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Loyez M, Fasseaux H, Lobry M, Wattiez R, Caucheteur C. Insulin biotrapping using plasmofluidic optical fiber chips: A benchmark. Biosens Bioelectron 2024; 254:116189. [PMID: 38507927 DOI: 10.1016/j.bios.2024.116189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/02/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
Plasmonic optical fiber-based biosensors are currently in their early stages of development as practical and integrated devices, gradually making their way towards the market. While the majority of these biosensors operate using white light and multimode optical fibers (OFs), our approach centers on single-mode OFs coupled with tilted fiber Bragg gratings (TFBGs) in the near-infrared wavelength range. Our objective is to enhance surface sensitivity and broaden sensing capabilities of OF-based sensors to develop in situ sensing with remote interrogation. In this study, we comprehensively assess their performance in comparison to the gold-standard plasmonic reference, a commercial device based on the Kretschmann-Raether prism configuration. We present their refractive index sensitivity and their capability for insulin sensing using a dedicated microfluidics approach. By optimizing a consistent surface biotrapping methodology, we elucidate the dynamic facets of both technologies and highlight their remarkable sensitivity to variations in bulk and surface properties. The one-to-one comparison between both technologies demonstrates the reliability of optical fiber-based measurements, showcasing similar experimental trends obtained with both the prismatic configuration and gold-coated TFBGs, with an even enhanced limit of detection for the latter. This study lays the foundation for the detection of punctual molecular interactions and opens the way towards the detection of spatially and temporally localized events on the surface of optical probes.
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Affiliation(s)
- Médéric Loyez
- Proteomics and Microbiology Department, University of Mons (UMONS), 7000, Belgium; Electromagnetism and Telecom. Department, University of Mons (UMONS), 7000, Belgium.
| | - Hadrien Fasseaux
- Electromagnetism and Telecom. Department, University of Mons (UMONS), 7000, Belgium
| | - Maxime Lobry
- Electromagnetism and Telecom. Department, University of Mons (UMONS), 7000, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons (UMONS), 7000, Belgium
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2
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Jiang S, Qian S, Zhu S, Lu J, Hu Y, Zhang C, Geng Y, Chen X, Guo Y, Chen Z, Pu J, Guo Z, Liu S. A Point-of-Care Testing Device Utilizing Graphene-Enhanced Fiber Optic SPR Sensor for Real-Time Detection of Infectious Pathogens. BIOSENSORS 2023; 13:1029. [PMID: 38131789 PMCID: PMC10741924 DOI: 10.3390/bios13121029] [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: 11/16/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
Timely detection of highly infectious pathogens is essential for preventing and controlling public health risks. However, most traditional testing instruments require multiple tedious steps and ultimately testing in hospitals and third-party laboratories. The sample transfer process significantly prolongs the time to obtain test results. To tackle this aspect, a portable fiber optic surface plasmon resonance (FO-SPR) device was developed for the real-time detection of infectious pathogens. The portable device innovatively integrated a compact FO-SPR sensing component, a signal acquisition and processing system, and an embedded power supply unit. A gold-plated fiber is used as the FO-SPR sensing probe. Compared with traditional SPR sensing systems, the device is smaller size, lighter weight, and higher convenience. To enhance the detection capacity of pathogens, a monolayer graphene was coated on the sensing region of the FO-SPR sensing probe. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was used to evaluate the performance of the portable device. The device can accurately detect the SARS-CoV-2 spike S1 protein in phosphate-buffered saline (PBS) and artificial saliva within just 20 min, and the device successfully detected cultured SARS-CoV-2 virus. Furthermore, the FO-SPR probe has long-term stability, remaining stable for up to 8 days. It could distinguish between the SARS-CoV-2 spike protein and the MERS-CoV spike protein. Hence, this FO-SPR device provides reliable, rapid, and portable access to test results. It provides a promising point-of-care testing (POCT) tool for on-site screening of infectious pathogens.
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Affiliation(s)
- Shiyu Jiang
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
- School of Electronic Engineering, Heilongjiang University, Harbin 150080, China
| | - Siyu Qian
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Shunning Zhu
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Jinxin Lu
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Yunxin Hu
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
- School of Electronic Engineering, Heilongjiang University, Harbin 150080, China
| | - Cheng Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.Z.); (Z.C.); (J.P.); (Z.G.)
| | - Yikai Geng
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Xuefeng Chen
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Ying Guo
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Zhaoliang Chen
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.Z.); (Z.C.); (J.P.); (Z.G.)
| | - Jie Pu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.Z.); (Z.C.); (J.P.); (Z.G.)
| | - Zhendong Guo
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.Z.); (Z.C.); (J.P.); (Z.G.)
