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Kaur G, Tintelott M, Suranglikar M, Masurier A, Vu XT, Gines G, Rondelez Y, Ingebrandt S, Coffinier Y, Pachauri V, Vlandas A. Time-encoded electrical detection of trace RNA biomarker by integrating programmable molecular amplifier on chip. Biosens Bioelectron 2024; 257:116311. [PMID: 38677018 DOI: 10.1016/j.bios.2024.116311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 04/02/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
One of the serious challenges facing modern point-of-care (PoC) molecular diagnostic platforms relate to reliable detection of low concentration biomarkers such as nucleic acids or proteins in biological samples. Non-specific analyte-receptor interactions due to competitive binding in the presence of abundant molecules, inefficient mass transport and very low number of analyte molecules in sample volume, in general pose critical hurdles for successful implementation of such PoC platforms for clinical use. Focusing on these specific challenges, this work reports a unique PoC biosensor that combines the advantages of nanoscale biologically-sensitive field-effect transistor arrays (BioFET-arrays) realized in a wafer-scale top-down nanofabrication as high sensitivity electrical transducers with that of sophisticated molecular programs (MPs) customized for selective recognition of analyte miRNAs and amplification resulting in an overall augmentation of signal transduction strategy. The MPs realize a programmable universal molecular amplifier (PUMA) in fluidic matrix on chip and provide a biomarker-triggered exponential release of small nucleic acid sequences easily detected by receptor-modified BioFETs. A common miRNA biomarker LET7a was selected for successful demonstration of this novel biosensor, achieving limit of detection (LoD) down to 10 fM and wide dynamic ranges (10 pM-10 nM) in complex physiological solutions. As the determination of biomarker concentration is implemented by following the electrical signal related to analyte-triggered PUMA in time-domain instead of measuring the threshold shifts of BioFETs, and circumvents direct hybridization of biomarkers at transducer surface, this new strategy also allows for multiple usage (>3 times) of the biosensor platform suggesting exceptional cost-effectiveness for practical use.
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Affiliation(s)
- Gurpreet Kaur
- Institut D'Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR CNRS 8520, Univ. Lille Avenue Poincaré, BP 60069, Villeneuve D'Ascq, Cedex, 59652, France
| | - Marcel Tintelott
- Institute of Materials in Electrical Engineering 1, RWTH Aachen University, Sommerfeldstrasse 24, 52074, Aachen, Germany
| | - Mohit Suranglikar
- Institute of Materials in Electrical Engineering 1, RWTH Aachen University, Sommerfeldstrasse 24, 52074, Aachen, Germany
| | - Antoine Masurier
- Laboratoire Gulliver, Ecole Supérieure de Physique et de Chimie Industrielles, PSL Research University, and CNRS, Paris, France
| | - Xuan-Thang Vu
- Institute of Materials in Electrical Engineering 1, RWTH Aachen University, Sommerfeldstrasse 24, 52074, Aachen, Germany
| | - Guillaume Gines
- Laboratoire Gulliver, Ecole Supérieure de Physique et de Chimie Industrielles, PSL Research University, and CNRS, Paris, France
| | - Yannick Rondelez
- Laboratoire Gulliver, Ecole Supérieure de Physique et de Chimie Industrielles, PSL Research University, and CNRS, Paris, France
| | - Sven Ingebrandt
- Institute of Materials in Electrical Engineering 1, RWTH Aachen University, Sommerfeldstrasse 24, 52074, Aachen, Germany
| | - Yannick Coffinier
- Institute of Materials in Electrical Engineering 1, RWTH Aachen University, Sommerfeldstrasse 24, 52074, Aachen, Germany
| | - Vivek Pachauri
- Institute of Materials in Electrical Engineering 1, RWTH Aachen University, Sommerfeldstrasse 24, 52074, Aachen, Germany.
| | - Alexis Vlandas
- Institut D'Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR CNRS 8520, Univ. Lille Avenue Poincaré, BP 60069, Villeneuve D'Ascq, Cedex, 59652, France
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2
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Ngoc LTN, Lee YC. Current Trends in RNA Virus Detection via Nucleic Acid Isothermal Amplification-Based Platforms. BIOSENSORS 2024; 14:97. [PMID: 38392016 PMCID: PMC10886876 DOI: 10.3390/bios14020097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Ribonucleic acid (RNA) viruses are one of the major classes of pathogens that cause human diseases. The conventional method to detect RNA viruses is real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), but it has some limitations. It is expensive and time-consuming, with infrastructure and trained personnel requirements. Its high throughput requires sophisticated automation and large-scale infrastructure. Isothermal amplification methods have been explored as an alternative to address these challenges. These methods are rapid, user-friendly, low-cost, can be performed in less specialized settings, and are highly accurate for detecting RNA viruses. Microfluidic technology provides an ideal platform for performing virus diagnostic tests, including sample preparation, immunoassays, and nucleic acid-based assays. Among these techniques, nucleic acid isothermal amplification methods have been widely integrated with microfluidic platforms for RNA virus detection owing to their simplicity, sensitivity, selectivity, and short analysis time. This review summarizes some common isothermal amplification methods for RNA viruses. It also describes commercialized devices and kits that use isothermal amplification techniques for SARS-CoV-2 detection. Furthermore, the most recent applications of isothermal amplification-based microfluidic platforms for RNA virus detection are discussed in this article.
