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Ben Aissa A, Madaboosi N, Nilsson M, Pividori MI. Electrochemical Genosensing of E. coli Based on Padlock Probes and Rolling Circle Amplification. SENSORS (BASEL, SWITZERLAND) 2021; 21:1749. [PMID: 33802488 PMCID: PMC7959471 DOI: 10.3390/s21051749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 11/16/2022]
Abstract
Isothermal amplification techniques are emerging nowadays for the rapid and accurate detection of pathogenic bacteria in low resource settings, where many infectious diseases are endemic, and the lack of reliable power supply, trained personnel and specialized facilities pose critical barriers for timely diagnosis. This work addresses the detection of E. coli based on DNA isothermal amplification performed on magnetic particles (MPs) followed by electrochemical genosensing on disposable electrodes by square-wave voltammetry. In this approach, the bacterial DNA is preconcentrated using a target-specific magnetic probe and then amplified on the MPs by rolling circle amplification (RCA). Two different electrochemical readout methods for the RCA amplicons are tested. The first one relied on the labelling of the magnetic RCA product with a digoxigenin probe followed by the incubation with antiDIG-HRP antibody as electrochemical reporter. In the second case, the direct detection with an HRP-probe was performed. This latter strategy showed an improved analytical performance, while simultaneously avoiding the use of thermocyclers or bulky bench top equipment.
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Affiliation(s)
- Alejandra Ben Aissa
- Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
| | - Narayanan Madaboosi
- IIT Madras Bioincubator, Indian Institute of Technology, Chennai 600113, India; or
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 11419 Stockholm, Sweden;
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 11419 Stockholm, Sweden;
| | - Maria Isabel Pividori
- Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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2
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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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3
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Smolina IV, Broude NE. Ultrasensitive detection of DNA and protein markers in cancer cells. Cancer Biol Med 2015; 12:143-9. [PMID: 26487959 PMCID: PMC4607821 DOI: 10.7497/j.issn.2095-3941.2015.0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Cancer cells differ from normal cells in various parameters, and these differences are caused by genomic mutations and consequential altered gene expression. The genetic and functional heterogeneity of tumor cells is a major challenge in cancer research, detection, and effective treatment. As such, the use of diagnostic methods is important to reveal this heterogeneity at the single-cell level. Droplet microfluidic devices are effective tools that provide exceptional sensitivity for analyzing single cells and molecules. In this review, we highlight two novel methods that employ droplet microfluidics for ultra-sensitive detection of nucleic acids and protein markers in cancer cells. We also discuss the future practical applications of these methods.
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Affiliation(s)
- Irina V Smolina
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Natalia E Broude
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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4
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Russell C, Roy S, Ganguly S, Qian X, Caruthers MH, Nilsson M. Formation of Silver Nanostructures by Rolling Circle Amplification Using Boranephosphonate-Modified Nucleotides. Anal Chem 2015; 87:6660-6. [PMID: 26059318 DOI: 10.1021/acs.analchem.5b00783] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We investigate the efficiency of incorporation of boranephosphonate-modified nucleotides by phi29 DNA polymerase and present a simple method for forming large defined silver nanostructures by rolling circle amplification (RCA) using boranephosphonate internucleotide linkages. RCA is a linear DNA amplification technique that can use specifically circularized DNA probes for detection of target nucleic acids and proteins. The resulting product is a collapsed single-stranded DNA molecule with tandem repeats of the DNA probe. By substituting each of the natural nucleotides with the corresponding 5'-(α-P-borano)deoxynucleosidetriphosphate, only a small reduction in amplification rate is observed. Also, by substituting all four natural nucleotides, it is possible to enzymatically synthesize a micrometer-sized, single-stranded DNA molecule with only boranephosphonate internucleotide linkages. Well-defined silver particles are then readily formed along the rolling circle product.
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Affiliation(s)
- Camilla Russell
- †Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, SE-751 85, Sweden
| | - Subhadeep Roy
- ‡Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Saheli Ganguly
- ‡Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Xiaoyan Qian
- §Science for Life laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-171 21, Sweden
| | - Marvin H Caruthers
- ‡Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Mats Nilsson
- †Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, SE-751 85, Sweden.,§Science for Life laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-171 21, Sweden
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5
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Xie L, Cheng H, Qi H, Wang T, Zhao H, Huang G, Du Y. Nanostructural morphology master-regulated the cell capture efficiency of multivalent aptamers. RSC Adv 2015. [DOI: 10.1039/c5ra01919b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The nanostructural features of stretched multivalent aptamers significantly improve the cell enrichment efficiency to about 16 fold higher than normal multivalent aptamers.
