifs by Nuclease Protection with Ion-Tagged Oligonucleotide Probes and Matrix-Assisted Laser Desorption Ionization Mass Spectrometry. Genes (Basel) 2022; 13:genes13061008. [PMID: 35741770 PMCID: PMC9222981 DOI: 10.3390/genes13061008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/24/2022] [Accepted: 05/31/2022] [Indexed: 12/10/2022] Open
Abstract
The reversible and substoichiometric modification of RNA has recently emerged as an additional layer of translational regulation in normal biological function and disease. Modifications are often enzymatically deposited in and removed from short (~5 nt) consensus motif sequences to carefully control the translational output of the cell. Although characterization of modification occupancy at consensus motifs can be accomplished using RNA sequencing methods, these approaches are generally time-consuming and do not directly detect post-transcriptional modifications. Here, we present a nuclease protection assay coupled with matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) to rapidly characterize modifications in consensus motifs, such as GGACU, which frequently harbor N6-methyladenosine (m6A). While conventional nuclease protection methods rely on long (~30 nt) oligonucleotide probes that preclude the global assessment of consensus motif modification stoichiometry, we investigated a series of ion-tagged oligonucleotide (ITO) probes and found that a benzylimidazolium-functionalized ITO (ABzIM-ITO) conferred significantly improved nuclease resistance for GGACU targets. After optimizing the conditions of the nuclease protection assay, we applied the ITO and MALDI-MS-based method for determining the stoichiometry of GG(m6A)CU and GGACU in RNA mixtures. Overall, the ITO-based nuclease protection and MALDI-MS method constitutes a rapid and promising approach for determining modification stoichiometries of consensus motifs.
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Emaus MN, Cagliero C, Gostel MR, Johnson G, Anderson JL. Simple and efficient isolation of plant genomic DNA using magnetic ionic liquids. PLANT METHODS 2022; 18:37. [PMID: 35321738 PMCID: PMC8943943 DOI: 10.1186/s13007-022-00860-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/17/2022] [Indexed: 06/13/2023]
Abstract
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.
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Affiliation(s)
- Miranda N. Emaus
- Department of Chemistry, Iowa State University, Ames, IA 50011 USA
| | - Cecilia Cagliero
- Dipartimento Di Scienza E Tecnologia del Farmaco, Università Degli Studi Di Torino, 10125 Turin, Italy
| | | | | | - Jared L. Anderson
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA 50011 USA
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Alves MS, Neto LCF, Scheid C, Merib J. An overview of magnetic ionic liquids: From synthetic strategies to applications in microextraction techniques. J Sep Sci 2021; 45:258-281. [PMID: 34726337 DOI: 10.1002/jssc.202100599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/24/2021] [Accepted: 10/27/2021] [Indexed: 11/06/2022]
Abstract
Remarkable progress has been achieved in the application of magnetic ionic liquids in microextraction-based procedures. These materials exhibit unique physicochemical properties of ionic liquids featuring additional responses to magnetic fields by incorporating a paramagnetic component within the chemical structure. This intriguing property can open new horizons in analytical extractions because the solvent manipulation is facilitated. Moreover, the tunable chemical structures of magnetic ionic liquids also allow for task-specific extractions that can significantly increase the method selectivity. This review aimed at providing an up-to-date overview of articles involving synthesis, physicochemical properties, and applications of magnetic ionic liquids highlighting recent developments and configurations. Moreover, a section containing critical evaluation and future trends in magnetic ionic liquid-based extractions is included.
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Affiliation(s)
- Mônica Silva Alves
- Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Luiz Carlos Ferreira Neto
- Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Camila Scheid
- Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Josias Merib
- Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
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Varona M, Eor P, Ferreira Neto LC, Merib J, Anderson JL. Metal-containing and magnetic ionic liquids in analytical extractions and gas separations. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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7
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Emaus MN, Anderson JL. Selective extraction of low-abundance BRAF V600E mutation from plasma, urine, and sputum using ion-tagged oligonucleotides and magnetic ionic liquids. Anal Bioanal Chem 2021; 414:277-286. [PMID: 33644840 DOI: 10.1007/s00216-021-03216-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Sequence-specific DNA extractions have the potential to improve the detection of low-abundance mutations from complex matrices, making them ideal for circulating tumor DNA analysis during the early stages of cancer. Ion-tagged oligonucleotides (ITOs) are oligonucleotides modified with an allylimidazolium salt via thiolene click chemistry. The allylimidazolium-based tag allows the ITO-DNA duplex to be selectively captured by a hydrophobic magnetic ionic liquid (MIL). In this study, the selectivity of the ITO-MIL method was examined by extracting low abundance of the BRAF V600E mutation-a common single-nucleotide polymorphism associated with several different cancers-from diluted human plasma, artificial urine, and diluted artificial sputum. Quantitative polymerase chain reaction (qPCR) was not able to distinguish a 9% BRAF V600E standard (50 fg·μL-1 BRAF V600E, 500 fg·μL-1 wild-type BRAF) from the 100% wild-type BRAF (50 fg·μL-1) standard. However, introducing the ITO-MIL extraction prior to qPCR allowed for samples consisting of 0.1% BRAF V600E (50 fg·μL-1 V600E BRAF, 50,000 fg·μL-1 wild-type BRAF) to be distinguished from the 100% wild-type BRAF standard. Ion-tagged oligonucleotides (ITOs) are combined with magnetic ionic liquids (MILs) to extract low-abundance BRAF V600E mutation from diluted human plasma, artificial urine, and diluted artificial sputum. The ITO-MIL extraction prior to qPCR allowed for samples consisting of 0.1% BRAF V600E to be distinguished from the 100% wild-type BRAF standard.
