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Shi YJ, Che YN, Zhao YM, Ran RX, Zhao YQ, Yu SS, Chen MY, Dong LY, Zhao ZY, Wang XH. High-efficient separation of deoxyribonucleic acid from pathogenic bacteria by hedgehog-inspired magnetic nanoparticles microextraction. J Chromatogr A 2024; 1724:464923. [PMID: 38653039 DOI: 10.1016/j.chroma.2024.464923] [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: 02/07/2024] [Revised: 03/28/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
Efficient separation of deoxyribonucleic acid (DNA) through magnetic nanoparticles (MN) is a widely used biotechnology. Hedgehog-inspired MNs (HMN) possess a high-surface-area due to the distinct burr-like structure of hedgehog, but there is no report about the usage of HMN for DNA extraction. Herein, to improve the selection of MN and illustrate the performance of HMN for DNA separation, HMN and silica-coated Fe3O4 nanoparticles (Fe3O4@SiO2) were fabricated and compared for the high-efficient separation of pathogenic bacteria of DNA. Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) are typical Gram-negative and Gram-positive bacteria and are selected as model pathogenic bacteria. To enhance the extraction efficiency of two kinds of MNs, various parameters, including pretreatment, lysis, binding and elution conditions, have been optimized in detail. In most separation experiments, the DNA yield of HMN was higher than that of Fe3O4@SiO2. Therefore, a HMN-based magnetic solid-phase microextraction (MSPE) and quantitative real-time PCR (qPCR) were integrated and used to detect pathogenic bacteria in real samples. Interestingly, the HMN-based MSPE combined qPCR strategy exhibited high sensitivity with a limit of detection of 2.0 × 101 CFU mL-1 for E. coli and 4.0 × 101 CFU mL-1 for S. aureus in orange juice, and 2.8 × 102 CFU mL-1 for E. coli and 1.1 × 102 CFU mL-1 for S. aureus in milk, respectively. The performance of the proposed strategy was significantly better than that of commercial kit. This work could prove that the novel HMN could be applicable for the efficient separation of DNA from complex biological samples.
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Affiliation(s)
- Yu-Jun Shi
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China; NHC Key Laboratory of Hormones and Development / Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital / Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Ya-Ning Che
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China; NHC Key Laboratory of Hormones and Development / Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital / Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Yi-Mei Zhao
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China; NHC Key Laboratory of Hormones and Development / Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital / Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Rui-Xue Ran
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Ya-Qi Zhao
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China; NHC Key Laboratory of Hormones and Development / Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital / Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Shi-Song Yu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China; NHC Key Laboratory of Hormones and Development / Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital / Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Meng-Ying Chen
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China; NHC Key Laboratory of Hormones and Development / Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital / Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Lin-Yi Dong
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
| | - Zhen-Yu Zhao
- NHC Key Laboratory of Hormones and Development / Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital / Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China.
| | - Xian-Hua Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
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Wang X, Guo Q, Guo J, Wang C. Magnetic composite microspheres with a controlled mesoporous shell for highly efficient DNA extraction and fragment screening. J Mater Chem B 2024; 12:4899-4908. [PMID: 38682549 DOI: 10.1039/d4tb00104d] [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: 05/01/2024]
Abstract
Rapid extraction and screening of high-purity DNA fragments is an indispensable technology in advanced molecular biology. In this article, mesoporous magnetic composite microspheres (MSP@mTiO2) with tunable pore sizes were successfully fabricated for high-purity DNA extraction and fragment screening. Owing to the strong complexation ability of Ti ions with DNA phosphate groups and the high specific surface area of mesoporous microspheres, the MSP@mTiO2 microspheres possess excellent adsorption performance, where the saturated loading capacity of MSP@mTiO2 with a specific surface area of 122 m2 g-1 is as high as 575 μg mg-1 for a salmon sperm specimen. ITC experiments demonstrated that DNA adsorption on MSP@mTiO2 microspheres is mainly driven by entropy, which gives us more potential ways to regulate the balance of adsorption and desorption. Meanwhile, the mesoporous MSP@mTiO2 microspheres exhibit a much higher extraction efficiency compared with non-porous MSP@TiO2 for whole genome DNA from Arabidopsis thaliana plants. Interestingly, DNA fragments with different lengths could be screened by simply regulating the pore size of MSP@mTiO2 or the concentration of Na3PO4 in the eluent. A small pore size and low phosphate concentration are advantageous for the extraction of short-stranded DNA fragments, and DNA fragments (≤1000 bp) can be efficiently extracted when the mesopore size of MSP@mTiO2 is lower than 7.6 nm. The extraction results from the mesoporous composite microspheres provide new promising insights into the purification and screening of DNA from complex biological samples.
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Affiliation(s)
- Xiuli Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China.
| | - Qilin Guo
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China.
| | - Jia Guo
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China.
| | - Changchun Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China.
