1
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Wang Z, Yan B, Ni Y, Cao Y, Qiu J, He R, Dong Y, Hao M, Wang W, Wang C, Su H, Yi B, Chang L. A portable, integrated microfluidics for rapid and sensitive diagnosis of Streptococcus agalactiae in resource-limited environments. Biosens Bioelectron 2024; 247:115917. [PMID: 38101186 DOI: 10.1016/j.bios.2023.115917] [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: 09/27/2023] [Revised: 11/23/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
Streptococcus agalactiae (Group B Streptococcus, GBS) has been the leading cause of infections in newborns. Rapid and accurate diagnosis of GBS in pregnant women is a deterministic strategy to prevent newborn infection. Conventional detection methods based on nucleic acid amplification assay have been applied in GBS diagnosis in central laboratories, with demonstrated high sensitivity. However, their heavy dependence on instrumentation and trained technicians forms remarkable obstacles to GBS detection in wide scenarios, including self-testing, and bedside-/community-screening. Furthermore, the structures of GBS bring about extra challenges to the nucleic acid extraction and purification. Novel GBS diagnosis platforms integrating sample processing, amplification, and read-out, are highly desired in clinical. Here, we report a portable, integrated microfluidics that enables rapid extraction of DNA from sampling swabs (<10 min), power-free DNA amplification (<30 min), and simple read-out in GBS detection. The platform works without an external pump, achieving rapid and highly efficient DNA extraction from clinical samples, with a significantly reduced time from 6 h to less than 50 min. Systematic clinical tests based on 47 patient samples validated the high performance of the platform, highlighted with a low limit of detection (LOD, 103 copies/ml), high sensitivity (100%), and specificity (100%). Head-to-head comparisons showed that the device improved the LOD by an order of magnitude than the traditional PCR method, showing a simple yet powerful POCT platform for home-/community-based testing towards GBS (and other pathogens) prevention in remote areas.
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Affiliation(s)
- Zhiying Wang
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Bo Yan
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; Gansu Province Clinical Research Center for Infertility, Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Yali Ni
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; Gansu Province Clinical Research Center for Infertility, Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Yafei Cao
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; Gansu Province Clinical Research Center for Infertility, Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; The First Clinical Medical College of Gansu University of Chinese Medicine, Lanzhou, 730000, China
| | - Jie Qiu
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Rui He
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Yan Dong
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Man Hao
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Weikai Wang
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; Gansu Province Clinical Research Center for Pediatric, Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Cheng Wang
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Haixiang Su
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China.
| | - Bin Yi
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; Gansu Province Clinical Research Center for Pediatric, Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China.
| | - Lingqian Chang
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China.
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2
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Malburet C, Carboni A, Guinamand S, Naik H, Fertier-Prizzon S. mRNA extraction from lipid nanoparticles. J Chromatogr A 2024; 1714:464545. [PMID: 38070303 DOI: 10.1016/j.chroma.2023.464545] [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: 10/03/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Messenger RiboNucleic Acid (mRNA) vaccines have recently shown considerable promises for both prophylactic and therapeutic vaccines. These vaccines do not carry an antigen but the information for producing it using the cell machinery, turning the human body into an antigen factory. However, mRNA is an unstable molecule, susceptible to physical, chemical and enzymatic degradation by exo- and endonucleases. If the mRNA is degraded, it can no longer be translated correctly into the antigen of interest and the vaccine lose its efficacy. To protect from nucleases degradation and allow it to get into the cells, mRNA can be encapsulated in lipid nanoparticles (LNPs). As part of the manufacturing process, the quality of the mRNAs should be controlled before the encapsulation (at the drug substance stage) as well as after formulation on the final vaccine product (at the drug product stage). Therefore, it is necessary to be able to extract the mRNA from the LNPs, that is to deformulate the final vaccine product. In this work, different deformulation methods have been compared: spin column extraction, magnetic particle extraction, organic extraction, and direct disruption. Advantages and disadvantages of each of these methods are highlighted.
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Affiliation(s)
- Camille Malburet
- Sanofi, 1541 Avenue Marcel Mérieux, 69280 Marcy l'Etoile, France.
| | - Aurelien Carboni
- Sanofi, 1541 Avenue Marcel Mérieux, 69280 Marcy l'Etoile, France
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3
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Gall-David SL, Boudry G, Buffet-Bataillon S. Comparison of four DNA extraction kits efficiency for 16SrDNA microbiota profiling of diverse human samples. Future Sci OA 2023; 9:FSO837. [PMID: 37006230 PMCID: PMC10051199 DOI: 10.2144/fsoa-2022-0072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/14/2023] [Indexed: 03/11/2023] Open
Abstract
Aim: The current study investigated the performance of 4 widely used DNA extraction kits using different types of high (stool) and low biomass samples (chyme, broncho alveolar lavage and sputum). Methods: Qiagen Powerfecal Pro DNA kit, Macherey Nucleospin Soil kit, Macherey Nucleospin Tissue Kit and MagnaPure LC DNA isolation kit III were evaluated in terms of DNA quantity, quality, diversity and composition profiles. Results: The quantity and quality of DNA varied among the four kits. The microbiota of the stool samples showed similar diversity and compositional profiles for the 4 kits. Conclusion: Despite differences in DNA quality and quantity, the 4 kits yielded similar results for stool samples, while all kits were not sensitive enough for low biomass samples.
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Affiliation(s)
| | - Gaëlle Boudry
- Institut Numecan, INSERM, INRAE, Univ Rennes, Rennes, France
| | - Sylvie Buffet-Bataillon
- Institut Numecan, INSERM, INRAE, Univ Rennes, Rennes, France
- Bacteriology, Pontchaillou University Hospital, Rennes, France
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4
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Ghouneimy A, Mahas A, Marsic T, Aman R, Mahfouz M. CRISPR-Based Diagnostics: Challenges and Potential Solutions toward Point-of-Care Applications. ACS Synth Biol 2022; 12:1-16. [PMID: 36508352 PMCID: PMC9872163 DOI: 10.1021/acssynbio.2c00496] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The COVID-19 pandemic has challenged the conventional diagnostic field and revealed the need for decentralized Point of Care (POC) solutions. Although nucleic acid testing is considered to be the most sensitive and specific disease detection method, conventional testing platforms are expensive, confined to central laboratories, and are not deployable in low-resource settings. CRISPR-based diagnostics have emerged as promising tools capable of revolutionizing the field of molecular diagnostics. These platforms are inexpensive, simple, and do not require the use of special instrumentation, suggesting they could democratize access to disease diagnostics. However, there are several obstacles to the use of the current platforms for POC applications, including difficulties in sample processing and stability. In this review, we discuss key advancements in the field, with an emphasis on the challenges of sample processing, stability, multiplexing, amplification-free detection, signal interpretation, and process automation. We also discuss potential solutions for revolutionizing CRISPR-based diagnostics toward sample-to-answer diagnostic solutions for POC and home use.