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Affiliation(s)
- Le Thi Nhu Ngoc
- Department of Nano Science and Technology Convergence, Gachon University, 1342 Seongnam-Daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
| | - Young-Chul Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
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3
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Sato Y, Suzuki Y. DNA nanotechnology provides an avenue for the construction of programmable dynamic molecular systems. Biophys Physicobiol 2021; 18:116-126. [PMID: 34123692 PMCID: PMC8164909 DOI: 10.2142/biophysico.bppb-v18.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/23/2021] [Indexed: 12/01/2022] Open
Abstract
Self-assembled supramolecular structures in living cells and their dynamics underlie various cellular events, such as endocytosis, cell migration, intracellular transport, cell metabolism, and gene expression. Spatiotemporally regulated association/dissociation and generation/degradation of assembly components is one of the remarkable features of biological systems. The significant advancement in DNA nanotechnology over the last few decades has enabled the construction of various-shaped nanostructures via programmed self-assembly of sequence-designed oligonucleotides. These nanostructures can further be assembled into micrometer-sized structures, including ordered lattices, tubular structures, macromolecular droplets, and hydrogels. In addition to being a structural material, DNA is adopted to construct artificial molecular circuits capable of activating/inactivating or producing/decomposing target DNA molecules based on strand displacement or enzymatic reactions. In this review, we provide an overview of recent studies on artificially designed DNA-based self-assembled systems that exhibit dynamic features, such as association/dis-sociation of components, phase separation, stimulus responsivity, and DNA circuit-regulated structural formation. These biomacromolecule-based, bottom-up approaches for the construction of artificial molecular systems will not only throw light on bio-inspired nano/micro engineering, but also enable us to gain insights into how autonomy and adaptability of living systems can be realized.
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Affiliation(s)
- Yusuke Sato
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
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4
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Climent E, Gotor R, Tobias C, Bell J, Martin-Sanchez PM, Rurack K. Dip Sticks Embedding Molecular Beacon-Functionalized Core-Mesoporous Shell Particles for the Rapid On-Site Detection of Microbiological Fuel Contamination. ACS Sens 2021; 6:27-34. [PMID: 33356175 DOI: 10.1021/acssensors.0c01178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Microbial contamination of fuels by fungi and bacteria presents risks of corrosion and fuel system fouling. In this work, a rapid test for the determination of microbial genomic DNA from aqueous fuel extracts is presented. It combines test strips coated with polystyrene core/mesoporous silica shell particles, to the surface of which modified fluorescent molecular beacons are covalently grafted, with a smartphone detection system. In the hairpin loop, the beacons incorporate a target sequence highly conserved in all bacteria, corresponding to a fragment of the 16S ribosomal RNA gene, which is also present to a significant extent in the 18S rRNA gene of fungi, allowing for broadband microbial detection. In the developed assay, the presence of genomic DNA extracts from bacteria and fungi down to ca. 20-50 μg L-1 induced a distinct fluorescence response. The optical read-out was adapted for on-site monitoring by combining a 3D-printed case with a conventional smartphone, taking advantage of the sensitivity of contemporary complementary metal oxide semiconductor (CMOS) detectors. Such an embedded assembly allowed to detect microbial genomic DNA in aqueous extracts down to ca. 0.2-0.7 mg L-1 and presents an important step toward the on-site uncovering of fuel contamination in a rapid and simple fashion.
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Affiliation(s)
- Estela Climent
- Department 1 Analytical Chemistry, Reference Materials, Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| | - Raúl Gotor
- Department 1 Analytical Chemistry, Reference Materials, Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| | - Charlie Tobias
- Department 1 Analytical Chemistry, Reference Materials, Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| | - Jérémy Bell
- Department 1 Analytical Chemistry, Reference Materials, Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| | - Pedro M. Martin-Sanchez
- Department 4 Materials & Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 87, 12205 Berlin, Germany
- Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, P.O.
