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Gong W, Sun Y, Tu T, Huang J, Zhu C, Zhang J, Salah M, Zhao L, Xia X, Wang Y. Chitosan inhibits Penicillium expansum possibly by binding to DNA and triggering apoptosis. Int J Biol Macromol 2024; 259:129113. [PMID: 38181919 DOI: 10.1016/j.ijbiomac.2023.129113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/05/2023] [Accepted: 12/26/2023] [Indexed: 01/07/2024]
Abstract
Chitosan is a natural polysaccharide that is abundant, biocompatible and exhibits effective antifungal activity against various pathogenic fungi. However, the potential intracellular targets of chitosan in pathogenic fungi and the way of activity of chitosan are far from well known. The present work demonstrated that chitosan could inhibit Penicillium expansum, the principal causal agent of postharvest blue mold decay on apple fruits, by binding to DNA and triggering apoptosis. UV-visible spectroscopy, fluorescence spectroscopy and electrophoretic mobility assay proved the interaction between chitosan and DNA, while atomic force microscope (AFM) observation revealed the binding morphology of chitosan to DNA. Chitosan could inhibit in vitro DNA replication, and cell cycle analysis employing flow cytometry demonstrated that cell cycle was retarded by chitosan treatment. Furthermore, the reactive oxygen species (ROS) assay and membrane potential analysis showed that apoptosis was induced in P. expansum cells after exposure to chitosan. In conclusion, our results confirmed that chitosan interacts with DNA and induces apoptosis. These findings are expected to provide a feasible theoretical basis and practical direction for the promoting and implementing of chitosan in plant protection and further illuminate the possible antifungal mechanisms of chitosan against fungal pathogens.
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Affiliation(s)
- Weifeng Gong
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yemei Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Tingting Tu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Juanying Huang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Chenyang Zhu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jiaqi Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Mahmoud Salah
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; Department of Environmental Agricultural Science, Faculty of Graduate Studies and Environmental Research, Ain Shams University, Cairo 11566, Egypt
| | - Luning Zhao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xiaoshuang Xia
- Center of Analysis, Jiangsu University, Zhenjiang 212013, China
| | - Yun Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
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2
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Grammatikos S, Svoliantopoulos I, Gizeli E. Naked-Eye Detection of LAMP-Produced Nucleic Acids in Saliva Using Chitosan-Capped AuNPs in a Single-Tube Assay. Anal Chem 2023; 95:18514-18521. [PMID: 38065570 PMCID: PMC10733902 DOI: 10.1021/acs.analchem.3c03878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/30/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a low-technology molecular assay that is highly adaptable to point-of-care (POC) applications. However, achieving sensitive naked-eye detection of the amplified target in a crude sample is challenging. Herein, we report a simple yet highly efficient and sensitive methodology for the colorimetric visualization of a single target copy in saliva using chitosan-capped gold nanoparticles (Chit-AuNPs) synthesized via a green chemistry approach. The presence or absence of free Chit in the Chit-AuNPs solution was shown to affect LAMP colorimetric detection oppositely: the observed stabilization in the negative samples and aggregation in the positive samples in the presence of free Chit were reversed in the case of neat Chit-AuNPs. The mechanism of the two assays was investigated and attributed to electrostatic and depletion effects exerted between the Chit-AuNPs, free Chit, and the solution components. The developed contamination-free, one-tube assay successfully amplified and detected down to 1-5 cfu of Salmonella and 10 copies of SARS-CoV-2 per reaction (25 μL) used, respectively, as model DNA and RNA targets in the presence of 20% saliva, making the method suitable for POC applications. Compared to the commonly used pH-sensitive dyes, Chit-AuNPs are shown to have an enhanced sensitivity toward naked-eye colorimetric observation owing to the direct detection of DNA amplicons. Thus, this is a simple, highly sensitive, fast, and versatile naked-eye detection methodology that could be coupled to any LAMP or RT-LAMP assay, avoiding the need of using complicated sample pretreatments and/or AuNPs long and laborious functionalization processes.
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Affiliation(s)
- Stylianos Grammatikos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013 Heraklion, Greece
- Department
of Biology, University of Crete, Voutes, 70013 Heraklion, Greece
| | - Ioannis Svoliantopoulos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013 Heraklion, Greece
- Department
of Chemistry, University of Crete, Voutes, 70013 Heraklion, Greece
| | - Electra Gizeli
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013 Heraklion, Greece
- Department
of Biology, University of Crete, Voutes, 70013 Heraklion, Greece
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3
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Avlani D, Kumar A, H N S. Development of Dispersible Vaginal Tablets of Tenofovir Loaded Mucoadhesive Chitosan Microparticles for Anti-HIV Pre-Exposure Prophylaxis. Mol Pharm 2023; 20:5006-5018. [PMID: 37656937 DOI: 10.1021/acs.molpharmaceut.3c00288] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Tenofovir disoproxil fumarate (TDF)-loaded bioadhesive chitosan microparticles (CM) were developed by an emulsification internal gelation technique. Among different batches produced, ECH-4 was found to display a high % entrapment efficiency (68.93 ± 1.76%) and sustained drug release of 88.05 ± 0.38% at 24 h. Solid state characterization of ECH-4 employing DSC and PXRD indicated that the TDF existed in an amorphous state as a solid-solid solution in chitosan. Scanning electron microscopy revealed CM of ECH-4 was spherical in shape with a rough surface topography. Laser scattering analysis using Malvern Master sizer indicated that particle size of ECH-4 was in the range of 0.52 ± 0.10 μm to 284.79 ± 21.42 μm with a surface-mean diameter of 12.41 ± 0.06 μm. Ex vivo mucoadhesion studies using rabbit mucosa as a substrate indicated that 10.34 ± 2.08% of CM of ECH-4 was retained at the end of 24 h. The microparticles of ECH-4 were incorporated into dispersible tablets (DT-TCM) intended for intravaginal administration, in view to arrest the pre-exposure transmission of HIV during sexual intercourse. In vitro release from the dispersible tablet (F3) into simulated vaginal fluid (pH 4.5) displayed a sustained release profile of TDF as 89.98 ± 1.61% of TDF was released at 24 h. The in vitro dissolution profile of the DT-TCM was found to be similar to that of TDF loaded CM with the values of f1 (difference factor) and f2 (similarity factor) being 1.52 and 78.02, respectively. Therefore, DT-TCM would be a promising novel drug delivery platform for pre-exposure prophylaxis against HIV.
