1
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Olave B. DNA nanotechnology in ionic liquids and deep eutectic solvents. Crit Rev Biotechnol 2024; 44:941-961. [PMID: 37518062 DOI: 10.1080/07388551.2023.2229950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/28/2023] [Accepted: 06/01/2023] [Indexed: 08/01/2023]
Abstract
Nucleic acids have the ability to generate advanced nanostructures in a controlled manner and can interact with target sequences or molecules with high affinity and selectivity. For this reason, they have applications in a variety of nanotechnology applications, from highly specific sensors to smart nanomachines and even in other applications such as enantioselective catalysis or drug delivery systems. However, a common disadvantage is the use of water as the ubiquitous solvent. The use of nucleic acids in non-aqueous solvents offers the opportunity to create a completely new toolbox with unprecedented degrees of freedom. Ionic liquids (ILs) and deep eutectic solvents (DESs) are the most promising alternative solvents due to their unique electrolyte and solvent roles, as well as their ability to maintain the stability and functionality of nucleic acids. This review aims to be a comprehensive, critical, and accessible evaluation of how much this goal has been achieved and what are the most critical parameters for accomplishing a breakthrough.
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Affiliation(s)
- Beñat Olave
- University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain
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2
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De Silva S, Cagliero C, Gostel MR, Johnson G, Anderson JL. Versatile DNA extraction from diverse plant taxa using ionic liquids and magnetic ionic liquids: a methodological breakthrough for enhanced sample utility. PLANT METHODS 2024; 20:91. [PMID: 38877523 PMCID: PMC11177442 DOI: 10.1186/s13007-024-01217-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/01/2024] [Indexed: 06/16/2024]
Abstract
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.
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Affiliation(s)
- Shashini De Silva
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Cecilia Cagliero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Turin, I-10125, Italy
| | - Morgan R Gostel
- Botanical Research Institute of Texas, Fort Worth, TX, 76107-3400, USA
| | | | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA.
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3
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Ren F, Fei Q, Qiu K, Zhang Y, Zhang H, Sun L. Liquid biopsy techniques and lung cancer: diagnosis, monitoring and evaluation. J Exp Clin Cancer Res 2024; 43:96. [PMID: 38561776 PMCID: PMC10985944 DOI: 10.1186/s13046-024-03026-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/24/2024] [Indexed: 04/04/2024] Open
Abstract
Lung cancer stands as the most prevalent form of cancer globally, posing a significant threat to human well-being. Due to the lack of effective and accurate early diagnostic methods, many patients are diagnosed with advanced lung cancer. Although surgical resection is still a potential means of eradicating lung cancer, patients with advanced lung cancer usually miss the best chance for surgical treatment, and even after surgical resection patients may still experience tumor recurrence. Additionally, chemotherapy, the mainstay of treatment for patients with advanced lung cancer, has the potential to be chemo-resistant, resulting in poor clinical outcomes. The emergence of liquid biopsies has garnered considerable attention owing to their noninvasive nature and the ability for continuous sampling. Technological advancements have propelled circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), extracellular vesicles (EVs), tumor metabolites, tumor-educated platelets (TEPs), and tumor-associated antigens (TAA) to the forefront as key liquid biopsy biomarkers, demonstrating intriguing and encouraging results for early diagnosis and prognostic evaluation of lung cancer. This review provides an overview of molecular biomarkers and assays utilized in liquid biopsies for lung cancer, encompassing CTCs, ctDNA, non-coding RNA (ncRNA), EVs, tumor metabolites, TAAs and TEPs. Furthermore, we expound on the practical applications of liquid biopsies, including early diagnosis, treatment response monitoring, prognostic evaluation, and recurrence monitoring in the context of lung cancer.
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Affiliation(s)
- Fei Ren
- Department of Geriatrics, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Qian Fei
- Department of Oncology, Shengjing Hospital of China Medical University, Shen Yang, 110000, China
| | - Kun Qiu
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Yuanjie Zhang
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Heyang Zhang
- Department of Hematology, The First Hospital of China Medical University, Shen Yang, 110000, China.
| | - Lei Sun
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China.