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Affiliation(s)
- Liping Xie
- College of Life and Health Science
- Northeastern University
- Shenyang 110819
- China
| | - Hao Cheng
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| | - Hao Qi
- Key Laboratory of Systems Bioengineering
- Ministry of Education (Tianjin University)
- Tianjin
- China
- School of Chemical Engineering and Technology
| | - Tongzhou Wang
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| | - Hui Zhao
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| | - Guoliang Huang
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| | - Yanan Du
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
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6
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Abstract
Effective prevention of HIV/AIDS requires early diagnosis, initiation of therapy, and regular plasma viral load monitoring of the infected individual. In addition, incidence estimation using accurate and sensitive assays is needed to facilitate HIV prevention efforts in the public health setting. Therefore, more affordable and accessible point-of-care (POC) technologies capable of providing early diagnosis, HIV viral load measurements, and CD4 counts in settings where HIV is most prevalent are needed to enable appropriate intervention strategies and ultimately stop transmission of the virus within these populations to achieve the future goal of an AIDS-free generation. This review discusses the available and emerging POC technologies for future application to these unmet public health needs.
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7
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Yaroslavsky AI, Smolina IV. Fluorescence imaging of single-copy DNA sequences within the human genome using PNA-directed padlock probe assembly. ACTA ACUST UNITED AC 2013; 20:445-53. [PMID: 23521801 DOI: 10.1016/j.chembiol.2013.02.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 12/24/2012] [Accepted: 02/07/2013] [Indexed: 01/07/2023]
Abstract
We present an approach for fluorescent in situ detection of short, single-copy sequences within genomic DNA in human cells. The single-copy sensitivity and single-base specificity of our method is achieved due to the combination of three components. First, a peptide nucleic acid (PNA) probe locally opens a chosen target site, which allows a padlock DNA probe to access the site and become ligated. Second, rolling circle amplification (RCA) generates thousands of single-stranded copies of the target sequence. Finally, fluorescent in situ hybridization (FISH) is used to visualize the amplified DNA. We validate this technique by successfully detecting six single-copy target sites on human mitochondrial and autosomal DNA. We also demonstrate the high selectivity of this method by detecting X- and Y-specific sequences on human sex chromosomes and by simultaneously detecting three sequence-specific target sites. Finally, we discriminate two target sites that differ by 2 nt. The PNA-RCA-FISH approach is a distinctive in situ hybridization method capable of multitarget visualization within human chromosomes and nuclei that does not require DNA denaturation and is extremely sequence specific.
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8
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Konry T, Lerner A, Yarmush ML, Smolina IV. Target DNA detection and quantitation on a single cell with single base resolution. TECHNOLOGY 2013; 1:88. [PMID: 24977169 PMCID: PMC4073798 DOI: 10.1142/s2339547813500088] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In this report, we present a new method for sensitive detection of short DNA sites in single cells with single base resolution. The method combines peptide nucleic acid (PNA) openers as the tagging probes, together with isothermal rolling circle amplification (RCA) and fluorescence-based detection, all performed in a cells-in-flow format. Bis-PNAs provide single base resolution, while RCA ensures linear signal amplification. We applied this method to detect the oncoviral DNA inserts in cancer cell lines using a flow-cytometry system. We also demonstrated quantitative detection of the selected signature sites within single cells in microfluidic nano-liter droplets. Our results show single-nucleotide polymorphism (SNP) discrimination and detection of copy-number variations (CNV) under isothermal non-denaturing conditions. This new method is ideal for many applications in which ultra-sensitive DNA characterization with single base resolution is desired on the level of single cells.