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Affiliation(s)
- Dhruti Avlani
- Department of Pharmaceutics, Dr. Prabhakar B Kore Basic Science Research Center, Off-campus, KLE College of Pharmacy (A constituent unit of KAHER-Belagavi), Rajajinagar, Bengaluru 560010 Karnataka, India
| | - Avichal Kumar
- Department of Pharmaceutics, Dr. Prabhakar B Kore Basic Science Research Center, Off-campus, KLE College of Pharmacy (A constituent unit of KAHER-Belagavi), Rajajinagar, Bengaluru 560010 Karnataka, India
| | - Shivakumar H N
- Department of Pharmaceutics, Dr. Prabhakar B Kore Basic Science Research Center, Off-campus, KLE College of Pharmacy (A constituent unit of KAHER-Belagavi), Rajajinagar, Bengaluru 560010 Karnataka, India
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4
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Heinrich T, Toepfer S, Steinmetzer K, Ruettger M, Walz I, Kanitz L, Lemuth O, Hubold S, Fritsch F, Loncarevic-Barcena I, Klingner S, Bocker HT, Ermantraut E. DNA-Binding Magnetic Nanoreactor Beads for Digital PCR Analysis. Anal Chem 2023; 95:14175-14183. [PMID: 37646599 PMCID: PMC10534990 DOI: 10.1021/acs.analchem.3c01418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Digital PCR (dPCR) is based on the separation of target amplification reactions into many compartments with randomly distributed template molecules. Here, we present a novel digital PCR format based on DNA binding magnetic nanoreactor beads (mNRBs). Our approach relies on the binding of all nucleic acids present in a sample to the mNRBs, which both provide a high-capacity binding matrix for capturing nucleic acids from a sample and define the space available for PCR amplification by the internal volume of their hydrogel core. Unlike conventional dPCR, this approach does not require a precise determination of the volume of the compartments used but only their number to calculate the number of amplified targets. We present a procedure in which genomic DNA is bound, the nanoreactors are loaded with PCR reagents in an aqueous medium, and amplification and detection are performed in the space provided by the nanoreactor suspended in fluorocarbon oil. mNRBs exhibit a high DNA binding capacity of 1.1 ng DNA/mNRB (95% CI 1.0-1.2) and fast binding kinetics with ka = 0.21 s-1 (95% CI 0.20-0.23). The dissociation constant KD was determined to be 0.0011 μg/μL (95% CI 0.0007-0.0015). A simple disposable chamber plate is used to accommodate the nanoreactor beads in a monolayer formation for rapid thermocycling and fluorescence detection. The performance of the new method was compared with conventional digital droplet PCR and found to be equivalent in terms of the precision and linearity of quantification. In addition, we demonstrated that mNRBs provide quantitative capture and loss-free analysis of nucleic acids contained in samples in different volumes.
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Affiliation(s)
| | | | | | | | - Ines Walz
- BLINK AG, Bruesseler Strasse 20, 07747 Jena, Germany
| | - Lea Kanitz
- BLINK AG, Bruesseler Strasse 20, 07747 Jena, Germany
| | - Oliver Lemuth
- BLINK AG, Bruesseler Strasse 20, 07747 Jena, Germany
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5
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Jiang S, Li B, Zhao J, Wu D, Zhang Y, Zhao Z, Zhang Y, Yu H, Shao K, Zhang C, Li R, Chen C, Shen Z, Hu J, Dong B, Zhu L, Li J, Wang L, Chu J, Hu Y. Magnetic Janus origami robot for cross-scale droplet omni-manipulation. Nat Commun 2023; 14:5455. [PMID: 37673871 PMCID: PMC10482950 DOI: 10.1038/s41467-023-41092-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/22/2023] [Indexed: 09/08/2023] Open
Abstract
The versatile manipulation of cross-scale droplets is essential in many fields. Magnetic excitation is widely used for droplet manipulation due to its distinguishing merits. However, facile magnetic actuation strategies are still lacked to realize versatile multiscale droplet manipulation. Here, a type of magnetically actuated Janus origami robot is readily fabricated for versatile cross-scale droplet manipulation including three-dimensional transport, merging, splitting, dispensing and release of daughter droplets, stirring and remote heating. The robot allows untethered droplet manipulation from ~3.2 nL to ~51.14 μL. It enables splitting of droplet, precise dispensing (minimum of ~3.2 nL) and release (minimum of ~30.2 nL) of daughter droplets. The combination of magnetically controlled rotation and photothermal properties further endows the robot with the ability to stir and heat droplets remotely. Finally, the application of the robot in polymerase chain reaction (PCR) is explored. The extraction and purification of nucleic acids can be successfully achieved.
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Affiliation(s)
- Shaojun Jiang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China
| | - Bo Li
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027, China
| | - Jun Zhao
- Center of Engineering Technology Research for Biomedical Optical Instrument, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Dong Wu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China.
| | - Yiyuan Zhang
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China
| | - Zhipeng Zhao
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China
| | - Yiyuan Zhang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Hao Yu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027, China
| | - Kexiang Shao
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Cong Zhang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Rui Li
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Chao Chen
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Zuojun Shen
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Jie Hu
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Bin Dong
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Ling Zhu
- Center of Engineering Technology Research for Biomedical Optical Instrument, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Jiawen Li
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Liqiu Wang
- Department of Mechanical Engineering, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Jiaru Chu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Yanlei Hu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China.
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6
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Hapsianto BN, Kojima N, Kurita R, Yamagata H, Fujita H, Fujii T, Kim SH. Direct Capture and Amplification of Small Fragmented DNAs Using Nitrogen-Mustard-Coated Microbeads. Anal Chem 2022; 94:7594-7600. [PMID: 35578745 DOI: 10.1021/acs.analchem.2c00531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Circulating cell-free DNA (cfDNA) has been implicated as an important biomarker and has been intensively studied for "liquid biopsy" applications in cancer diagnostics. Owing to its small fragment size and its low concentration in circulation, cfDNA extraction and purification from serum samples are complicated, and the extraction yield affects the precision of subsequent molecular diagnostic tests. Here, we report a novel approach using nitrogen-mustard-coated DNA capture beads (NMD beads) that covalently capture DNA and allow direct subsequent polymerase chain reaction (PCR) amplification from the NMD bead without elusion. The complex DNA extraction and purification processes are not required. To illustrate the diagnostic use of the NMD beads, we detected short DNA fragments (142 bp) that were spiked into fetal bovine serum (as a model serum sample). The spiked DNAs were captured directly from serum samples and detected using real-time PCR at concentrations as low as 10 fg/mL. We anticipate that this DNA capture bead technique has the potential to simplify the preanalytical processes required for cfDNA detection, which could significantly expand the diagnostic applications of liquid biopsy.