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Cui YB, Yan H, Sun Z, Ling Y, Luo HQ, Li NB. A photoelectrochemical biosensor based on ZnIn2S4@AuNPs coupled with circular bipedal DNA walker for signal-on detection of circulating tumor DNA. Biosens Bioelectron 2023; 231:115295. [PMID: 37058959 DOI: 10.1016/j.bios.2023.115295] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/22/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023]
Abstract
The circulating tumor DNA (ctDNA) is a crucial cancer marker, its sensitive monitoring is useful for early diagnose and therapy of tumor-related diseases. Herein, a bipedal DNA walker with multiple recognition sites is designed through the transition of dumbbell-shaped DNA nanostructure to realize the dual amplification of the signal and achieve ultrasensitive photoelectrochemical (PEC) detection of ctDNA. Initially, the ZnIn2S4@AuNPs is obtained by combining the drop coating method with electrodeposition method. When the target is present, the dumbbell-shaped DNA structure transforms into an annular bipedal DNA walker that can walk unrestrictedly on the modified electrode. After the cleavage endonuclease (Nb.BbvCI) was added to the sensing system, the ferrocene (Fc) on the substrate is released from the electrode surface, and the transfer efficiency of photogenerated electron-hole pairs is extremely improved, enabling the "signal on" testing of ctDNA. The detection limit of the prepared PEC sensor is 0.31 fM, and the recovery of actual samples varied between 96.8 and 103.6% with an average relative standard deviation of about 8%. Meaningfully, the prepared PEC biosensor with an innovative bipedal DNA walker has potential application value for ultrasensitive detection of other nucleic acid-related biomarker.
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5
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Xu X, Gao J, Zhang Y, Zhang L. Tailored novel multifunctional benzyl-functionalized magnetic ionic liquid for rapid and efficient monitoring of trace fluoroquinolones in food samples. Food Chem 2023; 404:134654. [DOI: 10.1016/j.foodchem.2022.134654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 10/01/2022] [Accepted: 10/15/2022] [Indexed: 11/22/2022]
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6
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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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7
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Ultrahigh sensitive and selective detection of single nucleotide polymorphism using peptide nucleic acid and ribonuclease H assembled DNA amplification (PRADA). Anal Chim Acta 2022; 1233:340423. [DOI: 10.1016/j.aca.2022.340423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/06/2022] [Accepted: 09/19/2022] [Indexed: 11/22/2022]
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8
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Wei J, Wang Y, Gao J, Li Z, Pang R, Zhai T, Ma Y, Wang Z, Meng X. Detection of BRAFV600E mutation of thyroid cancer in circulating tumor DNA by an electrochemical-enrichment assisted ARMS-qPCR assay. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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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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10
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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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11
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Magnetic ionic liquids as microRNA extraction solvents and additives for the exponential amplification reaction. Anal Chim Acta 2021; 1181:338900. [PMID: 34556230 DOI: 10.1016/j.aca.2021.338900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 12/24/2022]
Abstract
The detection of microRNAs (miRNAs) from highly complex matrices has become an area of immense interest as their characterization in biological samples has been utilized for disease diagnosis and body fluid identification. However, conventional northern blotting miRNA detection lacks the sensitivity required to detect circulating miRNAs. Additionally, polymerase chain reaction-based methods for miRNA detection require modified oligonucleotides that are difficult to design. Exponential amplification reaction (EXPAR) is an isothermal amplification method used for miRNA detection that is simple to design but suffers from non-specific amplification that masks low concentration miRNAs. Previous studies have shown that magnetic ionic liquids (MILs) are a promising alternative to traditional nucleic acid extraction methods capable of preconcentrating DNA from complex matrices. In this study, three hydrophobic magnetic ionic liquids (MILs) were investigated as EXPAR additives and miRNA extraction solvents. The addition of MIL to the EXPAR buffer decreased the background signal from non-specific amplification and increased the reaction rate. Reactions containing MIL could detect miRNA at concentration levels down to 10 aM. In comparison, reactions that did not contain MIL could not discriminate 10 fM lethal-7a (let-7a) standards from the no trigger control (NTC). All three MILs extracted miRNA from 2-fold diluted plasma, artificial urine, and artificial saliva with only a 1 min dispersion step. By integrating the miRNA-enriched MIL into the EXPAR buffer, the extraction and detection of femtomolar concentrations of miRNA required only 10 min. In contrast, conventional spin column kits require at least 20 min to isolate miRNA, indicating that a dispersive MIL-based extraction is ideal for high throughput analysis of miRNA.