Box 1066 Blindern, 0316 Oslo, Norway
| | - Knut Rurack
- Department 1 Analytical Chemistry, Reference Materials, Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str. 11, 12489 Berlin, Germany
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5
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Zeng Y, Koo KM, Shen AG, Hu JM, Trau M. Nucleic Acid Hybridization-Based Noise Suppression for Ultraselective Multiplexed Amplification of Mutant Variants. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2006370. [PMID: 33325632 DOI: 10.1002/smll.202006370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/11/2020] [Indexed: 06/12/2023]
Abstract
The analysis of mutant nucleic acid (NA) variants can provide crucial clinical and biological insights for many diseases. Yet, existing analysis techniques are generally constrained by nonspecific "noise" signals from excessive wildtype background sequences, especially under rapid isothermal multiplexed target amplification conditions. Herein, the molecular hybridization chemistry between NA bases is manipulated to suppress noise signals and achieve ultraselective multiplexed detection of cancer gene fusion NA variants. Firstly, modified locked NA (LNA) bases are rationally introduced into oligonucleotide sequences as designed "locker probes" for high affinity hybridization to wildtype sequences, leading to enrichment of mutant variants for multiplexed isothermal amplification. Secondly, locker probes are coupled with a customized "proximity-programmed" (SERS) readout which allows precise control of hybridization-based plasmonic signaling to specifically detect multiple target amplicons within a single reaction. Moreover, the use of triple bond Raman reporters endows NA noise signal-free quantification in the Raman silent region (≈1800-2600 cm-1 ). With this dual molecular hybridization-based strategy, ultraselective multiplexed detection of gene fusion NA variants in cancer cellular models is actualized with successful noise suppression of native wildtype sequences. The distinct benefits of isothermal NA amplification and SERS multiplexing ability are simultaneously harnessed.
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Affiliation(s)
- Yi Zeng
- School of Printing and Packaging, Wuhan University, Wuhan, 430079, P. R. China
- The Centre of Analysis and Measurement of Wuhan University, Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kevin M Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
- XING Technologies Pty Ltd, Sinnamon Park, Brisbane, QLD, 4073, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, QLD, 4029, Australia
| | - Ai-Guo Shen
- School of Printing and Packaging, Wuhan University, Wuhan, 430079, P. R. China
| | - Ji-Ming Hu
- The Centre of Analysis and Measurement of Wuhan University, Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
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Shoji K, Kawano R. Recent Advances in Liposome-Based Molecular Robots. MICROMACHINES 2020; 11:E788. [PMID: 32825332 PMCID: PMC7569806 DOI: 10.3390/mi11090788] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 01/03/2023]
Abstract
A molecular robot is a microorganism-imitating micro robot that is designed from the molecular level and constructed by bottom-up approaches. As with conventional robots, molecular robots consist of three essential robotics elements: control of intelligent systems, sensors, and actuators, all integrated into a single micro compartment. Due to recent developments in microfluidic technologies, DNA nanotechnologies, synthetic biology, and molecular engineering, these individual parts have been developed, with the final picture beginning to come together. In this review, we describe recent developments of these sensors, actuators, and intelligence systems that can be applied to liposome-based molecular robots. First, we explain liposome generation for the compartments of molecular robots. Next, we discuss the emergence of robotics functions by using and functionalizing liposomal membranes. Then, we discuss actuators and intelligence via the encapsulation of chemicals into liposomes. Finally, the future vision and the challenges of molecular robots are described.
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Affiliation(s)
- Kan Shoji
- Department of Mechanical Engineering, Nagaoka University of Technology, Kamitomioka 1603-1, Nagaoka, Niigata 940-2188, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo 184-8588, Japan
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7
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Emerging isothermal amplification technologies for microRNA biosensing: Applications to liquid biopsies. Mol Aspects Med 2020; 72:100832. [DOI: 10.1016/j.mam.2019.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 11/06/2019] [Accepted: 11/10/2019] [Indexed: 02/07/2023]
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Gines G, Menezes R, Nara K, Kirstetter AS, Taly V, Rondelez Y. Isothermal digital detection of microRNAs using background-free molecular circuit. SCIENCE ADVANCES 2020; 6:eaay5952. [PMID: 32010788 PMCID: PMC6976291 DOI: 10.1126/sciadv.aay5952] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/20/2019] [Indexed: 05/04/2023]
Abstract
MicroRNAs, a class of transcripts involved in the regulation of gene expression, are emerging as promising disease-specific biomarkers accessible from tissues or bodily fluids. However, their accurate quantification from biological samples remains challenging. We report a sensitive and quantitative microRNA detection method using an isothermal amplification chemistry adapted to a droplet digital readout. Building on molecular programming concepts, we design a DNA circuit that converts, thresholds, amplifies, and reports the presence of a specific microRNA, down to the femtomolar concentration. Using a leak absorption mechanism, we were able to suppress nonspecific amplification, classically encountered in other exponential amplification reactions. As a result, we demonstrate that this isothermal amplification scheme is adapted to digital counting of microRNAs: By partitioning the reaction mixture into water-in-oil droplets, resulting in single microRNA encapsulation and amplification, the method provides absolute target quantification. The modularity of our approach enables to repurpose the assay for various microRNA sequences.