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Affiliation(s)
- Benediktus N Hapsianto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8654, Japan
| | - Naoshi Kojima
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB/DAICENTER, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Ibaraki, Japan
| | - Ryoji Kurita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB/DAICENTER, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Ibaraki, Japan
| | - Hitoshi Yamagata
- Advanced Research Laboratory (ARL), Canon Medical Systems Corporation, 1385 Shimoishigami, Otawara 324-8550, Tochigi, Japan
| | - Hiroyuki Fujita
- Advanced Research Laboratory (ARL), Canon Medical Systems Corporation, 1385 Shimoishigami, Otawara 324-8550, Tochigi, Japan
| | - Teruo Fujii
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| | - Soo Hyeon Kim
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
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7
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Bessey C, Gao Y, Truong YB, Miller H, Jarman SN, Berry O. Comparison of materials for rapid passive collection of environmental
DNA. Mol Ecol Resour 2022; 22:2559-2572. [PMID: 35570323 PMCID: PMC9544503 DOI: 10.1111/1755-0998.13640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/24/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022]
Abstract
Passive collection is an emerging sampling method for environmental DNA (eDNA) in aquatic systems. Passive eDNA collection is inexpensive and efficient, and requires minimal equipment, making it suited to high‐density sampling and remote deployment. Here, we compare the effectiveness of nine membrane materials for passively collecting fish eDNA from a 3‐million‐litre marine mesocosm. We submerged materials (cellulose, cellulose with 1% and 3% chitosan, cellulose overlayed with electrospun nanofibres and 1% chitosan, cotton fibres, hemp fibres, and sponge with either zeolite or active carbon) for intervals between 5 and 1080 min. We show that for most materials, with as little as 5 min of submersion, mitochondrial fish eDNA measured with qPCR, and fish species richness measured with metabarcoding, was comparable to that collected by conventional filtering. Furthermore, PCR template DNA concentrations and species richness were generally not improved significantly by longer submersion. Species richness detected for all materials ranged between 11 and 37 species, with a median of 27, which was comparable to the range for filtered eDNA (19–32). Using scanning electron microscopy, we visualized biological matter adhering to the surface of materials, rather than entrapped, with images also revealing a diversity in size and structure of putative eDNA particles. eDNA can be collected rapidly from seawater with a passive approach and using a variety of materials. This will suit cost‐ and time‐sensitive biological surveys, and where access to equipment is limited.
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Affiliation(s)
- Cindy Bessey
- Commonwealth Scientific and Industrial Research Organisation, Indian Oceans Marine Research Centre, Oceans and Atmosphere, 64 Fairway Crawley WA Australia
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, 64 Fairway Crawley WA Australia
- University of Western Australia UWA Oceans Institute, 35 Stirling Highway Crawley WA Australia
| | - Yuan Gao
- Commonwealth Scientific and Industrial Research Organization, Manufacturing, Research Way Clayton Australia
| | - Yen Bach Truong
- Commonwealth Scientific and Industrial Research Organization, Manufacturing, Research Way Clayton Australia
| | - Haylea Miller
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, 64 Fairway Crawley WA Australia
| | - Simon Neil Jarman
- University of Western Australia UWA Oceans Institute, 35 Stirling Highway Crawley WA Australia
- University of Western Australia School of Biological Sciences and the UWA Oceans Institute Crawley WA Australia
| | - Oliver Berry
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, 64 Fairway Crawley WA Australia
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8
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Tripathy S, Chalana AK, Talukdar A, Rajesh PV, Saha A, Pramanik G, Ghosh S. Limited-resource preparable chitosan magnetic particles for extracting amplification-ready nucleic acid from complex biofluids. Analyst 2021; 147:165-177. [PMID: 34870658 DOI: 10.1039/d1an01150b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Extraction and concentration of pure nucleic acid from complex biofluids are the prerequisite for nucleic acid amplification test (NAAT) applications in pathogen detection, biowarfare prevention, and genetic diseases. However, conventional spin-column mediated nucleic acid extraction is constricted by the requirement for costly power-intensive centralized lab infrastructure, making it unsuitable for limited-resource settings. Significant progress in lab-on-a-chip devices or cartridges (e.g., Cepheid GeneXpert®) that integrate nucleic acid extraction and amplification has been made, but these approaches either require additional equipment or are costly. Similarly, their complexities make them difficult to fabricate in low-resource settings by the end-user themselves. The application of magnetic particles such as silica-coated iron oxide beads for nucleic acid extraction is relatively instrument-free, rapid, user-friendly, and amenable to automation. But, they rely on hazardous chaotropic salt chemistry and ethanol desalting that could limit their efficacy for downstream NAATs. Recent advances in several types of novel material (e.g., polyamine) coated magnetic bead-based chaotropic salt-free extraction methods offer a possible solution to this problem. However, these materials also involve multistep synthesis impermissible in limited-resource settings. To offer a possible instrument-free magnetic particle-based nucleic acid extraction doable at limited-resource settings, we investigated the nucleic acid capture ability of two chitosan-coated magnetic particles that are preparable by minimally trained personnel using only a water bath and a magnetic stirrer within 6-8 h. We quantitatively probed the efficiency of the passive (without any electrical shaking or vortex-aided) DNA magnetocapture (i.e., binding to chitosan magnetic particles, physical separation from its sample of origin, and release from the particles) using UV260. To explore their suitability towards clinically relevant sensitive downstream NAATs, 100-1000 copies (i.e., in the order of zeptomole) of Escherichia coli (E. coli) or human genomic DNA from aqueous solution, crude cell lysate, and fetal bovine serum were extracted by them and then successfully detected using quantitative real-time loop-mediated isothermal amplification (LAMP) or real-time polymerase chain reaction (PCR). Alongside, their suitability with gel-based LAMP, colorimetric LAMP, and in situ (on beads) LAMP was also probed. The required optimization of the amplification methods has been discussed. Overall, the turnaround time for the magnetocapture combined with NAAT was 1.5-2 h and is thus expected to aid in rapid clinical decision making. With the ease of preparation, reproducibility, and compatibility with downstream NAATs, we anticipate that these magnetic particles would facilitate the expansion and decentralization of nucleic acid-based diagnosis for limited-resource settings.