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9
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Chang CM, Chang WH, Wang CH, Wang JH, Mai JD, Lee GB. Nucleic acid amplification using microfluidic systems. LAB ON A CHIP 2013; 13:1225-42. [PMID: 23407669 DOI: 10.1039/c3lc41097h] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In the post-human-genome-project era, the development of molecular diagnostic techniques has advanced the frontiers of biomedical research. Nucleic-acid-based technology (NAT) plays an especially important role in molecular diagnosis. However, most research and clinical protocols still rely on the manual analysis of individual samples by skilled technicians which is a time-consuming and labor-intensive process. Recently, with advances in microfluidic designs, integrated micro total-analysis-systems have emerged to overcome the limitations of traditional detection assays. These microfluidic systems have the capability to rapidly perform experiments in parallel and with a high-throughput which allows a NAT analysis to be completed in a few hours or even a few minutes. These features have a significant beneficial influence on many aspects of traditional biological or biochemical research and this new technology is promising for improving molecular diagnosis. Thus, in the foreseeable future, microfluidic systems developed for molecular diagnosis using NAT will become an important tool in clinical diagnosis. One of the critical issues for NAT is nucleic acid amplification. In this review article, recent advances in nucleic acid amplification techniques using microfluidic systems will be reviewed. Different approaches for fast amplification of nucleic acids for molecular diagnosis will be highlighted.
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Affiliation(s)
- Chen-Min Chang
- Institute of Oral Medicine, National Cheng Kung University, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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10
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Zanoli LM, Spoto G. Isothermal amplification methods for the detection of nucleic acids in microfluidic devices. BIOSENSORS 2013; 3:18-43. [PMID: 25587397 PMCID: PMC4263587 DOI: 10.3390/bios3010018] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 12/07/2012] [Accepted: 12/24/2012] [Indexed: 12/05/2022]
Abstract
Diagnostic tools for biomolecular detection need to fulfill specific requirements in terms of sensitivity, selectivity and high-throughput in order to widen their applicability and to minimize the cost of the assay. The nucleic acid amplification is a key step in DNA detection assays. It contributes to improving the assay sensitivity by enabling the detection of a limited number of target molecules. The use of microfluidic devices to miniaturize amplification protocols reduces the required sample volume and the analysis times and offers new possibilities for the process automation and integration in one single device. The vast majority of miniaturized systems for nucleic acid analysis exploit the polymerase chain reaction (PCR) amplification method, which requires repeated cycles of three or two temperature-dependent steps during the amplification of the nucleic acid target sequence. In contrast, low temperature isothermal amplification methods have no need for thermal cycling thus requiring simplified microfluidic device features. Here, the use of miniaturized analysis systems using isothermal amplification reactions for the nucleic acid amplification will be discussed.
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Affiliation(s)
- Laura Maria Zanoli
- Istituto Biostrutture e Bioimmagini, CNR, Viale A. Doria 6, Catania, Italy; E-Mail:
| | - Giuseppe Spoto
- Istituto Biostrutture e Bioimmagini, CNR, Viale A. Doria 6, Catania, Italy; E-Mail: ; Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125 Catania, Italy
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11
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Jang K, Tanaka Y, Wakabayashi J, Ishii R, Sato K, Mawatari K, Nilsson M, Kitamori T. Selective cell capture and analysis using shallow antibody-coated microchannels. BIOMICROFLUIDICS 2012; 6:44117. [PMID: 24339850 PMCID: PMC3555508 DOI: 10.1063/1.4771968] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/28/2012] [Indexed: 06/03/2023]
Abstract
Demand for analysis of rare cells such as circulating tumor cells in blood at the single molecule level has recently grown. For this purpose, several cell separation methods based on antibody-coated micropillars have been developed (e.g., Nagrath et al., Nature 450, 1235-1239 (2007)). However, it is difficult to ensure capture of targeted cells by these methods because capture depends on the probability of cell-micropillar collisions. We developed a new structure that actively exploits cellular flexibility for more efficient capture of a small number of cells in a target area. The depth of the sandwiching channel was slightly smaller than the diameter of the cells to ensure contact with the channel wall. For cell selection, we used anti-epithelial cell adhesion molecule antibodies, which specifically bind epithelial cells. First, we demonstrated cell capture with human promyelocytic leukemia (HL-60) cells, which are relatively homogeneous in size; in situ single molecule analysis was verified by our rolling circle amplification (RCA) method. Then, we used breast cancer cells (SK-BR-3) in blood, and demonstrated selective capture and cancer marker (HER2) detection by RCA. Cell capture by antibody-coated microchannels was greater than with negative control cells (RPMI-1788 lymphocytes) and non-coated microchannels. This system can be used to analyze small numbers of target cells in large quantities of mixed samples.
