1
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Li H, Li Y, Gui C, Chen D, Chen L, Luo L, Huang G, Yuan Y, He R, Xia F, Wang J. Bare glassy nanopore for length-resolution reading of PCR amplicons from various pathogenic bacteria and viruses. Talanta 2023; 256:124275. [PMID: 36701856 DOI: 10.1016/j.talanta.2023.124275] [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: 10/01/2022] [Revised: 11/16/2022] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
In this study, it is confirmed that without addition of organic solvent and embedding polymer hydrogel into glass nanopore, bare glass nanopore can faithfully measure various lengths of DNA duplexes from 200 to 3000 base pairs with 200 base pairs resolution, showing well-separated peak amplitudes of blockage currents. Furthermore, motivated by this readout capability of duplex DNA, amplicons from Polymerase Chain Reaction (PCR) amplification are straightforwardly discriminated by bare glassy nanopore without fluorescent labeling. Except simultaneous discrimination of up to 7 different segments of the same lambda genome, various pathogenic bacteria and viruses including SARS-CoV-2 and its mutants in clinical samples can be discriminated at high resolution. Moreover, quantitative measurement of PCR amplicons is obtained with detection range spanning from 0.75 aM to 7.5 pM and detection limit of 7.5 aM, which reveals that bare glass nanopore can faithfully disclose PCR results without any extra labeling.
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Affiliation(s)
- Huizhen Li
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Yunhui Li
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Cenlin Gui
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Daqi Chen
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Lanfang Chen
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Le Luo
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Guobao Huang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, College of Chemistry and Food Science, Yulin Normal University, Yulin, Guangxi, 537000, China
| | - Yang Yuan
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Rong He
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, 510440, China.
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei, 430074, China.
| | - Jiahai Wang
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China.
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2
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Zhang C, Belwal T, Luo Z, Su B, Lin X. Application of Nanomaterials in Isothermal Nucleic Acid Amplification. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2102711. [PMID: 34626064 DOI: 10.1002/smll.202102711] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/29/2021] [Indexed: 05/26/2023]
Abstract
Because of high sensitivity and specificity, isothermal nucleic acid amplification are widely applied in many fields. To facilitate and improve their performance, various nanomaterials, like nanoparticles, nanowires, nanosheets, nanotubes, and nanoporous films are introduced in isothermal nucleic acid amplification. However, the specific application, roles, and prospect of nanomaterials in isothermal nucleic acid amplification have not been comprehensively reviewed. Here, the application of different nanomaterials (0D, 1D, 2D, and 3D) in isothermal nucleic acid amplification is comprehensively discussed and recent progress in the field is summarized. The nanomaterials are mainly used for reaction enhancer, signal generation/amplification, or surface loading carriers. In addition, 3D nanomaterials can be also functioned as isolated chambers for digital nucleic acid amplification and the tools for DNA sequencing of amplified products. Challenges and future recommendations are also proposed to be better used for recent covid-19 detection, point-of-care diagnostic, food safety, and other fields.