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Affiliation(s)
- Sayantan Tripathy
- Department of Chemistry, Bennett University, Greater Noida, Uttar Pradesh 201310, India.
| | - Ashish Kumar Chalana
- Department of Chemistry, Bennett University, Greater Noida, Uttar Pradesh 201310, India.
| | - Arunansu Talukdar
- Department of Medicine, Medical College and Hospital, Kolkata, West Bengal, India
| | - P V Rajesh
- UGC-DAE CSR, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata - 700 106, India
| | - Abhijit Saha
- UGC-DAE CSR, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata - 700 106, India
| | - Goutam Pramanik
- UGC-DAE CSR, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata - 700 106, India
| | - Souradyuti Ghosh
- Department of Chemistry, Bennett University, Greater Noida, Uttar Pradesh 201310, India. .,Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh 201310, India
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9
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François C, Martinez C, Faye C, Pansu N, Dunyach-Remy C, Garrelly L, Roig B, Cadiere A. The Utilization of Linear Polylysine Coupled with Mechanic Forces to Extract Microbial DNA from Different Matrices. Microorganisms 2020; 8:microorganisms8121901. [PMID: 33266082 PMCID: PMC7760326 DOI: 10.3390/microorganisms8121901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 11/16/2022] Open
Abstract
Molecular approaches are powerful tools that are used for medical or environmental diagnoses. However, the main limitations of such a tools are that they extract low levels of DNA and they do not remove the inhibitors of polymerase chain reaction (PCR). Although the use of polycation to complex and purify DNA has been described in the literature, elution often requires a high ionic strength or pH levels not compatible with molecular analyses. In this paper, we described a new process that is based on the complexation of DNA with linear polylysine, followed by capturing the complex by a cation exchange resin. The originality of the process consisted of using mechanic force to elute DNA from the complex. The extraction method showed several advantages when compared to existing methods, such as being compatible with pH levels that range from 5 to 11, as well as high levels of DNA recovery and elimination of PCR inhibitors from complex samples. This method was successfully applied to different types of samples, such as environmental samples, beverage samples, and medical samples. Furthermore, it was proven to be a good solution for removing PCR inhibitors and assuring good DNA recovery yield.
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Affiliation(s)
- Celia François
- Gl-Biocontrol, 34830 Clapiers, France; (C.F.); (C.M.); (C.F.); (L.G.)
| | - Celia Martinez
- Gl-Biocontrol, 34830 Clapiers, France; (C.F.); (C.M.); (C.F.); (L.G.)
| | - Clement Faye
- Gl-Biocontrol, 34830 Clapiers, France; (C.F.); (C.M.); (C.F.); (L.G.)
| | - Nathalie Pansu
- Institute National de la Santé et de la Recherche Médicale, U1047, University Montpellier, UFR de Médecine, 30908 Nimes, France; (N.P.); (C.D.-R.)
- Department of Microbiology, CHU Nimes, University Montpellier, 30029 Nimes, France
| | - Catherine Dunyach-Remy
- Institute National de la Santé et de la Recherche Médicale, U1047, University Montpellier, UFR de Médecine, 30908 Nimes, France; (N.P.); (C.D.-R.)
- Department of Microbiology, CHU Nimes, University Montpellier, 30029 Nimes, France
| | - Laurent Garrelly
- Gl-Biocontrol, 34830 Clapiers, France; (C.F.); (C.M.); (C.F.); (L.G.)
| | - Benoit Roig
- EA7352 CHROME, University Nimes, Rue du Dr G. Salan, CEDEX 1, 30021 Nimes, France;
| | - Axelle Cadiere
- EA7352 CHROME, University Nimes, Rue du Dr G. Salan, CEDEX 1, 30021 Nimes, France;
- Correspondence: ; Tel.: +33-466-27-95-71
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10
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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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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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12
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A Novel Microfluidic Device Integrated with Chitosan-Modified Capillaries for Rapid ZIKV Detection. MICROMACHINES 2020; 11:mi11020186. [PMID: 32054007 PMCID: PMC7074674 DOI: 10.3390/mi11020186] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/29/2020] [Accepted: 02/03/2020] [Indexed: 02/08/2023]
Abstract
The outbreak of Zika virus (ZIKV) has posed a great challenge to public health in recent years. To address the urgent need of ZIKV RNA assays, we integrate the microfluidic chip embedded with chitosan-modified silicon dioxide capillaries, smartphone-based detection unit to be a C3-system for the rapid extraction and detection of ZIKV RNA. The C3-system is characterized by: (1) four chitosan-modified silicon dioxide capillaries integrated in the microfluidic chip for target ZIKV RNA enrichment and “in situ PCR” (polymerase chain reaction) amplification; (2) smartphone-based point of care (POC) device consisting of a pneumatic subsystem for controlling the nucleic acid extraction processes in the microfluidic chip, a heating subsystem for sample lysis and PCR amplification, and an optical subsystem for signal acquisition. The entire detection processes including sample lysis, ZIKV RNA enrichment, and reverse-transcription polymerase chain reaction (RT-PCR) is achieved in the microfluidic chip. Moreover, PCR buffers can be directly loaded into the chitosan-modified silicon dioxide capillaries for “in situ PCR”, in which the captured ZIKV RNA is directly used for downstream PCR without any loss. ZIKV RNA extracted by the C3-system can be successfully recovered at very low concentrations of 50 transducing units (TU)/mL from crude human saliva. This means that our method of detecting viremia in patients infected with ZIKV is reliable.
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13
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Sosa-Acosta JR, Iriarte-Mesa C, Ortega GA, Díaz-García AM. DNA–Iron Oxide Nanoparticles Conjugates: Functional Magnetic Nanoplatforms in Biomedical Applications. Top Curr Chem (Cham) 2020; 378:13. [DOI: 10.1007/s41061-019-0277-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/20/2019] [Indexed: 02/08/2023]
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14
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van Gelder MK, Jong JAW, Folkertsma L, Guo Y, Blüchel C, Verhaar MC, Odijk M, Van Nostrum CF, Hennink WE, Gerritsen KGF. Urea removal strategies for dialysate regeneration in a wearable artificial kidney. Biomaterials 2020; 234:119735. [PMID: 31958714 DOI: 10.1016/j.biomaterials.2019.119735] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/05/2019] [Accepted: 12/25/2019] [Indexed: 12/31/2022]
Abstract
The availability of a wearable artificial kidney (WAK) that provides dialysis outside the hospital would be an important advancement for dialysis patients. The concept of a WAK is based on regeneration of a small volume of dialysate in a closed-loop. Removal of urea, the primary waste product of nitrogen metabolism, is the major challenge for the realization of a WAK since it is a molecule with low reactivity that is difficult to adsorb while it is the waste solute with the highest daily molar production. Currently, no efficient urea removal technology is available that allows for miniaturization of the WAK to a size and weight that is acceptable for patients to carry. Several urea removal strategies have been explored, including enzymatic hydrolysis by urease, electro-oxidation and sorbent systems. However, thus far, these methods have toxic side effects, limited removal capacity or slow removal kinetics. This review discusses different urea removal strategies for application in a wearable dialysis device, from both a chemical and a medical perspective.