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Affiliation(s)
- Ahmed Ghouneimy
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ahmed Mahas
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tin Marsic
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Rashid Aman
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi Arabia,
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5
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Mannier C, Yoon JY. Progression of LAMP as a Result of the COVID-19 Pandemic: Is PCR Finally Rivaled? BIOSENSORS 2022; 12:492. [PMID: 35884295 PMCID: PMC9312731 DOI: 10.3390/bios12070492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 06/01/2023]
Abstract
Reflecting on the past three years and the coronavirus disease 19 (COVID-19) pandemic, varying global tactics offer insights into the most effective public-health responses. In the US, specifically, rapid and widespread testing was quickly prioritized to lower restrictions sooner. Essentially, only two types of COVID-19 diagnostic tests were publicly employed during the peak pandemic: the rapid antigen test and reverse transcription polymerase chain reaction (RT-PCR). However, neither test ideally suited the situation, as rapid antigen tests are far too inaccurate, and RT-PCR tests require skilled personnel and sophisticated equipment, leading to long wait times. Loop-mediated isothermal amplification (LAMP) is another exceptionally accurate nucleic acid amplification test (NAAT) that offers far quicker time to results. However, RT-LAMP COVID-19 tests have not been embraced as extensively as rapid antigen tests or RT-PCR. This review will investigate the performance of current RT-LAMP-based COVID-19 tests and summarize the reasons behind the hesitancy to embrace RT-LAMP instead of RT-PCR. We will also look at other LAMP platforms to explore possible improvements in the accuracy and portability of LAMP, which could be applied to COVID-19 diagnostics and future public-health outbreaks.
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Affiliation(s)
| | - Jeong-Yeol Yoon
- Department of Biomedical Engineering, the University of Arizona, Tucson, AZ 85721, USA;
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6
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Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost. mSystems 2021; 6:e0029421. [PMID: 34254828 PMCID: PMC8409480 DOI: 10.1128/msystems.00294-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
New approaches to characterizing microbiomes via high-throughput sequencing provide impressive gains in efficiency and cost reduction compared to approaches that were standard just a few years ago. However, the speed of method development has been such that staying abreast of the latest technological advances is challenging. Moreover, shifting laboratory protocols to include new methods can be expensive and time consuming. To facilitate adoption of new techniques, we provide a guide and review of recent advances that are relevant for single-locus sequence-based study of microbiomes—from extraction to library preparation—including a primer regarding the use of liquid-handling automation in small-scale academic settings. Additionally, we describe several amendments to published techniques to improve throughput, track contamination, and reduce cost. Notably, we suggest adding synthetic DNA molecules to each sample during nucleic acid extraction, thus providing a method of documenting incidences of cross-contamination. We also describe a dual-indexing scheme for Illumina sequencers that allows multiplexing of many thousands of samples with minimal PhiX input. Collectively, the techniques that we describe demonstrate that laboratory technology need not impose strict limitations on the scale of molecular microbial ecology studies. IMPORTANCE New methods to characterize microbiomes reduce technology-imposed limitations to study design, but many new approaches have not been widely adopted. Here, we present techniques to increase throughput and reduce contamination alongside a thorough review of current best practices.
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7
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Moehling TJ, Choi G, Dugan LC, Salit M, Meagher RJ. LAMP Diagnostics at the Point-of-Care: Emerging Trends and Perspectives for the Developer Community. Expert Rev Mol Diagn 2021; 21:43-61. [PMID: 33474990 DOI: 10.1080/14737159.2021.1873769] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Over the past decade, loop-mediated isothermal amplification (LAMP) technology has played an important role in molecular diagnostics. Amongst numerous nucleic acid amplification assays, LAMP stands out in terms of sample-to-answer time, sensitivity, specificity, cost, robustness, and accessibility, making it ideal for field-deployable diagnostics in resource-limited regions.Areas covered: In this review, we outline the front-end LAMP design practices for point-of-care (POC) applications, including sample handling and various signal readout methodologies. Next, we explore existing LAMP technologies that have been validated with clinical samples in the field. We summarize recent work that utilizes reverse transcription (RT) LAMP to rapidly detect SARS-CoV-2 as an alternative to standard PCR protocols. Finally, we describe challenges in translating LAMP from the benchtop to the field and opportunities for future LAMP assay development and performance reporting.Expert opinion: Despite the popularity of LAMP in the academic research community and a recent surge in interest in LAMP due to the COVID-19 pandemic, there are numerous areas for improvement in the fundamental understanding of LAMP, which are needed to elevate the field of LAMP assay development and characterization.
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Affiliation(s)
- Taylor J Moehling
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
| | - Gihoon Choi
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
| | - Lawrence C Dugan
- Lawrence Livermore National Laboratory, Biosciences & Biotechnology Div., Livermore, CA, USA
| | - Marc Salit
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Lab and Departments of Bioengineering and Pathology, Stanford University, Stanford, CA, USA
| | - Robert J Meagher
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
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8
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Zhang C, Liu WJ, Wang TY, Qian TT, Ain NU, Wu LQ, Wu XN, Cai XP, Zeng Q, Xie HP. Fabrication of surface charge pH-sensitive multi-bumpy small magnetic bead with ultrahigh magnetic content and its ultrahigh loading capacity and salt-free rapid isolation for DNA. J Pharm Biomed Anal 2020; 189:113439. [PMID: 32650194 DOI: 10.1016/j.jpba.2020.113439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 11/29/2022]
Abstract
Gene transfection vector polyethyleneimine (PEI) was used as a cross-linking agent to crosslink the surface epoxidized magnetic nanoparticles and aggregate them to form a small magnetic bead (MB) with multiple nanoscale bumps on its surface (i.e. the multi-bumpy small magnetic bead, mbsMB). As there is a very low content of non-magnetic components (the cross-linking agent) in the magnetic bead, the mbsMB has an ultrahigh magnetic content of 81.95 % and a smaller particle size of 1.4 μm when compared with the usual medical MB. Such a small MB also has a strong magnetic force allowing it to reach the rapid separating ability of the commonly used larger medical MB which has 8 times its volume. The mbsMB has an obvious pH sensitivity of positive and negative surface charges and the salt-free isolation of DNA has been achieved based on the electrostatic interactions between mbsMB and DNA. This avoids the desalting of the isolated DNA as well as the effects of high salt concentration on its long chain helix structure. Whether in an acidic absorbing medium, an alkalinous desorbing one or a near neutral particle-storing one, the mbsMB will have obvious surface electrostatic charges. There is also its good suspension stability in an aqueous medium which provides a good condition for isolating of DNA suitable for efficiently adsorbing and desorbing. The as-prepared MB has a unique surface structure and some excellent properties, all suitable for adsorbing DNA. In addition, a large amount of commonly used gene transfection vector PEI can be cross-linked and bonded on the surface of mbsMB, whilst still having an excellent DNA-loading ability. In summary, the mbsMB has an ultrahigh capacity of 629.49 mg/g for DNA load.