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Affiliation(s)
- Chao Zhang
- College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Tarun Belwal
- College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, China
- Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China
| | - Bin Su
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Xingyu Lin
- College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, China
- Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China
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3
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Liang X, Chen H, Li L, An R, Komiyama M. Ring-Structured DNA and RNA as Key Players In Vivoand In Vitro. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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4
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Tang H, Wang H, Yang C, Zhao D, Qian Y, Li Y. Nanopore-based Strategy for Selective Detection of Single Carcinoembryonic Antigen (CEA) Molecules. Anal Chem 2020; 92:3042-3049. [DOI: 10.1021/acs.analchem.9b04185] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Haoran Tang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P.R. China
| | - Hao Wang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P.R. China
| | - Cheng Yang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P.R. China
| | - Dandan Zhao
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P.R. China
| | - Yuanyuan Qian
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P.R. China
| | - Yongxin Li
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P.R. China
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5
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Venzac B, Diakité ML, Herthnek D, Cissé I, Bockelmann U, Descroix S, Malaquin L, Viovy JL. On-chip conductometric detection of short DNA sequences via electro-hydrodynamic aggregation. Analyst 2018; 143:190-199. [PMID: 29171594 DOI: 10.1039/c7an00798a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescence measurement is the main technology for post-amplification DNA detection in automated systems. Direct electrical reading of DNA concentration in solution could be an interesting alternative to go toward more miniaturized or less expensive devices, in particular in the pathogen detection field. Here we present the detection of short bacterial biomarkers with a direct impedancemetric measurement, within solutions of amplified and elongated DNA sequences in a microchannel. This technology relies on the electrohydrodynamic instability occurring in solutions of long charged macromolecules in a strong electric field. This instability specifically induces the aggregation of long DNAs and triggers conductivity variations that can be monitored by on-contact conductometry. An innovative isothermal amplification and elongation strategy was developed, combining SDA and HRCA reactions, in order to yield long DNAs suitable to be detected by the above principle, from a dilute initial DNA target. In contrast with previous label-free detection methods, this new strategy is very robust to matrix effects, thanks to the unique molecular weight dependence of the instability, coupled with this specific DNA amplification strategy. We demonstrate the detection of a 1 pM gene sequence specific to Staphylococcus aureus, in a portable system.
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Affiliation(s)
- B Venzac
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France.
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6
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Qu X, Bian F, Guo Q, Ge Q, Sun Q, Huang X. Ligation-Rolling Circle Amplification on Quantum Dot-Encoded Microbeads for Detection of Multiplex G-Quadruplex-Forming Sequences. Anal Chem 2018; 90:12051-12058. [DOI: 10.1021/acs.analchem.8b02820] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xiaojun Qu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Feika Bian
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingsheng Guo
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xuebin Huang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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7
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Neumann F, Hernández-Neuta I, Grabbe M, Madaboosi N, Albert J, Nilsson M. Padlock Probe Assay for Detection and Subtyping of Seasonal Influenza. Clin Chem 2018; 64:1704-1712. [PMID: 30257827 DOI: 10.1373/clinchem.2018.292979] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/31/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Influenza remains a constant threat worldwide, and WHO estimates that it affects 5% to 15% of the global population each season, with an associated 3 to 5 million severe cases and up to 500000 deaths. To limit the morbidity and the economic burden of influenza, improved diagnostic assays are needed. METHODS We developed a multiplexed assay for the detection and subtyping of seasonal influenza based on padlock probes and rolling circle amplification. The assay simultaneously targets all 8 genome segments of the 4 circulating influenza variants-A(H1N1), A(H3N2), B/Yamagata, and B/Victoria-and was combined with a prototype cartridge for inexpensive digital quantification. Characterized virus isolates and patient nasopharyngeal swabs were used for assay design and analytical validation. The diagnostic performance was assessed by blinded testing of 50 clinical samples analyzed in parallel with a commercial influenza assay, Simplexa™ Flu A/B & RSV Direct. RESULTS The assay had a detection limit of 18 viral RNA copies and achieved 100% analytical and clinical specificity for differential detection and subtyping of seasonal circulating influenza variants. The diagnostic sensitivity on the 50 clinical samples was 77.5% for detecting influenza and up to 73% for subtyping seasonal variants. CONCLUSIONS We have presented a proof-of-concept padlock probe assay combined with an inexpensive digital readout for the detection and subtyping of seasonal influenza strains A and B. The demonstrated high specificity and multiplexing capability, together with the digital quantification, established the assay as a promising diagnostic tool for seasonal influenza.
