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Yajima S, Koto A, Koda M, Sakamoto H, Takamura E, Suye SI. Photo-Cross-Linked Probe-Modified Magnetic Particles for the Selective and Reliable Recovery of Nucleic Acids. ACS OMEGA 2022; 7:12701-12706. [PMID: 35474845 PMCID: PMC9026142 DOI: 10.1021/acsomega.1c07012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Polymerase chain reaction (PCR) assays are used to diagnose various infectious diseases such as Coronavirus disease 2019 by detecting the nucleic acids of the pathogen. However, in practice, the yield of the extraction process and the inhibition of the reverse transcription reaction and PCR by foreign substances reduce the sensitivity and may yield false negative results. The sensitivity of the PCR test can be improved by using technologies that can reliably capture the target nucleic acid and remove foreign substances. In this study, we developed photo-cross-linkable probe-modified magnetic particles (PPMPs) for the sequence-specific recovery of target nucleic acids using photo-cross-linkable artificial nucleic acid probes and magnetic particles. Nucleic acid probes modified with photo-cross-linkable artificial nucleic acids can hybridize with the target nucleic acids in a sequence-specific manner and then securely capture the target nucleic acids by UV irradiation-mediated covalent bonding. Then the target nucleic acid is detected by trapping the target-bound probe on the surface of the magnetic particles and subjecting these collected magnetic particles to PCR. Recovery of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) N gene pseudo-DNA (120 bp) was performed using PPMPs. We confirmed that the PPMPs captured the target consistently even after washes were done with denaturing agents and surfactants. Even in the presence of foreign DNA fragments, PPMPs were able to specifically recover the target DNA. This method allows for a more accurate detection by recovering only the target DNA for PCR. Hence, PPMPs can be successfully used for PCR-mediated detection of SARS-CoV-2 and other pathogens whose nucleic acid sequences are known.
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Affiliation(s)
- Shuto Yajima
- Department
of Frontier Fiber Technology and Science, Graduate School of Engineering, University of Fukui, 3-9-1, Bunkyo, Fukui 910-8507, Japan
| | - Ayako Koto
- Department
of Advanced Interdisciplinary Science and Technology, Graduate School
of Engineering, University of Fukui, 3-9-1, Bunkyo, Fukui 910-8507, Japan
- Advanced
Technology Research Department, Institute of Surface Science Technology, Nicca Chemical Co., Ltd., 4-23-1, Bunkyo, Fukui 910-8670, Japan
| | - Maho Koda
- Department
of Materials Science and Biotechnology, School of Engineering, University of Fukui, 3-9-1, Bunkyo, Fukui 910-8507, Japan
| | - Hiroaki Sakamoto
- Department
of Frontier Fiber Technology and Science, Graduate School of Engineering, University of Fukui, 3-9-1, Bunkyo, Fukui 910-8507, Japan
| | - Eiichiro Takamura
- Department
of Frontier Fiber Technology and Science, Graduate School of Engineering, University of Fukui, 3-9-1, Bunkyo, Fukui 910-8507, Japan
| | - Shin-ichiro Suye
- Department
of Frontier Fiber Technology and Science, Graduate School of Engineering, University of Fukui, 3-9-1, Bunkyo, Fukui 910-8507, Japan
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Jeong S, González-Grandío E, Navarro N, Pinals RL, Ledesma F, Yang D, Landry MP. Extraction of Viral Nucleic Acids with Carbon Nanotubes Increases SARS-CoV-2 Quantitative Reverse Transcription Polymerase Chain Reaction Detection Sensitivity. ACS NANO 2021; 15:10309-10317. [PMID: 34105936 PMCID: PMC8204751 DOI: 10.1021/acsnano.1c02494] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/04/2021] [Indexed: 05/25/2023]
Abstract
The global SARS-CoV-2 coronavirus pandemic has led to a surging demand for rapid and efficient viral infection diagnostic tests, generating a supply shortage in diagnostic test consumables including nucleic acid extraction kits. Here, we develop a modular method for high-yield extraction of viral single-stranded nucleic acids by using "capture" ssDNA sequences attached to carbon nanotubes. Target SARS-CoV-2 viral RNA can be captured by ssDNA-nanotube constructs via hybridization and separated from the liquid phase in a single-tube system with minimal chemical reagents, for downstream quantitative reverse transcription polymerase chain reaction (RT-qPCR) detection. This nanotube-based extraction method enables 100% extraction yield of target SARS-CoV-2 RNA from phosphate-buffered saline in comparison to ∼20% extraction yield when using a commercial silica-column kit. Notably, carbon nanotubes enable extraction of nucleic acids directly from 50% human saliva with a similar efficiency as achieved with commercial DNA/RNA extraction kits, thereby bypassing the need for further biofluid purification and avoiding the use of commercial extraction kits. Carbon nanotube-based extraction of viral nucleic acids facilitates high-yield and high-sensitivity identification of viral nucleic acids such as the SARS-CoV-2 viral genome with a reduced reliance on reagents affected by supply chain obstacles.