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Affiliation(s)
- Chen Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Wen-Juan Liu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Tian-Yu Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Ting-Ting Qian
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China; Faculty of Chemical Engineering, Huaiyin Institute of Technology, Huai'an, 223000, China
| | - Noor Ul Ain
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Lu-Qian Wu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Xiao-Ning Wu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Xue-Ping Cai
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China; Suzhou Institute for Drug Control, Suzhou, 215104, China
| | - Qi Zeng
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China; Dushuhu Public Hospital Affiliated to Soochow University, Suzhou, 215123, China.
| | - Hong-Ping Xie
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
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Lee Yu HL, Fan TW, Hsing IM. Oligonucleotide hybridization with magnetic separation assay for multiple SNP phasing. Anal Chim Acta X 2020; 5:100050. [PMID: 33117988 PMCID: PMC7587028 DOI: 10.1016/j.acax.2020.100050] [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: 12/11/2019] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 10/29/2022] Open
Abstract
Since humans have two copies of each gene, multiple mutations in different loci may or may not be found on the same strand of DNA (i.e., inherited from one parent). When a person is heterozygous at more than one position, the placement of these mutations, also called the haplotype phase, (i.e., cis for the same strand and trans for different strands) can result in the expression of different amount and type of proteins. In this work, we described an enzyme-free method to phase two single nucleotide polymorphisms (SNPs) using two fluorophore/quencher-labelled probes, where one of which was biotinylated. The fluorescence signal was obtained twice: first, after the addition of the labelled probes and second, after the addition of the magnetic beads. The first signal was shown to be proportional to the total number of SNP A and SNP B present in the target analyte, while the second signal showed a marked decrease of the fluorescence signal from the non-biotinylated probe when the SNPs were in trans, showing that the probe immobilized on the magnetic bead selectively captures targets with SNPs in a cis configuration. We then mimic the nature of the human genome which consists of two haplotype copies of each gene, and showed that 250 nM of the 10 possible pairs of haplotypes could be differentiated using a combination of fluorescence microscopy and fluorescence detection.
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Affiliation(s)
- Henson L. Lee Yu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Tsz Wing Fan
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - I-Ming Hsing
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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10
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Lee EY, Lee EJ, Yoon H, Lee DH, Kim KH. Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions. Diagnostics (Basel) 2020; 10:diagnostics10040234. [PMID: 32325682 PMCID: PMC7236016 DOI: 10.3390/diagnostics10040234] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 12/25/2022] Open
Abstract
Urinary cell-free DNA (cfDNA) is an attractive body fluid for liquid biopsy. In this study, we compared the efficiencies of four commercial kits for urinary cell-free DNA (cfDNA) isolation and of various sample storage conditions. Urinary cfDNA was isolated from 10 healthy individuals using four commercial kits: QIAamp Circulating Nucleic Acid Kit (QC; Qiagen), MagMAX™ Cell-Free DNA Isolation Kit (MM; Applied Biosystems), Urine Cell-Free Circulating DNA Purification Midi Kit (NU; Norgen Biotek), and Quick-DNA™ Urine Kit (ZQ; Zymo Research). To assess the isolation efficiency, an Agilent 2100 Bioanalyzer with High Sensitivity DNA chips was used, and cfDNA yield was defined as the amount of cfDNA obtained from 1 mL of urine. MM and QC provided the highest cfDNA yield in the 50–300 bp range, and MM and NU gave the highest cfDNA yield in the 50–100 bp range. In particular, the NU kit was efficient for isolation of more fragmented cfDNA in the range of 50–100 bp with the lowest cellular genomic DNA contamination. ZQ had the best cost-efficiency for isolating the same amount of urinary cfDNA. Samples stored at −70 °C with the addition of 10 mM EDTA resulted in the highest cfDNA yield 3 months after sample collection.
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Affiliation(s)
- Eun Young Lee
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
- Ewha Medical Research Institute, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Eun-Ju Lee
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
- Ewha Medical Research Institute, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Hana Yoon
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
| | - Dong Hyeon Lee
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
| | - Kwang Hyun Kim
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
- Correspondence: ; Tel.: +82-2-6986-1685; Fax: +82-2-6986-3258
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11
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Tong R, Zhang L, Hu C, Chen X, Song Q, Lou K, Tang X, Chen Y, Gong X, Gao Y, Wen W. An Automated and Miniaturized Rotating-Disk Device for Rapid Nucleic Acid Extraction. MICROMACHINES 2019; 10:E204. [PMID: 30909465 PMCID: PMC6471407 DOI: 10.3390/mi10030204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/08/2019] [Accepted: 03/20/2019] [Indexed: 11/20/2022]
Abstract
The result of molecular diagnostic and detection greatly dependent on the quality and integrity of the isolated nucleic acid. In this work, we developed an automated miniaturized nucleic acid extraction device based on magnetic beads method, consisting of four components including a sample processing disc and its associated rotary power output mechanism, a pipetting module, a magnet module and an external central controller to enable a customizable and automated robust nucleic acid sample preparation. The extracted nucleic acid using 293T cells were verified using real-time polymerase chain reaction (PCR) and the data implies a comparable efficiency to a manual process, with the advantages of performing a flexible, time-saving (~10 min), and simple nucleic acid sample preparation.
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Affiliation(s)
- Rui Tong
- The Nano Science and Technology (NSNT) Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Lijuan Zhang
- Shenzhen Shineway Hi-Tech Co., Ltd., Shenzhen 518112, China.
| | - Chuandeng Hu
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Xuee Chen
- The Nano Science and Technology (NSNT) Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Qi Song
- Guangzhou HKUST Fok Ying Tung Research Institute, Nansha, Guangzhou 511458, China.
| | - Kai Lou
- Shenzhen Shineway Hi-Tech Co., Ltd., Shenzhen 518112, China.
| | - Xin Tang
- Guangzhou HKUST Fok Ying Tung Research Institute, Nansha, Guangzhou 511458, China.
| | - Yongsheng Chen
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Xiuqing Gong
- Materials Genome Institute, University of Shanghai, Shanghai 200444, China.
| | - Yibo Gao
- Shenzhen Shineway Hi-Tech Co., Ltd., Shenzhen 518112, China.