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Affiliation(s)
- Maaike K van Gelder
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Jacobus A W Jong
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands; Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | - Laura Folkertsma
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands; BIOS-Lab on a Chip Group, MESA+ Institute of Nanotechnology, Technical Medical Center, Max Planck Center for Complex Fluid Dynamics, University of Twente, 7522 NH, Enschede, the Netherlands
| | - Yong Guo
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | | | - Marianne C Verhaar
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Mathieu Odijk
- BIOS-Lab on a Chip Group, MESA+ Institute of Nanotechnology, Technical Medical Center, Max Planck Center for Complex Fluid Dynamics, University of Twente, 7522 NH, Enschede, the Netherlands
| | - Cornelus F Van Nostrum
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | - Wim E Hennink
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | - Karin G F Gerritsen
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands.
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Minero GAS, Cangiano V, Garbarino F, Fock J, Hansen MF. Integration of microbead DNA handling with optomagnetic detection in rolling circle amplification assays. Mikrochim Acta 2019; 186:528. [DOI: 10.1007/s00604-019-3636-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/25/2019] [Indexed: 01/14/2023]
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16
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Gu Y, Zhuang B, Han J, Li Y, Song X, Zhou X, Wang L, Liu P. Modular-Based Integrated Microsystem with Multiple Sample Preparation Modules for Automated Forensic DNA Typing from Reference to Challenging Samples. Anal Chem 2019; 91:7435-7443. [PMID: 31050401 DOI: 10.1021/acs.analchem.9b01560] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The realization of an automated short tandem repeat (STR) analysis for forensic investigations is facing a unique challenge, that is DNA evidence with wide disparities in sample types, quality, and quantity. We developed a fully integrated microsystem in a modular-based architecture to accept and process various forensic samples in a "sample-in-answer-out" manner for forensic STR analysis. Two sample preparation modules (SPMs), the direct and the extraction SPM, were designed to be easily assembled with a capillary array electrophoresis (CAE) chip using a chip cartridge to efficiently achieve an adequate performance to different samples at a low cost. The direct SPM processed buccal swabs to produce STR profiles without DNA extraction in about 2 h. The extraction SPM analyzed more challenging blood samples based on chitosan-modified quartz filter paper for DNA extraction. This newly developed quartz filter provided a 90% DNA extraction efficiency and the "in situ" PCR capability, which enabled DNA extraction and PCR performed within a single chamber with all the DNA concentrated in the filter. We demonstrated that minute amounts of blood (0.25 μL), highly diluted blood (0.5 μL blood in 1 mL buffer), and latent bloodstains (5-μL bloodstain on cloth washed with detergent) can be automatically analyzed using our microsystem, reliably producing full STR profiles with a 100% calling of all the alleles. This modular-based microsystem with the capability of analyzing a wide range of samples should be able to play an increasing role in both urgent situations and routine forensic investigations, dramatically extending the applications and utility of automated DNA typing.
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Affiliation(s)
- Yin Gu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Tsinghua University , Beijing , 100084 , China.,State Key Laboratory of Space Medicine Fundamentals and Application , China Astronaut Research and Training Center , Beijing , 100094 , China
| | - Bin Zhuang
- Beijing CapitalBio Technology Ltd. Co. , Beijing , 101111 , China
| | - Junping Han
- Technology Department of Chaoyang Sub-bureau , Beijing Public Security Bureau , Beijing , 100102 , China
| | - Yi Li
- Beijing CapitalBio Technology Ltd. Co. , Beijing , 101111 , China
| | - Xiaoyu Song
- Beijing CapitalBio Technology Ltd. Co. , Beijing , 101111 , China
| | - Xinying Zhou
- CapitalBio Corporation , Beijing , 102206 , China
| | - Lei Wang
- CapitalBio Corporation , Beijing , 102206 , China
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Tsinghua University , Beijing , 100084 , China
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Emaus MN, Varona M, Anderson JL. Sequence-specific preconcentration of a mutation prone KRAS fragment from plasma using ion-tagged oligonucleotides coupled to qPCR compatible magnetic ionic liquid solvents. Anal Chim Acta 2019; 1068:1-10. [PMID: 31072469 DOI: 10.1016/j.aca.2019.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 01/22/2023]
Abstract
Circulating tumor DNA (ctDNA) is a source of mutant DNA found in plasma and holds great promise in guiding cancer diagnostics, prognostics, and treatment. However, ctDNA fragments are challenging to detect in plasma due to their low abundance compared to wild-type DNA. In this study, a series of ion-tagged oligonucleotides (ITO) were synthesized using thiol-ene click chemistry and designed to selectively anneal target DNA. The ITO-DNA duplex was subsequently captured using a hydrophobic magnetic ionic liquid (MIL) as a liquid support. Extracted target DNA was quantified by adding the DNA-enriched MIL to the quantitative polymerase chain reaction (qPCR) buffer to streamline the extraction procedure. Clinically relevant concentrations of the mutation prone KRAS fragment, which has been linked to colorectal, lung, and bladder cancer, were preconcentrated using the ITO-MIL strategy allowing for enrichment factors as high as 19.49 ± 1.44 from pure water and 4.02 ± 0.50 from 10-fold diluted plasma after a 1 min extraction. Preconcentration could only be achieved when adding the ITO probe to the sample validating the selectivity of the ITO in the capture process. In addition, the amplification efficiency of qPCR was not affected when performing extractions from a diluted-plasma matrix demonstrating that the ITO-MIL approach coupled to direct-qPCR can be used to quantitate DNA from complex matrices. In comparison, commercially available steptavidin-coated magnetic beads were observed to lose selectivity when performing extractions from a 10-fold diluted plasma matrix. The selectivity of the ITO-MIL method, coupled with the ability to rapidly preconcentrate clinically relevant concentrations of target DNA from 10-fold diluted plasma, suggests that this method has the potential to be applied towards the extraction of ctDNA fragments from clinical samples.