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Affiliation(s)
- Kihoon Jang
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
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12
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Craw P, Balachandran W. Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review. LAB ON A CHIP 2012; 12:2469-86. [PMID: 22592150 DOI: 10.1039/c2lc40100b] [Citation(s) in RCA: 470] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Nucleic Acid Testing (NAT) promises rapid, sensitive and specific diagnosis of infectious, inherited and genetic disease. The next generation of diagnostic devices will interrogate the genetic determinants of such conditions at the point-of-care, affording clinicians prompt reliable diagnosis from which to guide more effective treatment. The complex biochemical nature of clinical samples, the low abundance of nucleic acid targets in the majority of clinical samples and existing biosensor technology indicate that some form of nucleic acid amplification will be required to obtain clinically relevant sensitivities from the small samples used in point-of-care testing (POCT). This publication provides an overview and thorough review of existing technologies for nucleic acid amplification. The different methods are compared and their suitability for POCT adaptation are discussed. Current commercial products employing isothermal amplification strategies are also investigated. In conclusion we identify the factors impeding the integration of the methods discussed in fully automated, sample-to-answer POCT devices.
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Affiliation(s)
- Pascal Craw
- Department of Electronic & Computer Engineering, School of Engineering & Design, Brunel University, London, UK.
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13
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Liu C, Qu Y, Luo Y, Fang N. Recent advances in single-molecule detection on micro- and nano-fluidic devices. Electrophoresis 2012; 32:3308-18. [PMID: 22134976 DOI: 10.1002/elps.201100159] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-molecule detection (SMD) allows static and dynamic heterogeneities from seemingly equal molecules to be revealed in the studies of molecular structures and intra- and inter-molecular interactions. Micro- and nanometer-sized structures, including channels, chambers, droplets, etc., in microfluidic and nanofluidic devices allow diffusion-controlled reactions to be accelerated and provide high signal-to-noise ratio for optical signals. These two active research frontiers have been combined to provide unprecedented capabilities for chemical and biological studies. This review summarizes the advances of SMD performed on microfluidic and nanofluidic devices published in the past five years. The latest developments on optical SMD methods, microfluidic SMD platforms, and on-chip SMD applications are discussed herein and future development directions are also envisioned.
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Affiliation(s)
- Chang Liu
- Ames Laboratory, US Department of Energy, Ames, Iowa, USA
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14
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Asiello PJ, Baeumner AJ. Miniaturized isothermal nucleic acid amplification, a review. LAB ON A CHIP 2011; 11:1420-30. [PMID: 21387067 DOI: 10.1039/c0lc00666a] [Citation(s) in RCA: 287] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Micro-Total Analysis Systems (µTAS) for use in on-site rapid detection of DNA or RNA are increasingly being developed. Here, amplification of the target sequence is key to increasing sensitivity, enabling single-cell and few-copy nucleic acid detection. The several advantages to miniaturizing amplification reactions and coupling them with sample preparation and detection on the same chip are well known and include fewer manual steps, preventing contamination, and significantly reducing the volume of expensive reagents. To-date, the majority of miniaturized systems for nucleic acid analysis have used the polymerase chain reaction (PCR) for amplification and those systems are covered in previous reviews. This review provides a thorough overview of miniaturized analysis systems using alternatives to PCR, specifically isothermal amplification reactions. With no need for thermal cycling, isothermal microsystems can be designed to be simple and low-energy consuming and therefore may outperform PCR in portable, battery-operated detection systems in the future. The main isothermal methods as miniaturized systems reviewed here include nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), and strand displacement amplification (SDA). Also, important design criteria for the miniaturized devices are discussed. Finally, the potential of miniaturization of some new isothermal methods such as the exponential amplification reaction (EXPAR), isothermal and chimeric primer-initiated amplification of nucleic acids (ICANs), signal-mediated amplification of RNA technology (SMART) and others is presented.