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Affiliation(s)
- Felix Neumann
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Iván Hernández-Neuta
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Malin Grabbe
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Narayanan Madaboosi
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jan Albert
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden;
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8
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Shi J, Zhou M. Probing the conformational switch of I-motif DNA using tunable resistive pulse sensing. Biochim Biophys Acta Gen Subj 2018; 1862:2564-2569. [PMID: 30048743 DOI: 10.1016/j.bbagen.2018.07.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 07/08/2018] [Accepted: 07/11/2018] [Indexed: 02/04/2023]
Abstract
I-motif DNA, which can fold and unfold reversibly in various environments, plays a significant role in DNA nanotechnology and biological functions. Thus, it is of fundamental importance to identify the different conformations of i-motif DNA. Here, we demonstrate that distinct structures of i-motif DNA conjugated to polystyrene spheres can be distinguished through tunable resistive pulse sensing technique. When dispersed in acidic buffer, i-motif DNA coating on polystyrene spheres would fold into quadruplex structure and subsequently induce an apparent increase in the translocation duration time upon passing through a nanopore due to the shielding effect of the surface charge of the nanospheres. However, if the DNA strands don't have conformational changes in acidic buffer, little shift can be observed in the translocation duration time of the DNA functionalized polystyrene spheres. A before-and-after assay was also performed to illustrate the fast speed of i-motif DNA folding using this technique. The successful implementation of tunable resistive pulse sensing to monitor the conformational transition of i-motif DNA provides a potential tool to detect the structural changes of DNA and an alternative approach to study the function of DNA structures.
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Affiliation(s)
- Jing Shi
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, People's Republic of China
| | - Ming Zhou
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, People's Republic of China.
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9
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Chen Z, Duan X, Wei H, Tang S, Xu C, Li Y, Guan Y, Zhao G. Screening oligonucleotide sequences for silver staining and d-galactose visual detection using RCA silver staining in a tube. Acta Biochim Biophys Sin (Shanghai) 2018; 50:507-515. [PMID: 29635339 DOI: 10.1093/abbs/gmy034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 03/07/2018] [Indexed: 02/04/2023] Open
Abstract
Oligonucleotides were screened for strongly silver-stained repetitive sequences. An 'AG'-clustered purine sequence showed strong staining, and the staining density can be compromised by disrupting the continuity of the 'AG'-clustered sequence. The staining-favored sequence was then employed in rolling circle amplification (RCA) for its product detection. A tube-staining method was developed for convenient and visual RCA assay. Moreover, by introducing GalR into RCA, d-galactose was detected by RCA tube-staining with naked eyes without any equipment. About 10 mM d-galactose can be easily identified, and the detection of d-galactose was specific in comparison with that of several other monosaccharides.
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Affiliation(s)
- Ziwei Chen
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Xuying Duan
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Hua Wei
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Suming Tang
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Chidong Xu
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Yanlei Li
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Yifu Guan
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Guojie Zhao
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
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10
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Kühnemund M, Hernández-Neuta I, Sharif MI, Cornaglia M, Gijs MAM, Nilsson M. Sensitive and inexpensive digital DNA analysis by microfluidic enrichment of rolling circle amplified single-molecules. Nucleic Acids Res 2017; 45:e59. [PMID: 28077562 PMCID: PMC5416848 DOI: 10.1093/nar/gkw1324] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/22/2016] [Indexed: 11/29/2022] Open
Abstract
Single molecule quantification assays provide the ultimate sensitivity and precision for molecular analysis. However, most digital analysis techniques, i.e. droplet PCR, require sophisticated and expensive instrumentation for molecule compartmentalization, amplification and analysis. Rolling circle amplification (RCA) provides a simpler means for digital analysis. Nevertheless, the sensitivity of RCA assays has until now been limited by inefficient detection methods. We have developed a simple microfluidic strategy for enrichment of RCA products into a single field of view of a low magnification fluorescent sensor, enabling ultra-sensitive digital quantification of nucleic acids over a dynamic range from 1.2 aM to 190 fM. We prove the broad applicability of our analysis platform by demonstrating 5-plex detection of as little as ∼1 pg (∼300 genome copies) of pathogenic DNA with simultaneous antibiotic resistance marker detection, and the analysis of rare oncogene mutations. Our method is simpler, more cost-effective and faster than other digital analysis techniques and provides the means to implement digital analysis in any laboratory equipped with a standard fluorescent microscope.