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Affiliation(s)
- Miranda N Emaus
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, United States
| | - Marcelino Varona
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, United States
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, United States.
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Pitakchatwong C, Chirachanchai S. pH Variation as a Simple and Selective Pathway for Obtaining Nanoparticle or Nanocapsule Polysaccharides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15820-15826. [PMID: 30509073 DOI: 10.1021/acs.langmuir.8b03443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The fabrication of polysaccharides to be nanoparticles or nanocapsules is quite specific due to various parameters and factors. The present work demonstrates a simple pathway to selectively prepare the ionic polysaccharide flakes to be nanoparticles or nanocapsules. The systematic studies on the model cases of cationic polysaccharide (i.e., chitosan) and anionic polysaccharide (i.e., alginate) confirm that p Ka is the key point to tune the polysaccharides to be nanoparticles or nanocapsules. When the ionic polysaccharides were in an oil/water emulsion system, the pH close to p Ka leads to the densely packed polysaccharide chains under the hydrogen bond networks, and as a result the cross-link occurs all through the chains to be nanoparticles. On the other hand, when pH was adjusted to the lower or higher than p Ka depending on the types of ionic polysaccharide, the polysaccharide chains are under charge-charge repulsive force, resulting in the alignment of polysaccharide chains to be hollow nanospheres, and at that time the cross-link initiates the formation of nanocapsules. The present work, for the first time, clarifies that pH variation is the key to selectively prepare nanoparticles or nanocapsules, and this is important for delivery systems, coatings, sensors, and so forth.
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19
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Maciel BG, da Silva RJ, Chávez-Guajardo AE, Medina-Llamas JC, Alcaraz-Espinoza JJ, de Melo CP. Magnetic extraction and purification of DNA from whole human blood using a γ-Fe2O3@Chitosan@Polyaniline hybrid nanocomposite. Carbohydr Polym 2018; 197:100-108. [DOI: 10.1016/j.carbpol.2018.05.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 11/27/2022]
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20
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Hui J, Gu Y, Zhu Y, Chen Y, Guo SJ, Tao SC, Zhang Y, Liu P. Multiplex sample-to-answer detection of bacteria using a pipette-actuated capillary array comb with integrated DNA extraction, isothermal amplification, and smartphone detection. LAB ON A CHIP 2018; 18:2854-2864. [PMID: 30105321 DOI: 10.1039/c8lc00543e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A pipette-actuated capillary array comb (PAAC) system operated on a smartphone-based hand-held device has been successfully developed for the multiplex detection of bacteria in a "sample-to-answer" manner. The PAAC consists of eight open capillaries inserted into a cylindrical plastic base with a piece of chitosan-modified glass filter paper embedded in each capillary. During the sample preparation, a PAAC was mounted into a 1 mL pipette tip with an enlarged opening and was operated with a 1 mL pipette for liquid handling. The cell lysate was drawn and expelled through the capillaries three times to facilitate the DNA capture on the embedded filter discs. Following washes with water, the loop-mediated isothermal amplification (LAMP) reagents were aspirated into the capillaries, in which the primers were pre-fixed with chitosan. After that, the PAAC was loaded into the smartphone-based device for a one-hour amplification at 65 °C and end-point detection of calcein fluorescence in the capillaries. The DNA capture efficiency of a 1.1 mm-diameter filter disc was determined to be 97% of λ-DNA and the coefficient of variation among the eight capillaries in the PAAC was only 2.2%. The multiplex detection of genomic DNA extracted from Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus provided limits of detection of 200, 500, and 500 copies, respectively, without any cross-contamination and cross reactions. "Sample-to-answer" detection of E. coli samples was successfully completed in 85 minutes, demonstrating a sensitivity of 200 cfu per capillary. The multiplex "sample-to-answer" detection, the streamlined operation, and the compact device should facilitate a broad range of applications of our PAAC system in point-of-care testing.
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Affiliation(s)
- Junhou Hui
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, China.
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Han J, Gan W, Zhuang B, Sun J, Zhao L, Ye J, Liu Y, Li CX, Liu P. A fully integrated microchip system for automated forensic short tandem repeat analysis. Analyst 2018; 142:2004-2012. [PMID: 28513665 DOI: 10.1039/c7an00295e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have successfully developed an integrated microsystem that combines two plastic microchips for DNA extraction and PCR amplification with a glass capillary array electrophoresis chip together in a compact control and detection instrument for automated forensic short tandem repeat (STR) analysis. DNA extraction followed by an "in situ PCR" was conducted in a single reaction chamber of the microchip based on a filter paper-based extraction methodology. PCR products were then mixed with sizing standards by an injection electrode and injected into the electrophoresis chip for four-color confocal fluorescence detection. The entire STR analysis can be completed in about two hours without any human intervention. Since the 15-plex STR system has a more stringent requirement for PCR efficiency, we optimized the structure of the plastic DNA extraction and amplification chip, in which the reaction chamber was formed by sandwiching a hollow structure layer with two blank cover layers, to reduce the adsorption of PCR reagents to the surfaces. In addition, PCR additives, bovine serum albumin, poly(ethylene glycol), and more magnesium chloride were included into the on-chip multiplex STR system. The limit-of-detection study demonstrated that our microsystem was able to produce full 15-plex STR profiles from 3.75 ng standard K562 DNA. Buccal swab and whole blood samples were also successfully typed by our system, validating the feasibility of performing rapid DNA typing in a "sample-in-answer-out" manner for on-site forensic human identification.
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Affiliation(s)
- Junping Han
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, China.