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Affiliation(s)
- Miranda N Emaus
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, USA
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, USA.
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Ionic liquid modification of metal-organic framework endows high selectivity for phosphoproteins adsorption. Anal Chim Acta 2021; 1147:144-154. [PMID: 33485572 DOI: 10.1016/j.aca.2020.12.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 02/02/2023]
Abstract
Zr-based metal-organic framework, UiO-66-NH2, provides favorable adsorption capacity to phosphoproteins, however, it exhibits obvious nonspecific adsorption to other proteins. In the present work, we report a facile strategy to reduce the nonspecific adsorption of nonphosphoproteins by modifying UiO-66-NH2 with imidazolium ionic liquids (ILs). With respect to bare UiO-66-NH2, the modified counterpart, UiO@IL, exhibits much improved selectivity to phosphoproteins while maintains comparable adsorption performance. The surface of UiO@IL presents a strong hydrophilicity due to the modification of ILs. Hydrophobic and electrostatic interaction between the absorbent and nonphosphoprotein is significantly reduced. In addition, the interaction between imidazole group of ILs moiety and phosphate group in phosphoprotein ensures the favorable adsorption capacity of UiO@IL for phosphoproteins. Anionic moieties of ILs, i.e., Cl-, Br-, BF4-, CF3SO3-, play negligible effect in the adsorption process. As a representative, phosphoprotein β-casein (β-ca) is selectively enriched at a mass ratio of BSA:β-ca = 100:1. UiO@IL was further applied for the selective enrichment of phosphoprotein in milk.
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Xu J, Chen D, Yang Y, Gong H, Gao W, Xiao H. A one step method for isolation of genomic DNA using multi-amino modified magnetic nanoparticles. RSC Adv 2021; 11:3324-3332. [PMID: 35424297 PMCID: PMC8693999 DOI: 10.1039/d0ra09409a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/29/2020] [Indexed: 12/29/2022] Open
Abstract
A simple and efficient approach for the rapid extraction of genomic DNA from blood using various amino-modified magnetic nanoparticles (AMNPs) has been described. The salmon sperm DNA was isolated from aqueous solution based on electrostatic interaction between the positively charged amino-groups of AMNPs and the negatively charged phosphate groups of the DNA. The results of ultraviolet-visible (UV-Vis) spectrometry showed that increasing number of amino groups on the AMNPs surface resulted in an improvement in DNA adsorption efficiency. Several variables including the extraction pH, adsorption time, ionic strength and quantity of AMNPs were optimized to achieve the best extraction efficiency with the proposed method. Acceptable adsorption efficiency of 92% and recovery of 91% were achieved using multi-amino modified MNPs (mAMNPs) with an extraction time of 10 min and an overall processing time of 30 min. The mAMNPs enabled genomic DNA capture from human whole blood, and the resulting mAMNP/DNA complexes could be directly used as templates for PCR amplification without the need for complex and time-consuming DNA elution and purification steps. Our results imply that this method can be used as an effective strategy for genomic DNA extraction and may be extended to other types of biological samples.