| | - Weijia Wen
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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Majoral J, Caminade A. Phosphorhydrazones as Useful Building Blocks for Special Architectures: Macrocycles and Dendrimers. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201801184] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jean‐Pierre Majoral
- Laboratoire de Chimie de Coordination CNRS 205, route de Narbonne 31077 Toulouse Cedex 04 France
- LCC‐CNRS Université de Toulouse CNRS Toulouse France
| | - Anne‐Marie Caminade
- Laboratoire de Chimie de Coordination CNRS 205, route de Narbonne 31077 Toulouse Cedex 04 France
- LCC‐CNRS Université de Toulouse CNRS Toulouse France
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13
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14
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Ma W, Lee Y, Li G, Row KH. Comparison of Three Multi-Dimensional Solid-Phase Extraction Methods with IL-based Silica Sorbent for Separation of Rutin, Quercetin, and Scoparone from Herba Artemisiae Scopariae. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Wanwan Ma
- Department of Chemistry and Chemical Engineering; Inha University; Incheon 402-701 Korea
| | - Yuri Lee
- Department of Chemistry and Chemical Engineering; Inha University; Incheon 402-701 Korea
| | - Guizhen Li
- Department of Chemistry and Chemical Engineering; Inha University; Incheon 402-701 Korea
| | - Kyung Ho Row
- Department of Chemistry and Chemical Engineering; Inha University; Incheon 402-701 Korea
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Current Nucleic Acid Extraction Methods and Their Implications to Point-of-Care Diagnostics. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9306564. [PMID: 28785592 PMCID: PMC5529626 DOI: 10.1155/2017/9306564] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/05/2017] [Indexed: 12/12/2022]
Abstract
Nucleic acid extraction (NAE) plays a vital role in molecular biology as the primary step for many downstream applications. Many modifications have been introduced to the original 1869 method. Modern processes are categorized into chemical or mechanical, each with peculiarities that influence their use, especially in point-of-care diagnostics (POC-Dx). POC-Dx is a new approach aiming to replace sophisticated analytical machinery with microanalytical systems, able to be used near the patient, at the point of care or point of need. Although notable efforts have been made, a simple and effective extraction method is still a major challenge for widespread use of POC-Dx. In this review, we dissected the working principle of each of the most common NAE methods, overviewing their advantages and disadvantages, as well their potential for integration in POC-Dx systems. At present, it seems difficult, if not impossible, to establish a procedure which can be universally applied to POC-Dx. We also discuss the effects of the NAE chemicals upon the main plastic polymers used to mass produce POC-Dx systems. We end our review discussing the limitations and challenges that should guide the quest for an efficient extraction method that can be integrated in a POC-Dx system.
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Yasmin R, Zhu H, Chen Z, Montagna RA. A modifiable microarray-based universal sensor: providing sample-to-results automation. Heliyon 2016; 2:e00179. [PMID: 27812551 PMCID: PMC5078625 DOI: 10.1016/j.heliyon.2016.e00179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/22/2016] [Accepted: 10/11/2016] [Indexed: 12/30/2022] Open
Abstract
A microfluidic system consisting of generic single use cartridges which interface with a workstation allows the automatic performance of all necessary sample preparation, PCR analysis and interpretation of multiplex PCR assays. The cartridges contain a DNA array with 20 different 16mer DNA “universal” probes immobilized at defined locations. PCR amplicons can be detected via hybridization of user-defined “reporter” probes that are complementary at their 3′ termini to one or more of the universal probes and complementary to the target amplicons at their 5′ termini. The system was able to detect single-plex and multiplex PCR amplicons from various infectious agents as well as wild type and mutant alleles of single nucleotide polymorphisms. The system's ease of use was further demonstrated by converting a published PCR assay for the detection of Mycobacterium genitalium in a fully automated manner. Excellent correlation between traditional manual methods and the automated analysis performed by the workstation suggests that the system can provide a means to easily design and implement a variety of customized PCR-based assays. The system will be useful to researchers or clinical investigators seeking to develop their own user defined assays. As the U.S. FDA continues to pursue regulatory oversight of LDTs, the system would also allow labs to continue to develop compliant assays.
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Affiliation(s)
| | - Hui Zhu
- Rheonix Inc., 10 Brown Road, Ithaca, NY 14850, USA
| | - Zongyuan Chen
- Rheonix Inc., 10 Brown Road, Ithaca, NY 14850, USA; Thermo Fisher Scientific, South San Francisco, CA, USA
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Gardner SN, Frey KG, Redden CL, Thissen JB, Allen JE, Allred AF, Dyer MD, Mokashi VP, Slezak TR. Targeted amplification for enhanced detection of biothreat agents by next-generation sequencing. BMC Res Notes 2015; 8:682. [PMID: 26572552 PMCID: PMC4647626 DOI: 10.1186/s13104-015-1530-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 09/28/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Historically, identification of causal agents of disease has relied heavily on the ability to culture the organism in the laboratory and/or the use of pathogen-specific antibodies or sequence-based probes. However, these methods can be limiting: Even highly sensitive PCR-based assays must be continually updated due to signature degradation as new target strains and near neighbors are sequenced. Thus, there has been a need for assays that do not suffer as greatly from these limitations and/or biases. Recent advances in library preparation technologies for Next-Generation Sequencing (NGS) are focusing on the use of targeted amplification and targeted enrichment/capture to ensure that the most highly discriminating regions of the genomes of known targets (organism-unique regions and/or regions containing functionally important genes or phylogenetically-discriminating SNPs) will be sequenced, regardless of the complex sample background. RESULTS In the present study, we have assessed the feasibility of targeted sequence enhancement via amplification to facilitate detection of a bacterial pathogen present in low copy numbers in a background of human genomic material. Our results indicate that the targeted amplification of signature regions can effectively identify pathogen genomic material present in as little as 10 copies per ml in a complex sample. Importantly, the correct species and strain calls could be made in amplified samples, while this was not possible in unamplified samples. CONCLUSIONS The results presented here demonstrate the efficacy of a targeted amplification approach to biothreat detection, using multiple highly-discriminative amplicons per biothreat organism that provide redundancy in case of variation in some primer regions. Importantly, strain level discrimination was possible at levels of 10 genome equivalents. Similar results could be obtained through use of panels focused on the identification of amplicons targeted for specific genes or SNPs instead of, or in addition to, those targeted for specific organisms (ongoing gene-targeting work to be reported later). Note that without some form of targeted enhancement, the enormous background present in complex clinical and environmental samples makes it highly unlikely that sufficient coverage of key pathogen(s) present in the sample will be achieved with current NGS technology to guarantee that the most highly discriminating regions will be sequenced.
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Affiliation(s)
- Shea N Gardner
- Bioinformatics, Global Security Program, Lawrence Livermore National Laboratory, 7000 East Avenue, L-174, Livermore, CA, 94550, USA.
| | - Kenneth G Frey
- Naval Medical Research Center, NMRC-Frederick, 8400 Research Plaza, Fort Detrick, MD, 21702, USA. .,Henry M. Jackson Foundation, 6720-A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA.
| | - Cassie L Redden
- Naval Medical Research Center, NMRC-Frederick, 8400 Research Plaza, Fort Detrick, MD, 21702, USA. .,Henry M. Jackson Foundation, 6720-A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA.
| | - James B Thissen
- Bioinformatics, Global Security Program, Lawrence Livermore National Laboratory, 7000 East Avenue, L-174, Livermore, CA, 94550, USA.
| | - Jonathan E Allen
- Bioinformatics, Global Security Program, Lawrence Livermore National Laboratory, 7000 East Avenue, L-174, Livermore, CA, 94550, USA.
| | - Adam F Allred
- Thermo Fisher Scientific, 180 Oyster Point Boulevard, Building 200, South San Francisco, CA, 94080, USA.
| | - Matthew D Dyer
- Thermo Fisher Scientific, 180 Oyster Point Boulevard, Building 200, South San Francisco, CA, 94080, USA.
| | - Vishwesh P Mokashi
- Naval Medical Research Center, NMRC-Frederick, 8400 Research Plaza, Fort Detrick, MD, 21702, USA.
| | - Tom R Slezak
- Bioinformatics, Global Security Program, Lawrence Livermore National Laboratory, 7000 East Avenue, L-174, Livermore, CA, 94550, USA.