| | - Shengchun Liu
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
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3
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Li X, Zhang H, Zhang Y, Zhao Y, Nguyen LV, Zhou X, Warren-Smith SC. Label-free DNA quantification using isothermal amplification on an exposed core optical fiber microfluidic platform. Analyst 2023; 148:4897-4904. [PMID: 37655735 DOI: 10.1039/d3an01047c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Isothermal amplification technology has triggered a surge in research due to its compatibility with small and portable equipment, simplicity, and high efficiency, especially in light of the COVID-19 pandemic where reliable widescale testing is critical to outbreak management. In this paper, a label-free isothermal deoxyribonucleic acid (DNA) amplification method based on refractive index (RI) quantification is proposed and demonstrated for the first time by combining optical fiber sensing, microfluidics, and isothermal amplification. A highly RI-sensitive Mach-Zehnder (MZ) interference is formed by splicing a short length of an exposed-core fiber between two lengths of a single-mode fiber while the microfluidic liquid channel on the exposed side of the ECF is filled with target DNA and the amplification solution. Real-time quantitative measurement of the target DNA is then realized by monitoring the change in RI of the solution during the isothermal DNA amplification process. The experimental results show that the platform successfully realizes real-time label-free monitoring of isothermal amplification of 0.16 aM DNA samples. This method is a breakthrough for applications in the fields of DNA detection and quantification where simple operation, rapid detection, portability, small size, high selectivity, and high sensitivity are required.
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Affiliation(s)
- Xuegang Li
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China.
- Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, 066004, China
| | - He Zhang
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China.
| | - Yanan Zhang
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China.
- Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, 066004, China
| | - Yong Zhao
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China.
- Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, 066004, China
| | - Linh Viet Nguyen
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
- Institute for Photonics and Advanced Sensing (IPAS) and School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Xue Zhou
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China.
| | - Stephen C Warren-Smith
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
- Institute for Photonics and Advanced Sensing (IPAS) and School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
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4
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Montserrat Pagès A, Hertog M, Nicolaï B, Spasic D, Lammertyn J. Unraveling the Kinetics of the 10-23 RNA-Cleaving DNAzyme. Int J Mol Sci 2023; 24:13686. [PMID: 37761982 PMCID: PMC10531344 DOI: 10.3390/ijms241813686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
DNA-based enzymes, or DNAzymes, are single-stranded DNA sequences with the ability to catalyze various chemical reactions, including the cleavage of the bond between two RNA nucleotides. Lately, an increasing interest has been observed in these RNA-cleaving DNAzymes in the biosensing and therapeutic fields for signal generation and the modulation of gene expression, respectively. Additionally, multiple efforts have been made to study the effects of the reaction environment and the sequence of the catalytic core on the conversion of the substrate into product. However, most of these studies have only reported alterations of the general reaction course, but only a few have focused on how each individual reaction step is affected. In this work, we present for the first time a mathematical model that describes and predicts the reaction of the 10-23 RNA-cleaving DNAzyme. Furthermore, the model has been employed to study the effect of temperature, magnesium cations and shorter substrate-binding arms of the DNAzyme on the different kinetic rate constants, broadening the range of conditions in which the model can be exploited. In conclusion, this work depicts the prospects of such mathematical models to study and anticipate the course of a reaction given a particular environment.
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Affiliation(s)
- Aida Montserrat Pagès
- Department of Biosystems, Biosensors Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Maarten Hertog
- Department of Biosystems, Postharvest Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Bart Nicolaï
- Department of Biosystems, Postharvest Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
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5
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Dillen A, Scarpellini C, Daenen W, Driesen S, Zijlstra P, Lammertyn J. Integrated Signal Amplification on a Fiber Optic SPR Sensor Using Duplexed Aptamers. ACS Sens 2023; 8:811-821. [PMID: 36734337 DOI: 10.1021/acssensors.2c02388] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Throughout the past decades, fiber optic surface plasmon resonance (FO-SPR)-based biosensors have proven to be powerful tools for both the characterization of biomolecular interactions and target detection. However, as FO-SPR signals are generally related to the mass that binds to the sensor surface, multistep processes and external reagents are often required to obtain significant signals for low molecular weight targets. This increases the time, cost, and complexity of the respective bioassays and hinders continuous measurements. To overcome these requirements, in this work, cis-duplexed aptamers (DAs) were implemented on FO-SPR sensors, which underwent a conformational change upon target binding. This induced a spatial redistribution of gold nanoparticles (AuNPs) upon specific target binding and resulted in an amplified and concentration-dependent signal. Importantly, the AuNPs were covalently conjugated to the sensor, so the principle does not rely on multistep processes or external reagents. To implement this concept, first, the thickness of the gold fiber coating was adapted to match the resonance conditions of the surface plasmons present on the FO-SPR sensors with those on the AuNPs. As a result, the signal obtained due to the spatial redistribution of the AuNPs was amplified by a factor of 3 compared to the most commonly used thickness. Subsequently, the cis-DAs were successfully implemented on the FO-SPR sensors, and it was demonstrated that the DA-based FO-SPR sensors could specifically and quantitatively detect an ssDNA target with a detection limit of 230 nM. Furthermore, the redistribution of the AuNPs was proven to be reversible, which is an important prerequisite for continuous measurements. Altogether, the established DA-based FO-SPR bioassay holds much promise for the detection of low molecular weight targets in the future and opens up possibilities for FO-SPR-based continuous biosensing.