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22
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Sosa-Acosta J, Silva J, Fernández-Izquierdo L, Díaz-Castañón S, Ortiz M, Zuaznabar-Gardona J, Díaz-García A. Iron Oxide Nanoparticles (IONPs) with potential applications in plasmid DNA isolation. Colloids Surf A Physicochem Eng Asp 2018. [DOI: 10.1016/j.colsurfa.2018.02.062] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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23
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Preconcentration of DNA using magnetic ionic liquids that are compatible with real-time PCR for rapid nucleic acid quantification. Anal Bioanal Chem 2018; 410:4135-4144. [PMID: 29704032 DOI: 10.1007/s00216-018-1092-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/10/2018] [Accepted: 04/16/2018] [Indexed: 12/19/2022]
Abstract
Nucleic acid extraction and purification represents a major bottleneck in DNA analysis. Traditional methods for DNA purification often require reagents that may inhibit quantitative polymerase chain reaction (qPCR) if not sufficiently removed from the sample. Approaches that employ magnetic beads may exhibit lower extraction efficiencies due to sedimentation and aggregation. In this study, four hydrophobic magnetic ionic liquids (MILs) were investigated as DNA extraction solvents with the goal of improving DNA enrichment factors and compatibility with downstream bioanalytical techniques. By designing custom qPCR buffers, we directly incorporated DNA-enriched MILs including trihexyl(tetradecyl)phosphonium tris(hexafluoroacetylaceto)nickelate(II) ([P6,6,6,14+][Ni(hfacac)3-]), [P6,6,6,14+] tris(hexafluoroacetylaceto)colbaltate(II) ([Co(hfacac)3-]), [P6,6,6,14+] tris(hexafluoroacetylaceto)manganate(II) ([Mn(hfacac)3-]), or [P6,6,6,14+] tetrakis(hexafluoroacetylaceto)dysprosate(III) ([Dy(hfacac)4-]) into reaction systems, thereby circumventing the need for time-consuming DNA recovery steps. Incorporating MILs into the reaction buffer did not significantly impact the amplification efficiency of the reaction (91.1%). High enrichment factors were achieved using the [P6,6,6,14+][Ni(hfacac)3-] MIL for the extraction of single-stranded and double-stranded DNA with extraction times as short as 2 min. When compared to a commercial magnetic bead-based platform, the [P6,6,6,14+][Ni(hfacac)3-] MIL was capable of producing higher enrichment factors for single-stranded DNA and similar enrichment factors for double-stranded DNA. The MIL-based method was applied for the extraction and direct qPCR amplification of mutation prone-KRAS oncogene fragment in plasma samples. Graphical abstract Magnetic ionic liquid solvents are shown to preconcentrate sufficient KRAS DNA template from an aqueous solution in as short as 2 min without using chaotropic salts or toxic organic solvents. By using custom-designed qPCR buffers, DNA can be directly amplified and quantified from four MILs examined in this study.
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Zou Y, Mason MG, Wang Y, Wee E, Turni C, Blackall PJ, Trau M, Botella JR. Nucleic acid purification from plants, animals and microbes in under 30 seconds. PLoS Biol 2017; 15:e2003916. [PMID: 29161268 PMCID: PMC5697807 DOI: 10.1371/journal.pbio.2003916] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/17/2017] [Indexed: 12/27/2022] Open
Abstract
Nucleic acid amplification is a powerful molecular biology tool, although its use outside the modern laboratory environment is limited due to the relatively cumbersome methods required to extract nucleic acids from biological samples. To address this issue, we investigated a variety of materials for their suitability for nucleic acid capture and purification. We report here that untreated cellulose-based paper can rapidly capture nucleic acids within seconds and retain them during a single washing step, while contaminants present in complex biological samples are quickly removed. Building on this knowledge, we have successfully created an equipment-free nucleic acid extraction dipstick methodology that can obtain amplification-ready DNA and RNA from plants, animals, and microbes from difficult biological samples such as blood and leaves from adult trees in less than 30 seconds. The simplicity and speed of this method as well as the low cost and availability of suitable materials (e.g., common paper towelling), means that nucleic acid extraction is now more accessible and affordable for researchers and the broader community. Furthermore, when combined with recent advancements in isothermal amplification and naked eye DNA visualization techniques, the dipstick extraction technology makes performing molecular diagnostic assays achievable in limited resource settings including university and high school classrooms, field-based environments, and developing countries.
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Affiliation(s)
- Yiping Zou
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St.Lucia, Australia
| | - Michael Glenn Mason
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St.Lucia, Australia
| | - Yuling Wang
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St.Lucia, Australia
| | - Eugene Wee
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St.Lucia, Australia
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St.Lucia, Australia
| | - Patrick J. Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St.Lucia, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St.Lucia, Australia
| | - Jose Ramon Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St.Lucia, Australia
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You JB, Kim YT, Lee KG, Choi Y, Choi S, Kim CH, Kim KH, Chang SJ, Lee TJ, Lee SJ, Im SG. Surface-Modified Mesh Filter for Direct Nucleic Acid Extraction and its Application to Gene Expression Analysis. Adv Healthc Mater 2017; 6. [PMID: 28714572 DOI: 10.1002/adhm.201700642] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Indexed: 12/23/2022]
Abstract
Rapid and convenient isolation of nucleic acids (NAs) from cell lysate plays a key role for onsite gene expression analysis. Here, this study achieves one-step and efficient capture of NA directly from cell lysate by developing a cationic surface-modified mesh filter (SMF). By depositing cationic polymer via vapor-phase deposition process, strong charge interaction is introduced on the surface of the SMF to capture the negatively charged NAs. The NA capturing capability of SMF is confirmed by X-ray photoelectron spectroscopy, fluorescent microscopy, and zeta potential measurement. In addition, the genomic DNAs of Escherichia Coli O157:H7 can be extracted by the SMF from artificially infected food, and fluorescent signal is observed on the surface of SMF after amplification of target gene. The proposed SMF is able to provide a more simplified, convenient, and fast extraction method and can be applied to the fields of food safety testing, clinical diagnosis, or environmental pollutant monitoring.