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12
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Zhang H, Yan Z, Wang X, Gaňová M, Chang H, Laššáková S, Korabecna M, Neuzil P. Determination of Advantages and Limitations of qPCR Duplexing in a Single Fluorescent Channel. ACS OMEGA 2021; 6:22292-22300. [PMID: 34497918 PMCID: PMC8412922 DOI: 10.1021/acsomega.1c02971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Real-time (quantitative) polymerase chain reaction (qPCR) has been widely applied in molecular diagnostics due to its immense sensitivity and specificity. qPCR multiplexing, based either on fluorescent probes or intercalating dyes, greatly expanded PCR capability due to the concurrent amplification of several deoxyribonucleic acid sequences. However, probe-based multiplexing requires multiple fluorescent channels, while intercalating dye-based multiplexing needs primers to be designed for amplicons having different melting temperatures. Here, we report a single fluorescent channel-based qPCR duplexing method on a model containing the sequence of chromosomes 21 (Chr21) and 18 (Chr18). We combined nonspecific intercalating dye EvaGreen with a 6-carboxyfluorescein (FAM) probe specific to either Chr21 or Chr18. The copy number (cn) of the target linked to the FAM probe could be determined in the entire tested range from the denaturation curve, while the cn of the other one was determined from the difference between the denaturation and elongation curves. We recorded the amplitude of fluorescence at the end of denaturation and elongation steps, thus getting statistical data set to determine the limit of the proposed method in detail in terms of detectable concentration ratios of both targets. The proposed method eliminated the fluorescence overspilling that happened in probe-based qPCR multiplexing and determined the specificity of the PCR product via melting curve analysis. Additionally, we performed and verified our method using a commercial thermal cycler instead of a self-developed system, making it more generally applicable for researchers. This quantitative single-channel duplexing method is an economical substitute for a conventional rather expensive probe-based qPCR requiring different color probes and hardware capable of processing these fluorescent signals.
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Affiliation(s)
- Haoqing Zhang
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Zhiqiang Yan
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Xinlu Wang
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Martina Gaňová
- Central
European Institute of Technology, Brno University
of Technology, Purkyňova 123, 612 00 Brno, Czech Republic
| | - Honglong Chang
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Soňa Laššáková
- Institute
of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital
in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Marie Korabecna
- Institute
of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital
in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Pavel Neuzil
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
- Central
European Institute of Technology, Brno University
of Technology, Purkyňova 123, 612 00 Brno, Czech Republic
- School
of Electrical Engineering and Computer Technology, Brno University of Technology, Technická 10, 612 00 Brno, Czech Republic
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Deng Y, Cao G, Chen X, Yang M, Huo D, Hou C. Ultrasensitive detection of gene-PIK3CA H1047R mutation based on cascaded strand displacement amplification and trans-cleavage ability of CRISPR/Cas12a. Talanta 2021; 232:122415. [PMID: 34074403 DOI: 10.1016/j.talanta.2021.122415] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/22/2021] [Accepted: 04/07/2021] [Indexed: 01/22/2023]
Abstract
Low abundance gene-PIK3CAH1047R mutation detection is crucial for the clinical diagnosis and treatment of breast cancer. Here, a fluorescent biosensor which combines cascaded strand displacement amplification (C-SDA) and trans-cleavage ability of CRISPR/Cas12a was established to ultra-sensitively detect gene-PIK3CAH1047R mutation. The mutated gene-PIK3CAH1047R can combine with complementary sequence to form an intact recognition site for endonuclease FspI. Mediated by FspI, it breaks at the mutation site to produce DNA fragment to trigger SDA or C-SDA. Then, the fluorescent biosensors based on SDA-CRISPR/Cas12a or C-SDA-CRISPR/Cas12a were constructed. Compared with biosensor based on SDA-CRISPR/Cas12a (5 pM), the minimum detection of the biosensor based on C-SDA-CRISPR/Cas12a is reduced two orders of magnitude (50 fM). In range of 0.001%-50%, we achieved the ultrasensitive detection of gene-PIK3CAH1047R mutation low to 0.001%. Besides, the proposed biosensor works well in human serum samples, showing its application potential in low-abundance gene-PIK3CAH1047R mutation detection.