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18
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Guo Y, Sheng S, Nie B, Tu Z. Development of magnetic capture hybridization and quantitative polymerase chain reaction for hepatitis B virus covalently closed circular DNA. HEPATITIS MONTHLY 2015; 15:e23729. [PMID: 25741372 PMCID: PMC4344652 DOI: 10.5812/hepatmon.23729] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 12/03/2014] [Accepted: 12/14/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) served as a vital role in the life cycle of the virus and persistent infection. However, specific and quantitative methods for cccDNA detection have not been available. OBJECTIVES Our aim was to develop and primarily evaluate a quantitative method for HBV cccDNA based on magnetic capture hybridization and quantitative PCR technology. MATERIALS AND METHODS The functionalized-nanoparticles specifically to capture HBV cccDNA, located on both sides of relaxed circle DNA (rcDNA) gap, were designed. Then, magnetic capture hybridization and quantitative PCR (MCH-qPCR) assay were developed and its performance was primarily evaluated with cccDNA standards and serum samples of patients with chronic hepatitis B. RESULTS Specific nanoparticles of cccDNA capture were prepared and a magnetic capture hybridization and quantitative assay method for cccDNA was developed successfully. The limit of detection was 90 IU/mL, and a good linear relationship in the range of 10(2)-10(6) IU/mL was revealed (r(2) = 0.994) with the MCH-qPCR. Compared with directly real-time PCR, a high content of HBV DNA did not affect the detection of cccDNA for the MCH-qPCR method, and there was no cross-reactivity between cccDNA and rcDNA. CONCLUSIONS The novel MCH-qPCR method has good sensitivity and specificity. It could meet the requirement of clinical routine detection.
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Affiliation(s)
- Yongcan Guo
- The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Shangchun Sheng
- The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Bin Nie
- The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Zhiguang Tu
- The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Chongqing Medical University, Chongqing, China
- Corresponding Author: Zhiguang Tu, The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Chongqing Medical University, Chongqing, China. Tel: +86-2368485759, Fax: +86-2368485239, E-mail:
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19
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Magnetic solid-phase extraction based on methylcellulose coated-Fe3O4–SiO2–phenyl for HPLC–DAD analysis of sildenafil and its metabolite in biological samples. Talanta 2014; 130:427-32. [DOI: 10.1016/j.talanta.2014.07.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/28/2014] [Accepted: 07/02/2014] [Indexed: 11/20/2022]
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20
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Li Y, Chen Y, Xiao C, Chen D, Xiao Y, Mei Z. Rapid screening and identification of α-amylase inhibitors from Garcinia xanthochymus using enzyme-immobilized magnetic nanoparticles coupled with HPLC and MS. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 960:166-73. [PMID: 24814002 DOI: 10.1016/j.jchromb.2014.04.041] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/18/2014] [Accepted: 04/22/2014] [Indexed: 12/30/2022]
Abstract
α-Amylase inhibitors play an important role in management of diabetes and obesity. In order to rapidly discover potent α-amylase inhibitors from medicinal plants, a ligands-screening method based on enzyme-immobilized magnetic nanoparticles integrated with HPLC was developed. Amine-terminated magnetic nanoparticles were prepared for the immobilization of α-amylase. Based on the affinity theory, the α-amylase-coated magnetic nanoparticles were employed to fish out the ligands from the extracts of Garcinia xanthochymus, and the elutes were examined by HPLC. As a result, three ligands were screened out. Isolation and identification were carried out subsequently. By analyzing the UV, MS and NMR spectra, they were identified as three biflavonoids including GB2a glucoside (2), GB2a (3) and fukugetin (4). The IC50 values of the three compounds were also determined. The results suggest the proposed approach is efficient and accurate, and has great potential in rapid discovery of drug candidates from medical plants.
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Affiliation(s)
- Yunfang Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; College of Pharmacy, South Central University for Nationalities, Wuhan 430074, China
| | - Yu Chen
- College of Chemistry and Material Sciences, South Central University for Nationalities, Wuhan 430074, China
| | - Chuying Xiao
- College of Pharmacy, South Central University for Nationalities, Wuhan 430074, China
| | - Dan Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yuxiu Xiao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
| | - Zhinan Mei
- College of Pharmacy, South Central University for Nationalities, Wuhan 430074, China.
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21
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Rödiger S, Liebsch C, Schmidt C, Lehmann W, Resch-Genger U, Schedler U, Schierack P. Nucleic acid detection based on the use of microbeads: a review. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1243-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Influence of Magnetic Microparticles Isolation on Adenine Homonucleotides Structure. MATERIALS 2014; 7:1455-1472. [PMID: 28788525 PMCID: PMC5453271 DOI: 10.3390/ma7031455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 12/16/2013] [Accepted: 02/17/2014] [Indexed: 02/07/2023]
Abstract
The electroactivity of purine and pyrimidine bases is the most important property of nucleic acids that is very useful for determining oligonucleotides using square wave voltammetry. This study was focused on the electrochemical behavior of adenine-containing oligonucleotides before and after their isolation using paramagnetic particles. Two peaks were detected-peak A related to the reduction of adenine base and another peak B involved in the interactions between individual adenine strands and contributes to the formation of various spatial structures. The influence of the number of adenine bases in the strand in the isolation process using paramagnetic particles was investigated too.