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Affiliation(s)
- Jia Xu
- Institute of Maternal and Child Health, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology Wuhan 430016 China
| | - Dan Chen
- Wuhan Institute for Food and Cosmetic Control Wuhan 430012 China
| | - Yuan Yang
- Institute of Maternal and Child Health, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology Wuhan 430016 China
| | - Hongjian Gong
- Institute of Maternal and Child Health, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology Wuhan 430016 China
| | - Wenqi Gao
- Institute of Maternal and Child Health, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology Wuhan 430016 China
| | - Han Xiao
- Institute of Maternal and Child Health, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology Wuhan 430016 China
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Safari M, Yamini Y. Application of magnetic nanomaterials in magnetic in-tube solid-phase microextraction. Talanta 2021; 221:121648. [PMID: 33076165 DOI: 10.1016/j.talanta.2020.121648] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022]
Abstract
Development of magnetic nanomaterials has greatly promoted the innovation of in-tube solid-phase microextraction. This review article gives an insight into recent advances in the modifications and applications of magnetic nanomaterials for in-tube solid-phase microextraction. Also, different magnetic nanomaterials which have recently been utilized as in-tube solid-phase microextraction sorbents are classified. This study shows that magnetic nanomaterials have gained significant attention owing to large specific surface area, selective absorption, and surface modification. Magnetic in-tube solid-phase microextraction has been applied for the analysis of food samples, biological, and environmental. However, for full development of magnetic in-tube SPME, effort is still needed to overcome limitations, such as mechanical stability, selectivity and low extraction efficiency. To achieve these objectives, research on magnetic in-tube SPME is mainly focused in the preparation of new extractive phases.
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Affiliation(s)
- Meysam Safari
- Department of Basic Sciences, Kermanshah University of Technology, Kermanshah, Iran
| | - Yadollah Yamini
- Department of Chemistry, Faculty of Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.
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Abdelaziz MA, Mansour FR, Danielson ND. A gadolinium-based magnetic ionic liquid for dispersive liquid-liquid microextraction. Anal Bioanal Chem 2020; 413:205-214. [PMID: 33095289 PMCID: PMC7581952 DOI: 10.1007/s00216-020-02992-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/01/2020] [Accepted: 10/06/2020] [Indexed: 11/30/2022]
Abstract
A hydrophobic gadolinium-based magnetic ionic liquid (MIL) was investigated for the first time as an extraction solvent in dispersive liquid–liquid microextraction (DLLME). The tested MIL was composed of trihexyl(tetradecyl)phosphonium cations and paramagnetic gadolinium chloride anions. The prepared MIL showed low water miscibility, reasonable viscosity, markedly high magnetic susceptibility, adequate chemical stability, low UV background, and compatibility with reversed-phase HPLC solvents. These features resulted in a more efficient extraction than the corresponding iron or manganese analogues. Accordingly, the overall method sensitivity and reproducibility were improved, and the analysis time was reduced. The applicability of the proposed MIL was examined through the microextraction of four sartan antihypertensive drugs from aqueous samples followed by reversed-phase HPLC with UV detection at 240 nm. The DLLME procedures were optimized for disperser solvent type, MIL mass, disperser solvent volume, as well as acid, base, and salt addition. The limits of quantitation (LOQs) obtained with the analysis of 1.2-mL samples after DLLME and HPLC were 80, 30, 40, and 160 ng/mL for azilsartan medoxomil, irbesartan, telmisartan, and valsartan, respectively. Correlation coefficients were greater than 0.9988 and RSD values were in the range of 2.48–4.07%. Under the optimized microextraction conditions and using a 5-mL sample volume, enrichment factors were raised from about 40 for all sartans using a 1.2-mL sample to 175, 176, 169, and 103 for azilsartan medoxomil, irbesartan, valsartan, and telmisartan, respectively. The relative extraction recoveries for the studied sartans in river water varied from 82.5 to 101.48% at a spiked concentration of 0.5 μg/mL for telmisartan and irbesartan and 1 μg/mL for azilsartan medoxomil and valsartan. Graphical abstract ![]()
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Affiliation(s)
- Mohamed A Abdelaziz
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, USA
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33511, Egypt
| | - Fotouh R Mansour
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, 31111, Egypt
- Pharmaceutical Services Center, Faculty of Pharmacy, Tanta University, Tanta, 31111, Egypt
| | - Neil D Danielson
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, USA.
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Emaus MN, Anderson JL. Allelic discrimination between circulating tumor DNA fragments enabled by a multiplex-qPCR assay containing DNA-enriched magnetic ionic liquids. Anal Chim Acta 2020; 1124:184-193. [PMID: 32534671 DOI: 10.1016/j.aca.2020.04.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/24/2020] [Accepted: 04/30/2020] [Indexed: 12/19/2022]
Abstract
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 [N8,8,8,Bz+][Ni(hfacac)3-]) and [P6,6,6,14+][Ni(Phtfacac)3-] MILs. DNA could still be preconcentrated from 2-fold diluted human plasma using the [N8,8,8,Bz+][Ni(hfacac)3-] MIL. Extractions from undiluted plasma were reproducible with the [P6,6,6,14+][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.
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Affiliation(s)
- Miranda N Emaus
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA.
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