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Affiliation(s)
- Sanghwa Jeong
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- School of Biomedical Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Eduardo González-Grandío
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Nicole Navarro
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Rebecca L Pinals
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Francis Ledesma
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Darwin Yang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Innovative Genomics Institute (IGI), Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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Anik MI, Hossain MK, Hossain I, Mahfuz AMUB, Rahman MT, Ahmed I. Recent progress of magnetic nanoparticles in biomedical applications: A review. NANO SELECT 2021. [DOI: 10.1002/nano.202000162] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Muzahidul I. Anik
- Chemical Engineering University of Rhode Island Kingston Rhode Island 02881 USA
| | - M. Khalid Hossain
- Interdisciplinary Graduate School of Engineering Science Kyushu University Fukuoka 816–8580 Japan
- Atomic Energy Research Establishment Bangladesh Atomic Energy Commission Dhaka 1349 Bangladesh
| | - Imran Hossain
- Institute for Micromanufacturing Louisiana Tech University Ruston Louisiana 71270 USA
| | - A. M. U. B. Mahfuz
- Biotechnology and Genetic Engineering University of Development Alternative Dhaka 1209 Bangladesh
| | - M. Tayebur Rahman
- Materials Science and Engineering University of Rajshahi Rajshahi 6205 Bangladesh
| | - Isteaque Ahmed
- Chemical Engineering University of Cincinnati Cincinnati Ohio 45221 USA
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Gopal H, Hassan HK, Rodríguez-Pérez MA, Toé LD, Lustigman S, Unnasch TR. Oligonucleotide based magnetic bead capture of Onchocerca volvulus DNA for PCR pool screening of vector black flies. PLoS Negl Trop Dis 2012; 6:e1712. [PMID: 22724041 PMCID: PMC3378604 DOI: 10.1371/journal.pntd.0001712] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 05/14/2012] [Indexed: 11/30/2022] Open
Abstract
Background Entomological surveys of Simulium vectors are an important component in the criteria used to determine if Onchocerca volvulus transmission has been interrupted and if focal elimination of the parasite has been achieved. However, because infection in the vector population is quite rare in areas where control has succeeded, large numbers of flies need to be examined to certify transmission interruption. Currently, this is accomplished through PCR pool screening of large numbers of flies. The efficiency of this process is limited by the size of the pools that may be screened, which is in turn determined by the constraints imposed by the biochemistry of the assay. The current method of DNA purification from pools of vector black flies relies upon silica adsorption. This method can be applied to screen pools containing a maximum of 50 individuals (from the Latin American vectors) or 100 individuals (from the African vectors). Methodology/Principal Findings We have evaluated an alternative method of DNA purification for pool screening of black flies which relies upon oligonucleotide capture of Onchocerca volvulus genomic DNA from homogenates prepared from pools of Latin American and African vectors. The oligonucleotide capture assay was shown to reliably detect one O. volvulus infective larva in pools containing 200 African or Latin American flies, representing a two-four fold improvement over the conventional assay. The capture assay requires an equivalent amount of technical time to conduct as the conventional assay, resulting in a two-four fold reduction in labor costs per insect assayed and reduces reagent costs to $3.81 per pool of 200 flies, or less than $0.02 per insect assayed. Conclusions/Significance The oligonucleotide capture assay represents a substantial improvement in the procedure used to detect parasite prevalence in the vector population, a major metric employed in the process of certifying the elimination of onchocerciasis. The absence of infective larvae of Onchocerca volvulus in the black fly vector of this parasite is a major criterion used to certify that transmission has been eliminated in a focus. This process requires screening large numbers of flies. Currently, this is accomplished by screening pools of flies using a PCR-based assay. The number of flies that may be included in each pool is currently limited by the DNA purification process to 50 flies for Latin American vectors and 100 flies for African vectors. Here, we describe a new method for DNA purification that relies upon a specific oligonucleotide to capture and immobilize the parasite DNA on a magnetic bead. This method permits the reliable detection of a single infective larva of O. volvulus in pools containing up to 200 individual flies. The method described here will dramatically improve the efficiency of pool screening of vector black flies, making the process of elimination certification easier and less expensive to implement.