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23
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Recent developments and future trends in solid phase microextraction techniques towards green analytical chemistry. J Chromatogr A 2013; 1321:1-13. [DOI: 10.1016/j.chroma.2013.10.030] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 09/19/2013] [Accepted: 10/09/2013] [Indexed: 01/17/2023]
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24
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Ghaemi M, Absalan G. Study on the adsorption of DNA on Fe3O4 nanoparticles and on ionic liquid-modified Fe3O4 nanoparticles. Mikrochim Acta 2013. [DOI: 10.1007/s00604-013-1040-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Lv YK, Zhao CX, Li P, He YD, Yang ZR, Sun HW. Preparation of doxycycline-imprinted magnetic microspheres by inverse-emulsion suspension polymerization for magnetic dispersion extraction of tetracyclines from milk samples. J Sep Sci 2013; 36:2656-63. [DOI: 10.1002/jssc.201300429] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/22/2013] [Accepted: 05/22/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Yun-Kai Lv
- Key Laboratory of Analytical Science and Technology, College of Chemistry and Environmental Science; Hebei University; Hebei Province; Baoding P. R. China
| | - Chen-Xi Zhao
- Key Laboratory of Analytical Science and Technology, College of Chemistry and Environmental Science; Hebei University; Hebei Province; Baoding P. R. China
| | - Pan Li
- Key Laboratory of Analytical Science and Technology, College of Chemistry and Environmental Science; Hebei University; Hebei Province; Baoding P. R. China
| | - Yan-Dong He
- Key Laboratory of Analytical Science and Technology, College of Chemistry and Environmental Science; Hebei University; Hebei Province; Baoding P. R. China
| | - Zhong-Rui Yang
- Key Laboratory of Analytical Science and Technology, College of Chemistry and Environmental Science; Hebei University; Hebei Province; Baoding P. R. China
| | - Han-Wen Sun
- Key Laboratory of Analytical Science and Technology, College of Chemistry and Environmental Science; Hebei University; Hebei Province; Baoding P. R. China
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26
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Rittich B, Španová A. SPE and purification of DNA using magnetic particles. J Sep Sci 2013; 36:2472-85. [DOI: 10.1002/jssc.201300331] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/13/2013] [Accepted: 05/13/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Bohuslav Rittich
- Faculty of Chemistry; Brno University of Technology; Brno Czech Republic
| | - Alena Španová
- Faculty of Chemistry; Brno University of Technology; Brno Czech Republic
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27
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Klamp T, Camps M, Nieto B, Guasch F, Ranasinghe RT, Wiedemann J, Petrášek Z, Schwille P, Klenerman D, Sauer M. Highly rapid amplification-free and quantitative DNA imaging assay. Sci Rep 2013; 3:1852. [PMID: 23677392 PMCID: PMC3655336 DOI: 10.1038/srep01852] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/29/2013] [Indexed: 12/24/2022] Open
Abstract
There is an urgent need for rapid and highly sensitive detection of pathogen-derived DNA in a point-of-care (POC) device for diagnostics in hospitals and clinics. This device needs to work in a 'sample-in-result-out' mode with minimum number of steps so that it can be completely integrated into a cheap and simple instrument. We have developed a method that directly detects unamplified DNA, and demonstrate its sensitivity on realistically sized 5 kbp target DNA fragments of Micrococcus luteus in small sample volumes of 20 μL. The assay consists of capturing and accumulating of target DNA on magnetic beads with specific capture oligonucleotides, hybridization of complementary fluorescently labeled detection oligonucleotides, and fluorescence imaging on a miniaturized wide-field fluorescence microscope. Our simple method delivers results in less than 20 minutes with a limit of detection (LOD) of ~5 pM and a linear detection range spanning three orders of magnitude.
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Affiliation(s)
- Tobias Klamp
- Department of Biotechnology & Biophysics, Biocenter, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Marta Camps
- Biokit, S. A., Can Malé s/n, 08186 LLiçà d'Amunt, Spain
| | | | | | - Rohan T. Ranasinghe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
| | - Jens Wiedemann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Zdeněk Petrášek
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany
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28
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Zhang H, Liu QS, Yang CL, Lv JZ, Xie LQ, Tang MJ, Yue ZF, Wan ZG. C18/C8-Functionalized Magnetic Silica Nanospheres (Fe3O4@Si-C8/C18) as Capture Probes for Highly Efficient and Rapid Purification of Veterinary Drug Residues. FOOD ANAL METHOD 2012. [DOI: 10.1007/s12161-012-9504-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Yang HW, Hua MY, Liu HL, Huang CY, Wei KC. Potential of magnetic nanoparticles for targeted drug delivery. Nanotechnol Sci Appl 2012; 5:73-86. [PMID: 24198498 DOI: 10.2147/nsa.s35506] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Nanoparticles (NPs) play an important role in the molecular diagnosis, treatment, and monitoring of therapeutic outcomes in various diseases. Their nanoscale size, large surface area, unique capabilities, and negligible side effects make NPs highly effective for biomedical applications such as cancer therapy, thrombolysis, and molecular imaging. In particular, nontoxic superparamagnetic magnetic NPs (MNPs) with functionalized surface coatings can conjugate chemotherapeutic drugs or be used to target ligands/proteins, making them useful for drug delivery, targeted therapy, magnetic resonance imaging, transfection, and cell/protein/DNA separation. To optimize the therapeutic efficacy of MNPs for a specific application, three issues must be addressed. First, the efficacy of magnetic targeting/guidance is dependent on particle magnetization, which can be controlled by adjusting the reaction conditions during synthesis. Second, the tendency of MNPs to aggregate limits their therapeutic use in vivo; surface modifications to produce high positive or negative charges can reduce this tendency. Finally, the surface of MNPs can be coated with drugs which can be rapidly released after injection, resulting in targeting of low doses of the drug. Drugs therefore need to be conjugated to MNPs such that their release is delayed and their thermal stability enhanced. This chapter describes the creation of nanocarriers with a high drug-loading capacity comprised of a high-magnetization MNP core and a shell of aqueous, stable, conducting polyaniline derivatives and their applications in cancer therapy. It further summarizes some newly developed methods to synthesize and modify the surfaces of MNPs and their biomedical applications.
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Affiliation(s)
- Hung-Wei Yang
- Molecular Medicine Research Center, Department of Chemical and Materials Engineering, Chang Gung University, Taoyuan, Taiwan ; Department of Neurosurgery, Chang Gung University and Memorial Hospital, Taoyuan, Taiwan
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Masarik M, Gumulec J, Sztalmachova M, Hlavna M, Babula P, Krizkova S, Ryvolova M, Jurajda M, Sochor J, Adam V, Kizek R. Isolation of metallothionein from cells derived from aggressive form of high-grade prostate carcinoma using paramagnetic antibody-modified microbeads off-line coupled with electrochemical and electrophoretic analysis. Electrophoresis 2011; 32:3576-88. [DOI: 10.1002/elps.201100301] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2011] [Revised: 06/30/2011] [Accepted: 07/02/2011] [Indexed: 12/18/2022]
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31
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Target-specific capture enhances sensitivity of electrochemical detection of bacterial pathogens. J Clin Microbiol 2011; 49:4293-6. [PMID: 21940468 DOI: 10.1128/jcm.01261-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the concentration and purification of bacterial 16S rRNA by the use of a biotinylated DNA target-specific capture (TSC) probe. For both cultivated bacterial and urine specimens from urinary tract infection patients, TSC resulted in a 5- to 8-fold improvement in the sensitivity of bacterial detection in a 16S rRNA electrochemical sensor assay.