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Affiliation(s)
- Jae Bem You
- Department of Chemical and Biomolecular Engineering; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Yong Tae Kim
- Department of Nano Bio Research; National NanoFab Center (NNFC); Daejeon 34141 Republic of Korea
| | - Kyoung G. Lee
- Department of Nano Bio Research; National NanoFab Center (NNFC); Daejeon 34141 Republic of Korea
| | - Yunho Choi
- Department of Chemical and Biomolecular Engineering; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Seongkyun Choi
- Department of Nano Bio Research; National NanoFab Center (NNFC); Daejeon 34141 Republic of Korea
| | - Chi Hyun Kim
- Department of Nano Bio Research; National NanoFab Center (NNFC); Daejeon 34141 Republic of Korea
| | - Kyung Hoon Kim
- Department of Nano Bio Research; National NanoFab Center (NNFC); Daejeon 34141 Republic of Korea
| | - Sung Jin Chang
- Department of Chemistry; Chung-Ang University; Seoul 06911 Republic of Korea
| | - Tae Jae Lee
- Department of Nano Bio Research; National NanoFab Center (NNFC); Daejeon 34141 Republic of Korea
| | - Seok Jae Lee
- Department of Nano Bio Research; National NanoFab Center (NNFC); Daejeon 34141 Republic of Korea
| | - Sung Gap Im
- Department of Chemical and Biomolecular Engineering; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
- Graphene Research Center in KAIST Institute for NanoCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
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26
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From Electrochemistry to Electroluminescence: Development and Application in a Ratiometric Aptasensor for Aflatoxin B1. Anal Chem 2017. [DOI: 10.1021/acs.analchem.7b01399] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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27
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Binding efficacy and kinetics of chitosan with DNA duplex: The effects of deacetylation degree and nucleotide sequences. Carbohydr Polym 2017; 169:451-457. [PMID: 28504168 DOI: 10.1016/j.carbpol.2017.04.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/13/2017] [Accepted: 04/18/2017] [Indexed: 11/24/2022]
Abstract
The binding process of DNA duplex with various types of chitosan polymers were studied at atomic level through molecular dynamics simulations. The interaction kinetics and binding strength, complex morphology and DNA structure evolution were systematically accessed. The binding efficacy of chitosan to DNA reduces (both in complexation speed and binding strength) when deacetylation degree is decreased, because protonated amine groups on chitosan backbone are more prone to bind with DNA, especially the phosphate oxygen, through coulomb interaction. The Watson Crick hydrogen bonds of A-T base pairs are more easily to break because chitosan is capable to form competitive hydrogen bonds with them. It is surprising to find that the G-C nucleotides have highly restrained kinetic motion than that of A-T nucleotides, which would be important for DNA-chitosan complexation and condensation to happen at the microscopic level. From our current results, the degree of chitosan deacetylation is found to play a certain role in regulating the DNA-chitosan complexation process, but is not as important as being believed before. Other types of chemical functionalization that can tune the chitosan's hydrophobicity should deserve more attentions in the experiment.
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28
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Magnetic- and pH-responsive κ-carrageenan/chitosan complexes for controlled release of methotrexate anticancer drug. Int J Biol Macromol 2017; 97:209-217. [DOI: 10.1016/j.ijbiomac.2017.01.012] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/09/2016] [Accepted: 01/02/2017] [Indexed: 12/15/2022]
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29
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Gan W, Gu Y, Han J, Li CX, Sun J, Liu P. Chitosan-Modified Filter Paper for Nucleic Acid Extraction and "in Situ PCR" on a Thermoplastic Microchip. Anal Chem 2017; 89:3568-3575. [PMID: 28230980 DOI: 10.1021/acs.analchem.6b04882] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Plastic microfluidic devices with embedded chitosan-modified Fusion 5 filter paper (unmodified one purchased from GE Healthcare) have been successfully developed for DNA extraction and concentration, utilizing two different mechanisms for DNA capture: the physical entanglement of long-chain DNA molecules with the fiber matrix of the filter paper and the electrostatic adsorption of DNA to the chitosan-modified filter fibers. This new method not only provided a high DNA extraction efficiency at a pH of 5 by synergistically combining these two capture mechanisms together, but also resisted the elution of DNA from filters at a pH > 8 due to the entanglement of DNA with fibers. As a result, PCR buffers can be directly loaded into the extraction chamber for "in situ PCR", in which the captured DNA were used for downstream analysis without any loss. We demonstrated that the capture efficiencies of a 3-mm-diameter filter disc in a microchip were 98% and 95% for K562 human genomic DNA and bacteriophage λ-DNA, respectively. The washes with DI water, PCR mixture, and TE buffer cannot elute the captured DNA. In addition, the filter disc can enrich 62% of λ-DNA from a diluted sample (0.05 ng/μL), providing a concentration factor more than 30-fold. Finally, a microdevice with a simple two-chamber structure was developed for on-chip cell lysis, DNA extraction, and 15-plex short tandem repeat amplification from blood. This DNA extraction coupled with "in situ PCR" has great potential to be utilized in fully integrated microsystems for rapid, near-patient nucleic acid testing.
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Affiliation(s)
- Wupeng Gan
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University , Beijing 100084, China
| | - Yin Gu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University , Beijing 100084, China
| | - Junping Han
- Technology Department of Chaoyang Sub-bureau, Beijing Public Security Bureau , Beijing 100102, China
| | - Cai-Xia Li
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Crime Scene Evidence Examination, Institute of Forensic Science , Beijing 100038, China
| | - Jing Sun
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Crime Scene Evidence Examination, Institute of Forensic Science , Beijing 100038, China
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University , Beijing 100084, China
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30
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Magnetic nanowires for rapid and ultrasensitive isolation of DNA from cervical specimens for the detection of multiple human papillomaviruses genotypes. Biosens Bioelectron 2016; 86:864-870. [DOI: 10.1016/j.bios.2016.07.066] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 11/22/2022]
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31
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Schlappi TS, McCalla SE, Schoepp NG, Ismagilov RF. Flow-through Capture and in Situ Amplification Can Enable Rapid Detection of a Few Single Molecules of Nucleic Acids from Several Milliliters of Solution. Anal Chem 2016; 88:7647-53. [PMID: 27429181 DOI: 10.1021/acs.analchem.6b01485] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Detecting nucleic acids (NAs) at zeptomolar concentrations (few molecules per milliliter) currently requires expensive equipment and lengthy processing times to isolate and concentrate the NAs into a volume that is amenable to amplification processes, such as PCR or LAMP. Shortening the time required to concentrate NAs and integrating this procedure with amplification on-device would be invaluable to a number of analytical fields, including environmental monitoring and clinical diagnostics. Microfluidic point-of-care (POC) devices have been designed to address these needs, but they are not able to detect NAs present in zeptomolar concentrations in short time frames because they require slow flow rates and/or they are unable to handle milliliter-scale volumes. In this paper, we theoretically and experimentally investigate a flow-through capture membrane that solves this problem by capturing NAs with high sensitivity in a short time period, followed by direct detection via amplification. Theoretical predictions guided the choice of physical parameters for a chitosan-coated nylon membrane; these predictions can also be applied generally to other capture situations with different requirements. The membrane is also compatible with in situ amplification, which, by eliminating an elution step enables high sensitivity and will facilitate integration of this method into sample-to-answer detection devices. We tested a wide range of combinations of sample volumes and concentrations of DNA molecules using a capture membrane with a 2 mm radius. We show that for nucleic acid detection, this approach can concentrate and detect as few as ∼10 molecules of DNA with flow rates as high as 1 mL/min, handling samples as large as 50 mL. In a specific example, this method reliably concentrated and detected ∼25 molecules of DNA from 50 mL of sample.
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Affiliation(s)
- Travis S Schlappi
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Stephanie E McCalla
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Nathan G Schoepp
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
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