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Affiliation(s)
- Malte Kühnemund
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 05 Upssala, Sweden.,Science for Life Laboratory, Department of Biophysics and Biochemistry, Stockholm University, SE- 171 65 Solna, Sweden
| | - Iván Hernández-Neuta
- Science for Life Laboratory, Department of Biophysics and Biochemistry, Stockholm University, SE- 171 65 Solna, Sweden
| | - Mohd Istiaq Sharif
- Science for Life Laboratory, Department of Biophysics and Biochemistry, Stockholm University, SE- 171 65 Solna, Sweden
| | - Matteo Cornaglia
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Martin A M Gijs
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Mats Nilsson
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 05 Upssala, Sweden.,Science for Life Laboratory, Department of Biophysics and Biochemistry, Stockholm University, SE- 171 65 Solna, Sweden
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11
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Carinelli S, Kühnemund M, Nilsson M, Pividori M. Yoctomole electrochemical genosensing of Ebola virus cDNA by rolling circle and circle to circle amplification. Biosens Bioelectron 2017; 93:65-71. [DOI: 10.1016/j.bios.2016.09.099] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/16/2016] [Accepted: 09/27/2016] [Indexed: 11/29/2022]
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12
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Song Y, Zhang J, Li D. Microfluidic and Nanofluidic Resistive Pulse Sensing: A Review. MICROMACHINES 2017; 8:E204. [PMID: 30400393 PMCID: PMC6190343 DOI: 10.3390/mi8070204] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/11/2017] [Accepted: 06/21/2017] [Indexed: 12/31/2022]
Abstract
The resistive pulse sensing (RPS) method based on the Coulter principle is a powerful method for particle counting and sizing in electrolyte solutions. With the advancement of micro- and nano-fabrication technologies, microfluidic and nanofluidic resistive pulse sensing technologies and devices have been developed. Due to the unique advantages of microfluidics and nanofluidics, RPS sensors are enabled with more functions with greatly improved sensitivity and throughput and thus have wide applications in fields of biomedical research, clinical diagnosis, and so on. Firstly, this paper reviews some basic theories of particle sizing and counting. Emphasis is then given to the latest development of microfuidic and nanofluidic RPS technologies within the last 6 years, ranging from some new phenomena, methods of improving the sensitivity and throughput, and their applications, to some popular nanopore or nanochannel fabrication techniques. The future research directions and challenges on microfluidic and nanofluidic RPS are also outlined.
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Affiliation(s)
- Yongxin Song
- Department of Marine Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Junyan Zhang
- Department of Marine Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Dongqing Li
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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13
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Zhu L, Li G, Sun S, Tan H, He Y. Digital immunoassay of a prostate-specific antigen using gold nanorods and magnetic nanoparticles. RSC Adv 2017. [DOI: 10.1039/c7ra00575j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have demonstrated a highly sensitive digital immunoassay for PSA detection.
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Affiliation(s)
- Liang Zhu
- Institute of Optical Imaging and Sensing
- Shenzhen Key Laboratory for Minimal Invasive Medical Technologies
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
| | - Guohua Li
- Institute of Optical Imaging and Sensing
- Shenzhen Key Laboratory for Minimal Invasive Medical Technologies
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
| | - Shuqing Sun
- Institute of Optical Imaging and Sensing
- Shenzhen Key Laboratory for Minimal Invasive Medical Technologies
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
| | - Hui Tan
- The First Affiliated Hospital of Shenzhen University
- Shenzhen Key Laboratory of Neurosurgery
- Shenzhen
- China
| | - Yonghong He
- Institute of Optical Imaging and Sensing
- Shenzhen Key Laboratory for Minimal Invasive Medical Technologies
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
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14
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Wei H, Hu B, Tang S, Zhao G, Guan Y. Repressor logic modules assembled by rolling circle amplification platform to construct a set of logic gates. Sci Rep 2016; 6:37477. [PMID: 27869177 PMCID: PMC5116584 DOI: 10.1038/srep37477] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/28/2016] [Indexed: 12/27/2022] Open
Abstract
Small molecule metabolites and their allosterically regulated repressors play an important role in many gene expression and metabolic disorder processes. These natural sensors, though valuable as good logic switches, have rarely been employed without transcription machinery in cells. Here, two pairs of repressors, which function in opposite ways, were cloned, purified and used to control DNA replication in rolling circle amplification (RCA) in vitro. By using metabolites and repressors as inputs, RCA signals as outputs, four basic logic modules were constructed successfully. To achieve various logic computations based on these basic modules, we designed series and parallel strategies of circular templates, which can further assemble these repressor modules in an RCA platform to realize twelve two-input Boolean logic gates and a three-input logic gate. The RCA-output and RCA-assembled platform was proved to be easy and flexible for complex logic processes and might have application potential in molecular computing and synthetic biology.