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Affiliation(s)
- Hemavathi Gopal
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, México
| | - Hassan K. Hassan
- Department of Global Health, Global Health Infectious Disease Research Program, University of South Florida, Tampa, Florida, United States of America
| | | | - Laurent D. Toé
- Multi-Disease Surveillance Centre, Ouagadougou, Burkina Faso
| | - Sara Lustigman
- Laboratory of Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York, United States of America
| | - Thomas R. Unnasch
- Department of Global Health, Global Health Infectious Disease Research Program, University of South Florida, Tampa, Florida, United States of America
- * E-mail:
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Abstract
PURPOSE OF REVIEW Molecular techniques offer the promise of improving diagnosis of lower respiratory tract infections. This review focuses on currently used molecular diagnostic techniques for various types of pneumonia and highlights potential future applications of this technology. RECENT FINDINGS Lower respiratory tract infections result in a high degree of morbidity and mortality, but a definitive microbiologic diagnosis is often not obtained by traditional culture or serologic methods. In addition, culture of certain organisms may be difficult or require extended periods of time. Molecular techniques have the potential to improve diagnostic yield and decrease time to pathogen identification. These techniques are also helpful in the determination of drug sensitivity and the understanding of transmission and outbreaks. Most currently used techniques employ some variation of the polymerase chain reaction. Limitations include high costs, the need for specialized equipment, and problems with false-positive and -negative results. SUMMARY Molecular diagnosis of pneumonia has the potential to improve identification of pathogens in patients with suspected lower respiratory tract infection. Limitations of molecular techniques currently prevent their widespread use, but future developments will likely lead to inclusion of these tests in routine diagnostic evaluations.
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Affiliation(s)
- Yvonne R Chan
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
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Berensmeier S. Magnetic particles for the separation and purification of nucleic acids. Appl Microbiol Biotechnol 2006; 73:495-504. [PMID: 17063328 PMCID: PMC7080036 DOI: 10.1007/s00253-006-0675-0] [Citation(s) in RCA: 308] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Revised: 09/04/2006] [Accepted: 09/12/2006] [Indexed: 11/16/2022]
Abstract
Nucleic acid separation is an increasingly important tool for molecular biology. Before modern technologies could be used, nucleic acid separation had been a time- and work-consuming process based on several extraction and centrifugation steps, often limited by small yields and low purities of the separation products, and not suited for automation and up-scaling. During the last few years, specifically functionalised magnetic particles were developed. Together with an appropriate buffer system, they allow for the quick and efficient purification directly after their extraction from crude cell extracts. Centrifugation steps were avoided. In addition, the new approach provided for an easy automation of the entire process and the isolation of nucleic acids from larger sample volumes. This review describes traditional methods and methods based on magnetic particles for nucleic acid purification. The synthesis of a variety of magnetic particles is presented in more detail. Various suppliers of magnetic particles for nucleic acid separation as well as suppliers offering particle-based kits for a variety of different sample materials are listed. Furthermore, commercially available manual magnetic separators and automated systems for magnetic particle handling and liquid handling are mentioned.
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Affiliation(s)
- Sonja Berensmeier
- Forschungszentrum Karlsruhe, Institute for Technical Chemistry, Water Technology and Geotechnology Division, Hermann-v.-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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