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Affiliation(s)
- Guillaume Gines
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - Roberta Menezes
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Kaori Nara
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - Anne-Sophie Kirstetter
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - Valerie Taly
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Corresponding author. (Y.R.); (V.T.)
| | - Yannick Rondelez
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
- Corresponding author. (Y.R.); (V.T.)
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Sato Y, Komiya K, Kawamata I, Murata S, Nomura SIM. Isothermal amplification of specific DNA molecules inside giant unilamellar vesicles. Chem Commun (Camb) 2019; 55:9084-9087. [PMID: 31287464 DOI: 10.1039/c9cc03277k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An isothermal amplification circuit for specific DNA molecules was implemented in giant unilamellar vesicles. Using this circuit, over 5000-fold amplification of output DNAs was achieved, and the amplification behaviour depended on the concentration of input signal DNAs in a cell-sized compartment. Moreover, initiation of the amplification by photo-stimulation was demonstrated.
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Affiliation(s)
- Yusuke Sato
- Department of Robotics, Tohoku University, Miyagi 980-8579, Japan.
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Komori M, Komiya K, Shirakawa T, Morikawa TJ, Yoshimura T. Measurement of microRNA with isothermal DNA amplification on fully automated immunoassay analyzers. Anal Bioanal Chem 2019; 411:3789-3800. [PMID: 31161320 PMCID: PMC6595071 DOI: 10.1007/s00216-019-01878-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/15/2019] [Accepted: 04/26/2019] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) in a blood sample are usually measured by quantitative reverse transcription PCR (qRT-PCR), microarray, and next-generation sequencing (NGS) which requires time-consuming pre-treatment, manual operation, and a stand-alone instrument. To overcome these disadvantages, miRNA testing has been developed using the automated analyzers routinely used in clinical laboratories. An isothermal DNA amplification reaction was adapted to a fully automated immunoassay analyzer that conducts extraction, amplification, and detection processes at 37 °C in 44 min. In a reaction vessel, a pre-designed single-stranded signal DNA was amplified in the presence of miRNA, using DNA templates, DNA polymerase, and nicking endonuclease. Then, the amplified signal DNA was hybridized by one DNA probe attached to a magnetic particle and another DNA probe labeled with acridinium ester. After the chemiluminescence reaction, luminescence intensity was automatically measured. The automated assays of cancer-related miRNAs were implemented on the analyzer with throughput of 66 tests per hour. In the assays with one-step amplification, three miRNAs (miR-21-5p, miR-18a-5p, and miR-500a-3p) at concentrations lower than 100 fM were automatically detected and the cross reactivity for miR-21-5p with fifteen similar miRNAs was not higher than 0.02%. In the assay with two-step amplification, detection sensitivity and amplification rate for miR-21-5p were 3 fM and 103-fold, respectively. The coefficient of variations (CVs) in the measurement at the target concentrations from 5 fM to 1000 pM were less than 8%. Furthermore, we also achieved automated nucleic acid detection in human serum. The proposed fully automated miRNA assays showed high sensitivity, low cross reactivity, and reproducibility suitable for clinical use. Graphical abstract.
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Affiliation(s)
- Makoto Komori
- Research and Development, Abbott Japan Co. Ltd, 278 Matsuhidai, Matsudo, Chiba, 270-2214, Japan.
| | - Ken Komiya
- School of Computing, Tokyo Institute of Technology, J2-51, 4259, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Takuma Shirakawa
- Research and Development, Abbott Japan Co. Ltd, 278 Matsuhidai, Matsudo, Chiba, 270-2214, Japan
| | - Takamitsu J Morikawa
- Research and Development, Abbott Japan Co. Ltd, 278 Matsuhidai, Matsudo, Chiba, 270-2214, Japan
| | - Toru Yoshimura
- Research and Development, Abbott Japan Co. Ltd, 278 Matsuhidai, Matsudo, Chiba, 270-2214, Japan
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