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Affiliation(s)
- Hua Wei
- Animal Science and Veterinary Medicine College, Shenyang Agricultural University, #120 Dongling Road, Shenyang, Liaoning, 110866, China.,Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Bo Hu
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Suming Tang
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Guojie Zhao
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Yifu Guan
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
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15
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Weatherall E, Hauer P, Vogel R, Willmott GR. Pulse Size Distributions in Tunable Resistive Pulse Sensing. Anal Chem 2016; 88:8648-56. [DOI: 10.1021/acs.analchem.6b01818] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | | | - Robert Vogel
- Izon Science Limited, 8C Homersham Place, P.O. Box 39168,
Burnside, Christchurch 8053, New Zealand
- School
of Mathematics and Physics, The University of Queensland, Brisbane 4072, Australia
| | - Geoff R. Willmott
- The
Departments of Physics and Chemistry, The University of Auckland, Auckland 1142, New Zealand
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16
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Sivakumaran M, Platt M. Tunable resistive pulse sensing: potential applications in nanomedicine. Nanomedicine (Lond) 2016; 11:2197-214. [PMID: 27480794 DOI: 10.2217/nnm-2016-0097] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
An accurate characterization of nanomaterials used in clinical diagnosis and therapeutics is of paramount importance to realize the full potential of nanotechnology in medicine and to avoid unexpected and potentially harmful toxic effects due to these materials. A number of technical modalities are currently in use to study the physical, chemical and biological properties of nanomaterials but they all have advantages and disadvantages. In this review, we discuss the potential of a relative newcomer, tunable resistive pulse sensing, for the characterization of nanomaterials and its applications in nanodiagnostics.
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Affiliation(s)
| | - Mark Platt
- Department of Chemistry, Loughborough University, Loughborough, LE11 3TU, UK
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Effect of Pore Geometry on Resistive-Pulse Sensing of DNA Using Track-Etched PET Nanopore Membrane. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.04.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Şen M, Demirci A. pH-Dependent ionic-current-rectification in nanopipettes modified with glutaraldehyde cross-linked protein membranes. RSC Adv 2016. [DOI: 10.1039/c6ra19263g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Highly specific DNA detection employing ligation on suspension bead array readout. N Biotechnol 2015; 32:504-10. [PMID: 25681158 DOI: 10.1016/j.nbt.2015.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 01/23/2015] [Accepted: 01/27/2015] [Indexed: 01/05/2023]
Abstract
We show for the first time that monomerized rolling circle amplification (RCA) products can be directly detected with the Luminex suspension bead array readout without the need of PCR amplification. Furthermore, using monomerized RCA products to guide ligation of the detection oligonucleotide (DO) to barcode sequences on the magnetic Luminex beads, combined with efficient washing and increased measurement temperature, yields a higher signal to noise ratio. As a proof-of-principle, we demonstrate detection of pathogenic DNA sequences with high reproducibility, sensitivity and a dynamic range over four orders of magnitude. Using padlock probes in combination with bead suspension arrays opens up the possibility for highly multiplexed DNA targeting and readout.
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Abstract
This Review focusses on the recent surge in applied research using tunable resistive pulse sensing, a technique used to analyse submicron colloids in aqueous solutions on a particle-by-particle basis.
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Affiliation(s)
- Eva Weatherall
- The MacDiarmid Institute for Advanced Materials and Nanotechnology
- School of Chemical and Physical Sciences
- Victoria University of Wellington
- New Zealand
- Callaghan Innovation
| | - Geoff R. Willmott
- The MacDiarmid Institute for Advanced Materials and Nanotechnology
- School of Chemical and Physical Sciences
- Victoria University of Wellington
- New Zealand
- The Departments of Physics and Chemistry
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