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32
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Specific magnetic isolation for direct detection of HPV16. Eur J Clin Microbiol Infect Dis 2011; 31:539-46. [DOI: 10.1007/s10096-011-1345-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 07/05/2011] [Indexed: 10/17/2022]
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33
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Development of a single-step subtraction method for eukaryotic 18S and 28S ribonucleic acids. J Biomed Biotechnol 2011; 2011:910369. [PMID: 21765639 PMCID: PMC3134377 DOI: 10.1155/2011/910369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 04/29/2011] [Indexed: 11/18/2022] Open
Abstract
The abundance of mammalian 18S and 28S ribosomal RNA can decrease the detection sensitivity of bacterial or viral targets in complex host-pathogen mixtures. A method to capture human RNA in a single step was developed and characterized to address this issue. For this purpose, capture probes were covalently attached to magnetic microbeads using a dendrimer linker and the solid phase was tested using rat thymus RNA (mammalian components) with Escherichia coli RNA (bacterial target) as a model system. Our results indicated that random capture probes demonstrated better performance than specific ones presumably by increasing the number of possible binding sites, and the use of a tetrame-thylammonium-chloride (TMA-Cl-) based buffer for the hybridization showed a beneficial effect in the selectivity. The subtraction efficiency determined through real-time RT-PCR revealed capture-efficiencies comparable with commercially available enrichment kits. The performance of the solid phase can be further fine tuned by modifying the annealing time and temperature.
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35
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Liu P, Li X, Greenspoon SA, Scherer JR, Mathies RA. Integrated DNA purification, PCR, sample cleanup, and capillary electrophoresis microchip for forensic human identification. LAB ON A CHIP 2011; 11:1041-8. [PMID: 21293830 DOI: 10.1039/c0lc00533a] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A fully integrated microdevice and process for forensic short tandem repeat (STR) analysis has been developed that includes sequence-specific DNA template purification, polymerase chain reaction (PCR), post-PCR cleanup and inline injection, and capillary electrophoresis (CE). Fragmented genomic DNA is hybridized with biotin-labeled capture oligos and pumped through a fluidized bed of magnetically immobilized streptavidin-coated beads in microchannels where the target DNA is bound to the beads. The bead-DNA conjugates are then transferred into a 250 nL PCR reactor for autosomal STR amplification using one biotin and one fluorescence-labeled primer. The resulting biotin-labeled PCR products are electrophoretically injected through a streptavidin-modified capture gel where they are captured to form a concentrated and purified injection plug. The thermally released sample plug is injected into a 14 cm long CE column for fragment separation and detection. The DNA template capture efficiency provided by the on-chip sequence-specific template purification is determined to be 5.4% using K562 standard DNA. This system can produce full 9-plex STR profiles from 2.5 ng input standard DNA and obtain STR profiles from oral swabs in about 3 hours. This fully integrated microsystem with sample-in-answer-out capability is a significant advance in the development of rapid, sensitive, and reliable micro-total analysis systems for on-site human identification.
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Affiliation(s)
- Peng Liu
- UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, Berkeley, CA 94720, USA
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Magnetic solids in analytical chemistry: A review. Anal Chim Acta 2010; 674:157-65. [DOI: 10.1016/j.aca.2010.06.043] [Citation(s) in RCA: 346] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 06/24/2010] [Accepted: 06/25/2010] [Indexed: 12/21/2022]
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Archer MJ, Long N, Lin B. Effect of probe characteristics on the subtractive hybridization efficiency of human genomic DNA. BMC Res Notes 2010; 3:109. [PMID: 20406484 PMCID: PMC2862039 DOI: 10.1186/1756-0500-3-109] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 04/20/2010] [Indexed: 12/04/2022] Open
Abstract
Background The detection sensitivity of low abundance pathogenic species by polymerase chain reaction (PCR) can be significantly enhanced by removing host nucleic acids. This selective removal can be performed using a magnetic bead-based solid phase with covalently immobilized capture probes. One of the requirements to attain efficient host background nucleic acids subtraction is the capture probe characteristics. Findings In this study we investigate how various capture probe characteristics influence the subtraction efficiency. While the primary focus of this report is the impact of probe length, we also studied the impact of probe conformation as well as the amount of capture probe attached to the solid phase. The probes were immobilized on magnetic microbeads functionalized with a phosphorous dendrimer. The subtraction efficiency was assessed by quantitative real time PCR using a single-step capture protocol and genomic DNA as target. Our results indicate that short probes (100 to 200 bp) exhibit the best subtraction efficiency. Additionally, higher subtraction efficiencies with these probes were obtained as the amount of probe immobilized on the solid phase decreased. Under optimal probes condition, our protocol showed a 90 - 95% subtraction efficiency of human genomic DNA. Conclusions The characteristics of the capture probe are important for the design of efficient solid phases. The length, conformation and abundance of the probes determine the capture efficiency of the solid phase.
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Affiliation(s)
- Marie J Archer
- US Naval Research Laboratory, Center for Bio/Molecular Science & Engineering, 4555 Overlook Avenue, S W, Washington, DC, 20375, USA.
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Gamper HA, van der Heijden MGA, Kowalchuk GA. Molecular trait indicators: moving beyond phylogeny in arbuscular mycorrhizal ecology. THE NEW PHYTOLOGIST 2010; 185:67-82. [PMID: 19863727 DOI: 10.1111/j.1469-8137.2009.03058.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi form symbiotic associations with the roots of most plants, thereby mediating nutrient and carbon fluxes, plant performance, and ecosystem dynamics. Although considerable effort has been expended to understand the keystone ecological position of AM symbioses, most studies have been limited in scope to recording organism occurrences and identities, as determined from morphological characters and (mainly) ribosomal sequence markers. In order to overcome these restrictions and circumvent the shortcomings of culture- and phylogeny-based approaches, we propose a shift toward plant and fungal protein-encoding genes as more immediate indicators of mycorrhizal contributions to ecological processes. A number of candidate target genes, involved in the uptake of phosphorus and nitrogen, carbon cycling, and overall metabolic activity, are proposed. We discuss the advantages and disadvantages of future protein-encoding gene marker and current (phylo-) taxonomic approaches for studying the impact of AM fungi on plant growth and ecosystem functioning. Approaches based on protein-encoding genes are expected to open opportunities to advance the mechanistic understanding of ecological roles of mycorrhizas in natural and managed ecosystems.
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Affiliation(s)
- Hannes A Gamper
- Botanical Institute, University of Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland.