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Wang X, Fei W, Zhou Z, Zhu M, Chang Y, Guo Q, Guo J, Wang C. Immobilization of Multivalent Titanium Cations on Magnetic Composite Microspheres for Highly Efficient DNA Extraction and Amplification. ACS APPLIED MATERIALS & INTERFACES 2023; 15:42170-42181. [PMID: 37654059 DOI: 10.1021/acsami.3c05502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Magnetic-assisted DNA testing technology has attracted much attention in genetics, clinical diagnostics, environmental microbiology, and molecular biology. However, achieving satisfying DNA adsorption and desorption efficiency in real samples is still a big challenge. In this paper, a new kind of high-quality magnetic composite microsphere of MM@PGMA-PA-Ti4+ was designed and prepared for DNA extraction and detection based on the strong interaction of Ti4+ and phosphate groups. By taking the advantages of high magnetic susceptibility and high Ti4+ content, the MM@PGMA-PA-Ti4+ microspheres possessed remarkable extraction capacity for mimic biological samples (salmon sperm specimens) with saturated loadings up to 533.0 mg/g. When the DNA feeding amount was 100 μg and the MM@PGMA-PA-Ti4+ dosage was 1 mg, the adsorption and desorption efficiencies were 80 and 90%, respectively. The kinetic and equilibrium extraction data were found to fit well with the pseudo-second-order model and Freundlich isotherm model. Furthermore, the MM@PGMA-PA-Ti4+ microspheres were successfully employed for DNA extraction from mouse epithelial-like fibroblasts. The extraction ability (84 ± 4 μg/mg) and DNA purity were superior to the comparative commercial spin kits, as evaluated by electrophoresis assays and qPCR analysis. The experimental results suggest that the MM@PGMA-PA-Ti4+ microspheres possess great potential as an adsorbent for DNA purification from complex biological samples.
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Affiliation(s)
- Xiuli Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China
| | - Weiwei Fei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China
| | - Zhifan Zhou
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China
| | - Mengjing Zhu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China
| | - Yinghao Chang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China
| | - Qilin Guo
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China
| | - Jia Guo
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China
| | - Changchun Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China
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Yuan Q, Wang Y, Wang S, Li R, Ma J, Wang Y, Sun R, Luo Y. Adenine imprinted beads as a novel selective extracellular DNA extraction method reveals underestimated prevalence of extracellular antibiotic resistance genes in various environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158570. [PMID: 36075418 DOI: 10.1016/j.scitotenv.2022.158570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/29/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Despite severe threats of extracellular antibiotic resistance genes (eARGs) towards public health in various environments, advanced studies have been hindered mainly by ineffective extracellular DNA (exDNA) extraction methods, which is challenged by trace levels of exDNA and inference from abundant coexisting compounds. This study developed a highly selective exDNA extraction method based on molecular imprinting technology (MIT) by using adenine as the template for the first time. Results suggested that adenine imprinted beads were rough spheres at an average size of 0.39 ± 0.07 μm. They effectively adsorbed DNA in the absence of chaotropic agents, with superior capacity (796.2 mg/g), rate (0.0066/s) and regarding DNA of variable lengths, even the ultra-short DNA (<100 bp). They were also highly selective towards DNA, circumventing the interference of competitive compounds' interference. These properties contribute to efficient exDNA extraction (71 %-119 %) from various environmental samples. Specifically, adenine imprinted beads enabled significantly higher extraction rates of eARGs from river, air and vegetable samples (69 %-95 %) compared to that by commercial DNA extraction products (16 %-62 %). The adenine imprinted beads-based method reveals underestimated eARG levels in the environment and the corresponding risks, and thus will thus be a powerful tool for advanced exDNA research.
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Affiliation(s)
- Qingbin Yuan
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Yi Wang
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Shangjie Wang
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ruiqing Li
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Junlu Ma
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yijing Wang
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ruonan Sun
- Department of Civil and Environmental Engineering, Rice University, Houston 77005, USA
| | - Yi Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
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Szymczyk A, Drozd M, Kamińska A, Matczuk M, Trzaskowski M, Mazurkiewicz-Pawlicka M, Ziółkowski R, Malinowska E. Comparative Evaluation of Different Surface Coatings of Fe3O4-Based Magnetic Nano Sorbent for Applications in the Nucleic Acids Extraction. Int J Mol Sci 2022; 23:ijms23168860. [PMID: 36012139 PMCID: PMC9408759 DOI: 10.3390/ijms23168860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/01/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
Nucleic acid extraction and purification are crucial steps in sample preparation for multiple diagnostic procedures. Routine methodologies of DNA isolation require benchtop equipment (e.g., centrifuges) and labor-intensive steps. Magnetic nanoparticles (MNPs) as solid-phase sorbents could simplify this procedure. A wide range of surface coatings employs various molecular interactions between dsDNA and magnetic nano-sorbents. However, a reliable, comparative evaluation of their performance is complex. In this work, selected Fe3O4 modifications, i.e., polyethyleneimine, gold, silica, and graphene derivatives, were comprehensively evaluated for applications in dsDNA extraction. A family of single batch nanoparticles was compared in terms of morphology (STEM), composition (ICP-MS/MS and elemental analysis), surface coating (UV-Vis, TGA, FTIR), and MNP charge (ζ-potential). ICP-MS/MS was also used to unify MNPs concentration allowing a reliable assessment of individual coatings on DNA extraction. Moreover, studies on adsorption medium (monovalent vs. divalent ions) and extraction buffer composition were carried out. As a result, essential relationships between nanoparticle coatings and DNA adsorption efficiencies have been noticed. Fe3O4@PEI MNPs turned out to be the most efficient nano sorbents. The optimized composition of the extraction buffer (medium containing 0.1 mM EDTA) helped avoid problems with Fe3+ stripping, which improved the validity of the spectroscopic determination of DNA recovery.
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Affiliation(s)
- Anna Szymczyk
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
- Doctoral School No. 1, Warsaw University of Technology, Plac Politechniki 1, 00-661 Warsaw, Poland
| | - Marcin Drozd
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
- Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
| | - Agnieszka Kamińska
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
| | - Magdalena Matczuk
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
| | - Maciej Trzaskowski
- Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
| | - Marta Mazurkiewicz-Pawlicka
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, Ludwika Waryńskiego 1, 00-645 Warsaw, Poland
| | - Robert Ziółkowski
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
- Correspondence:
| | - Elżbieta Malinowska
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
- Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
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