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Affiliation(s)
- Peter J Asiello
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
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15
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Tanaka Y, Xi H, Sato K, Mawatari K, Renberg B, Nilsson M, Kitamori T. Single-Molecule DNA Patterning and Detection by Padlock Probing and Rolling Circle Amplification in Microchannels for Analysis of Small Sample Volumes. Anal Chem 2011; 83:3352-7. [DOI: 10.1021/ac103185j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Yo Tanaka
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, 1-1-2, Otemachi, Chiyoda, Tokyo 100-0004, Japan
| | - Hui Xi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
| | - Kae Sato
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, 1-1-2, Otemachi, Chiyoda, Tokyo 100-0004, Japan
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women’s University, 2-8-1 Mejirodai, Bunkyo, Tokyo 112-8681, Japan
| | - Kazuma Mawatari
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, 1-1-2, Otemachi, Chiyoda, Tokyo 100-0004, Japan
| | - Björn Renberg
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
| | - Mats Nilsson
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Takehiko Kitamori
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, 1-1-2, Otemachi, Chiyoda, Tokyo 100-0004, Japan
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16
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Konry T, Smolina I, Yarmush JM, Irimia D, Yarmush ML. Ultrasensitive detection of low-abundance surface-marker protein using isothermal rolling circle amplification in a microfluidic nanoliter platform. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:395-400. [PMID: 21294269 PMCID: PMC3110589 DOI: 10.1002/smll.201001620] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 10/19/2010] [Indexed: 05/25/2023]
Abstract
With advances in immunology and cancer biology, there is an unmet need for increasingly sensitive systems to monitor the expression of specific cell markers for the development of new diagnostic and therapeutic tools. To address this challenge, a highly sensitive labeling method that translates antigen-antibody recognition processes into DNA detection events that can be greatly amplified via isothermal rolling circle amplification (RCA) is applied. By merging the single-molecule detection power of RCA reactions with microfluidic technology, it is demonstrated that the identification of specific protein markers can be achieved on tumor-cell surfaces in miniaturized nanoliter reaction droplets. Furthermore, this combined approach of signal amplification in a microfluidic format could extend the utility of existing methods by reducing sample and reagent consumption and enhancing the sensitivities and specificities for various applications, including early diagnosis of cancer.
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Affiliation(s)
- Tania Konry
- Center for Engineering in Medicine and Department of Surgery, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, Boston, MA, 02114, USA
| | - Irina Smolina
- Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA, 02215, USA
| | - Joel M. Yarmush
- Department of Anesthesiology, New York Methodist Hospital, Brooklyn, NY 11215, USA
| | - Daniel Irimia
- Center for Engineering in Medicine and Department of Surgery, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, Boston, MA, 02114, USA
| | - Martin L. Yarmush
- Center for Engineering in Medicine and Department of Surgery, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, Boston, MA, 02114, USA
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17
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Akhtar S, Strömberg M, Zardán Gómez de la Torre T, Russell C, Gunnarsson K, Nilsson M, Svedlindh P, Strømme M, Leifer K. Real-Space Transmission Electron Microscopy Investigations of Attachment of Functionalized Magnetic Nanoparticles to DNA-Coils Acting as a Biosensor. J Phys Chem B 2010; 114:13255-62. [DOI: 10.1021/jp105756b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sultan Akhtar
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Mattias Strömberg
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Teresa Zardán Gómez de la Torre
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Camilla Russell
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Klas Gunnarsson
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Mats Nilsson
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Peter Svedlindh
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Maria Strømme
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Klaus Leifer
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
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18
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Sato K, Tachihara A, Renberg B, Mawatari K, Sato K, Tanaka Y, Jarvius J, Nilsson M, Kitamori T. Microbead-based rolling circle amplification in a microchip for sensitive DNA detection. LAB ON A CHIP 2010; 10:1262-6. [PMID: 20445878 DOI: 10.1039/b927460j] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The sensitive detection and quantification of DNA targets in the food industry and in environmental and clinical settings are issues of utmost importance in ensuring contamination-free food, monitoring the environment, and battling disease. Selective probes coupled with powerful amplification techniques are therefore of major interest. In this study, we set out to create an integrated microchemical chip that benefits from microfluidic chip technology in terms of sensitivity and a strong detection methodology provided jointly by padlock probes and rolling circle amplification (RCA). Here, we have integrated padlock probes and RCA into a microchip. The chip uses solid phase capture in a microchannel to enable washing cycles and decrease analytical area, and employs on-bead RCA for single-molecule amplification and detection. We investigated the effects of reagent concentration and amount of padlock probes, and demonstrated the feasibility of detecting Salmonella.