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Affiliation(s)
- Yuanyi Deng
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Gaihua Cao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Xiaolong Chen
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, PR China.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, PR China.
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14
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Egorova KS, Posvyatenko AV, Larin SS, Ananikov V. Ionic liquids: prospects for nucleic acid handling and delivery. Nucleic Acids Res 2021; 49:1201-1234. [PMID: 33476366 PMCID: PMC7897475 DOI: 10.1093/nar/gkaa1280] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022] Open
Abstract
Operations with nucleic acids are among the main means of studying the mechanisms of gene function and developing novel methods of molecular medicine and gene therapy. These endeavours usually imply the necessity of nucleic acid storage and delivery into eukaryotic cells. In spite of diversity of the existing dedicated techniques, all of them have their limitations. Thus, a recent notion of using ionic liquids in manipulations of nucleic acids has been attracting significant attention lately. Due to their unique physicochemical properties, in particular, their micro-structuring impact and tunability, ionic liquids are currently applied as solvents and stabilizing media in chemical synthesis, electrochemistry, biotechnology, and other areas. Here, we review the current knowledge on interactions between nucleic acids and ionic liquids and discuss potential advantages of applying the latter in delivery of the former into eukaryotic cells.
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Affiliation(s)
- Ksenia S Egorova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow 119991, Russia
| | - Alexandra V Posvyatenko
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow 119991, Russia
- Molecular Immunology Laboratory, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samory Mashela St 1, Moscow 117997, Russia
| | - Sergey S Larin
- Molecular Immunology Laboratory, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samory Mashela St 1, Moscow 117997, Russia
| | - Valentine P Ananikov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow 119991, Russia
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15
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Will C, Huelsmann RD, Mafra G, Merib J, Anderson JL, Carasek E. High-throughput approach for the in situ generation of magnetic ionic liquids in parallel-dispersive droplet extraction of organic micropollutants in aqueous environmental samples. Talanta 2021; 223:121759. [PMID: 33298275 DOI: 10.1016/j.talanta.2020.121759] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 01/09/2023]
Abstract
In this work, a novel and high-throughput parallel-dispersive droplet extraction (Pa-DDE) based on in situ formation of the hydrophobic MILs ([Co(C4IM)4+2]2[NTf2-], [Ni(C4IM)4+2]2[NTf2-] and [Ni(BeIM)4+2]2[NTf2-]) is demonstrated, for the first time, for the determination of benzophenone, metolachlor, triclocarban, pendimethalin, 4-methylbenzylidene camphor, and 2-ethylhexyl-4-methoxycinnamate from aqueous environmental samples. This experimental setup is comprised of a 96-well plate system containing a set of magnetic pins which were used to collect the MIL droplet after in situ formation. This consolidated system enabled simultaneous extraction of up to 96 samples and MIL production in one step. Using this apparatus, sample preparation times of 0.78 min per sample was achieved. The experimental conditions were carefully optimized using uni and multivariate approaches. The optimal conditions were comprised of sample volume of 1.25 mL, 4 mg of [Co(C4IM)4+2]2[Cl-] and 40 μL of LiNTf2 for the in situ formation, and dilution in 20 μL of acetonitrile. The analytical parameters of merit were successfully determined with LODs ranging from 7.5 to 25 μg L-1 and coefficients of determination higher than 0.989. Intraday and interday precision ranged from 6.4 to 20.6% (n = 3) and 11.6-22.9% (n = 9), respectively, with analyte relative recovery ranging between 53.9 and 129.1%.
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Affiliation(s)
- Camila Will
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Ricardo Dagnoni Huelsmann
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Gabriela Mafra
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Josias Merib
- Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, 90050-170, Brazil.
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Eduardo Carasek
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil.
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16
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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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17
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Simultaneous cell lysis and DNA extraction from whole blood using magnetic ionic liquids. Anal Bioanal Chem 2020; 412:8039-8049. [PMID: 32918171 DOI: 10.1007/s00216-020-02941-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/27/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
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.
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