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Stankiewicz N, Gold A, Yüksel Y, Berensmeier S, Schwartz T. In vivo labeling and specific magnetic bead separation of RNA for biofilm characterization and stress-induced gene expression analysis in bacteria. J Microbiol Methods 2009; 79:344-52. [PMID: 19837116 DOI: 10.1016/j.mimet.2009.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 10/07/2009] [Accepted: 10/07/2009] [Indexed: 11/26/2022]
Abstract
The method of in vivo labeling and separation of bacterial RNA was developed as an approach to elucidating the stress response of natural bacterial populations. This technique is based on the incorporation of digoxigenin-11-uridine-5'-triphosphate (DIG-11-UTP) in the RNA of active bacteria. The digoxigenin fulfills a dual role as a label of de novo synthesized RNA and a target for magnetic bead separation from a total RNA extract. Depending on the growth conditions and the population's composition, the assembly rate of DIG-11-UTP ranged from 1.2% to 12.5% of the total RNA in gram-positive and gram-negative reference bacteria as well as in natural biofilms from drinking water, surface water, and lake sediment. Separation of DIG-RNA from total RNA extracts was performed with a biotinylated anti-digoxigenin antibody and streptavidin-functionalized magnetic particles. The average separation yield from total RNA extracts was about 95% of labeled RNA. The unspecific bindings of non-labeled nucleic acids were smaller than 0.2%, as was evaluated by spiking experiments with an unmarked DNA amplicon. Applicability of the method developed was demonstrated by rRNA-directed PCR-DGGE population analysis of natural biofilms and expression profiling of two stress-induced genes (vanA and rpoS) in reference bacteria.
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Affiliation(s)
- Nikolai Stankiewicz
- Karlsruhe Institute of Technology - KIT (former: Forschungszentrum Karlsruhe), Institute of Functional Interfaces (IFG), Microbiology of Natural and Technical Interfaces Department, P.O. Box 3640, D-76021 Karlsruhe, Germany
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Lien KY, Liu CJ, Kuo PL, Lee GB. Microfluidic System for Detection of α-Thalassemia-1 Deletion Using Saliva Samples. Anal Chem 2009; 81:4502-9. [DOI: 10.1021/ac900453d] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kang-Yi Lien
- Institute of Nanotechnology and Microsystems Engineering, Department of Engineering Science, Department of Obstetrics and Gynecology, Medical College, National Cheng Kung University, Tainan 701, Taiwan, and Medical Electronics and Device Technology Center, Industrial Technology Research Institute, Hsinchu 310, Taiwan
| | - Chien-Ju Liu
- Institute of Nanotechnology and Microsystems Engineering, Department of Engineering Science, Department of Obstetrics and Gynecology, Medical College, National Cheng Kung University, Tainan 701, Taiwan, and Medical Electronics and Device Technology Center, Industrial Technology Research Institute, Hsinchu 310, Taiwan
| | - Pao-Lin Kuo
- Institute of Nanotechnology and Microsystems Engineering, Department of Engineering Science, Department of Obstetrics and Gynecology, Medical College, National Cheng Kung University, Tainan 701, Taiwan, and Medical Electronics and Device Technology Center, Industrial Technology Research Institute, Hsinchu 310, Taiwan
| | - Gwo-Bin Lee
- Institute of Nanotechnology and Microsystems Engineering, Department of Engineering Science, Department of Obstetrics and Gynecology, Medical College, National Cheng Kung University, Tainan 701, Taiwan, and Medical Electronics and Device Technology Center, Industrial Technology Research Institute, Hsinchu 310, Taiwan
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Xie HY, Xie M, Zhang ZL, Long YM, Liu X, Tang ML, Pang DW, Tan Z, Dickinson C, Zhou W. Wheat germ agglutinin-modified trifunctional nanospheres for cell recognition. Bioconjug Chem 2007; 18:1749-55. [PMID: 17894449 DOI: 10.1021/bc060387g] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A simple and convenient strategy has been put forward to fabricate smart fluorescent magnetic wheat germ agglutinin-modified trifunctional nanospheres (WGA-TFNS) for recognition of human prostate carcinoma DU-145 cells which are surface-expressed with sialic acid and N-acetylglucosamine. These TFNS can be easily manipulated, tracked, and conveniently used to capture and separate target cells. The presence of wheat germ agglutinin on the surface of WGA-TFNS was confirmed by FTIR, biorecognition of carboxymethyl chitin-modified quantum dots (CM-CT-QDs), and bacterium Staphylococcus aureus. The success in recognizing DU-145 cells by the WGA-TFNS indicates that WGA-TFNS could be applicable.
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Affiliation(s)
- Hai-Yan Xie
- School of Life Science and Technology, Beijing Institute of Technology, Beijing, PR China
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Bencina K, Bencina M, Podgornik A, Strancar A. Influence of the methacrylate monolith structure on genomic DNA mechanical degradation, enzymes activity and clogging. J Chromatogr A 2007; 1160:176-83. [PMID: 17540390 DOI: 10.1016/j.chroma.2007.05.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 04/12/2007] [Accepted: 05/10/2007] [Indexed: 10/23/2022]
Abstract
The chromatography of mechanically sensitive macromolecules still represents a challenge. While larger pores can reduce the mechanically induced cleavage of large macromolecules and column clogging, the column performance inevitably decreases. To investigate the effect of pore size on the mechanical degradation of DNA, column permeability and enzyme biological activity, methacrylate monoliths with different pore sizes were tested. Monolith with a 143 nm pore radius mechanically damaged the DNA and was clogged at flow rates above 0.5 ml min(-1) (26 cm h(-1)). For monoliths with a pore radius of 634 nm and 2900 nm, no mechanical degradation of DNA was observed up to 5 ml min(-1) (265 cm h(-1)) above which the HPLC itself became the main source of damage. A decrease of a permeability appeared at flow rate 1.8 ml min(-1) (95 cm h(-1)) and 2.3 ml min(-1) (122 cm h(-1)), respectively. The effect of the pore size on enzyme biological activity was tested with immobilized DNase and trypsin on all three monoliths. Although the highest amount of enzyme was immobilized on the monolith with the smallest pores, monolith with the pore radius 634 nm exhibited the highest DNase biological activity probably due to restricted access for DNA molecules into the small pores. Interestingly, specific biological activity was increasing with a pore size decrease. This was attributed to higher number of contacts between a substrate and immobilized ligand.
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Affiliation(s)
- Katja Bencina
- BIA separations d.o.o., Teslova 30, SI-1001 Ljubljana, Slovenia
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Horák D, Babic M, Macková H, Benes MJ. Preparation and properties of magnetic nano- and microsized particles for biological and environmental separations. J Sep Sci 2007; 30:1751-72. [PMID: 17623453 DOI: 10.1002/jssc.200700088] [Citation(s) in RCA: 295] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The paper presents a critical overview on magnetic nanoparticles and microspheres used as separation media in different fields of chemistry, biochemistry, biology, and environment protection. The preparation of most widely used magnetic iron oxides in appropriate form, their coating or encapsulation in polymer microspheres, and functionalization is discussed in the first part. In the second part, new developments in the main application areas of magnetic composite particles for separation and catalytical purposes are briefly described. They cover separations and isolations of toxic inorganic and organic ions, proteins, and other biopolymers, cells, and microorganisms. Only selected number of relevant papers could be included due to the restricted extent of the review.
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Affiliation(s)
- Daniel Horák
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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Kehat T, Goren K, Portnoy M. Dendrons on insoluble supports: synthesis and applications. NEW J CHEM 2007. [DOI: 10.1039/b617855n] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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