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Affiliation(s)
- Kae Sato
- Center for Nanobio Integration, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
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19
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Stougaard M, Lohmann JS, Mancino A, Celik S, Andersen FF, Koch J, Knudsen BR. Single-molecule detection of human topoisomerase I cleavage-ligation activity. ACS NANO 2009; 3:223-233. [PMID: 19206270 DOI: 10.1021/nn800509b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In the present study, we demonstrate the conversion of a single human topoisomerase I mediated DNA cleavage-ligation event happening within nanometer dimensions to a micrometer-sized DNA molecule, readily detectable using standard fluorescence microscopy. This conversion is achieved by topoisomerase I mediated closure of a nicked DNA dumbbell structure, followed by rolling circle amplification. The resulting product consists of multiple tandem repeats of the DNA dumbbell and can subsequently be visualized by annealing to fluorescently labeled probes. Since amplification involves no thermal cycling, each fluorescent rolling circle product, which gives rise to an individual signal upon microscopic analysis, will correspond to a single human topoisomerase I mediated cleavage-ligation event. Regarding sensitivity, speed, and ease of performance, the presented activity assay based on single-molecule product detection is superior to current state of the art assays using supercoiled plasmids or radiolabeled oligonucleotides as the substrate for topoisomerase I activity. Moreover, inherent in the experimental design is the easy adaptation to multiplexed and/or high-throughput systems. Human topoisomerase I is the cellular target of clinically important anticancer drugs, and the effect of such drugs corresponds directly to the intracellular topoisomerase I cleavage-ligation activity level. We therefore believe that the presented setup, measuring directly the number of cleavage-ligation events in a given sample, has great diagnostic potential, adding considerably to the possibilities of accurate prognosis before treatment with topoisomerase I directed chemotherapeutics.
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Affiliation(s)
- Magnus Stougaard
- Department of Pathology and Interdisciplinary Nanoscience Center (iNano), Aarhus University Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark
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20
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Conze T, Shetye A, Tanaka Y, Gu J, Larsson C, Göransson J, Tavoosidana G, Söderberg O, Nilsson M, Landegren U. Analysis of genes, transcripts, and proteins via DNA ligation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2009; 2:215-239. [PMID: 20636060 DOI: 10.1146/annurev-anchem-060908-155239] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Analytical reactions in which short DNA strands are used in combination with DNA ligases have proven useful for measuring, decoding, and locating most classes of macromolecules. Given the need to accumulate large amounts of precise molecular information from biological systems in research and in diagnostics, ligation reactions will continue to offer valuable strategies for advanced analytical reactions. Here, we provide a basis for further development of methods by reviewing the history of analytical ligation reactions, discussing the properties of ligation reactions that render them suitable for engineering novel assays, describing a wide range of successful ligase-based assays, and briefly considering future directions.
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Affiliation(s)
- Tim Conze
- Department of Genetics and Pathology, The Rudbeck Lab, Uppsala University, Uppsala, Sweden
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21
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Melin J, Jarvius J, Larsson C, Söderberg O, Landegren U, Nilsson M. Ligation-based molecular tools for lab-on-a-chip devices. N Biotechnol 2008; 25:42-8. [DOI: 10.1016/j.nbt.2008.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Revised: 01/17/2008] [Accepted: 02/07/2008] [Indexed: 10/22/2022]
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22
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Kuhn H, Frank-Kamenetskii MD. Labeling of unique sequences in double-stranded DNA at sites of vicinal nicks generated by nicking endonucleases. Nucleic Acids Res 2008; 36:e40. [PMID: 18344522 PMCID: PMC2373456 DOI: 10.1093/nar/gkn107] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We describe a new approach for labeling of unique sequences within dsDNA under nondenaturing conditions. The method is based on the site-specific formation of vicinal nicks, which are created by nicking endonucleases (NEases) at specified DNA sites on the same strand within dsDNA. The oligomeric segment flanked by both nicks is then substituted, in a strand displacement reaction, by an oligonucleotide probe that becomes covalently attached to the target site upon subsequent ligation. Monitoring probe hybridization and ligation reactions by electrophoretic mobility retardation assay, we show that selected target sites can be quantitatively labeled with excellent sequence specificity. In these experiments, predominantly probes carrying a target-independent 3′ terminal sequence were employed. At target labeling, thus a branched DNA structure known as 3′-flap DNA is obtained. The single-stranded terminus in 3′-flap DNA is then utilized to prime the replication of an externally supplied ssDNA circle in a rolling circle amplification (RCA) reaction. In model experiments with samples comprised of genomic λ-DNA and human herpes virus 6 type B (HHV-6B) DNA, we have used our labeling method in combination with surface RCA as reporter system to achieve both high sequence specificity of dsDNA targeting and high sensitivity of detection. The method can find applications in sensitive and specific detection of viral duplex DNA.
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Affiliation(s)
- Heiko Kuhn
- Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, MA 02215, USA.
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