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Affiliation(s)
- Annelies Dillen
- Department of Biosystems─Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001Leuven, Belgium
| | - Claudia Scarpellini
- Department of Biosystems─Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001Leuven, Belgium
| | - Woud Daenen
- Department of Biosystems─Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001Leuven, Belgium
| | - Seppe Driesen
- Department of Biosystems─Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001Leuven, Belgium
| | - Peter Zijlstra
- Department of Applied Physics─Molecular Plasmonics, Eindhoven University of Technology, De Rondom 70, 5612 APEindhoven, The Netherlands
| | - Jeroen Lammertyn
- Department of Biosystems─Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001Leuven, Belgium
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6
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Ghafary Z, Hallaj R, Salimi A, Khosrowbakhsh F. A novel highly sensitive compilation-detachment fluorescence sensing strategy based on RNA-cleavage DNAzyme for MDA-MB-231 breast cancer biomarker determination. J Mater Chem B 2023; 11:1568-1579. [PMID: 36722940 DOI: 10.1039/d2tb02467e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Herein, we designed a novel and highly sensitive fluorescence multicomponent detachable platform for MDA-MB-231 breast cancer cell detection as a model. The RNA cleavage DNAzyme was used as a central operator of the multicomponent probe through which compilation and induced detachment of probe was done. During the compilation step, the dsDNA-Sybr green 1 complexes on gold nanoparticles (GNP@dsDNA@SG1) were assembled. The intercalated Sybr green in the DNA structure has been used as an amplified signal generator on one site of DNAzyme and magnetic nanoparticles (MNP) act as a biological carrier and probe collector on the opposite side. The enzyme activator co-factor (MDA-MB-231 cell cytoplasmic protein) provokes the activation of the catalytic core of enzyme sequence in the DNAzyme molecule, followed by cleavage reaction in the substrate sequence and releasing GNP@ dsDNA@SG1 into the solution. The results indicate that the Sybr green emission fluorescence (520 nm) increases with the increment of MDA-MB-231 protein concentration in the linear dynamic range of 8.10 × 10-2 to 1.95 ng ml-1 (0.77 × 10-3-0.019 cell ml-1) with a detection limit (LOD) of 1/72 × 10-2 pg ml-1 under optimal conditions. The proposed immunosensor has great potential in developing ultrasensitive and rapid diagnostic platforms.
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Affiliation(s)
- Zhaleh Ghafary
- Department of Chemistry, University of Kurdistan, P.O. Box 416, Sanandaj, Iran.
| | - Rahman Hallaj
- Department of Chemistry, University of Kurdistan, P.O. Box 416, Sanandaj, Iran. .,Nanotechnology Research Center, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - Abdollah Salimi
- Department of Chemistry, University of Kurdistan, P.O. Box 416, Sanandaj, Iran. .,Nanotechnology Research Center, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - Farnosh Khosrowbakhsh
- Department of Bioscience & Biotechnology, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
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7
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Zhang X, Xie S, Chen X, Wang L, Li F, Liu S. An allosteric DNA switch-mediated catalytic DNA circuit for ratiometric and sensitive nucleic acid detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 15:124-131. [PMID: 36504112 DOI: 10.1039/d2ay01751b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Herein, a new allosteric DNA switch-mediated catalytic DNA circuit reaction strategy has been proposed for ratiometric and sensitive nucleic acid detection. The sensing system was based on two DNA hybrid probes, each of which was constructed by annealing a reconfigurable DNA hairpin with single-stranded DNA. Upon target recognition by the first DNA hybrid probe, a reconfigurable DNA switch was liberated, triggering a toehold-mediated strand displacement reaction (TSDR) with the second DNA hybrid probe, which was accompanied by the release of another reconfigurable DNA switch. This released allosteric DNA switch could further interact with the first hybrid DNA probe via the TSDR strategy to form a reciprocal strand displacement network between the two DNA hybrid probes. Theoretically, this reciprocal strand displacement reaction would continue till the complete consumption of the reaction substrates. Thus, it provides a new signal amplification method leading toward target recognition. More interestingly, it creates a ratiometric signal response mode for target recognition, which involves the fluorescence increment of one fluorophore (Cy5) and concurrent decrement of another fluorophore (Cy3) accompanied by the target-triggered reciprocal strand displacement reaction. This process could achieve a low detection limit of about 0.1 pM toward the target nucleic acid and selective discrimination toward different mismatched targets. It could also be applied for detection in a serum sample. Thus, the developed catalytic DNA circuit reaction strategy together with ratiometric signal readout provides a new avenue for programmable, reliable and sensitive detection of nucleic acids and might also pave the way for developing more advanced DNA circuits or biosensors.
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Affiliation(s)
- Xiaofan Zhang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China.
| | - Shunjun Xie
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China.
| | - Xue Chen
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China.
| | - Li Wang
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai, 264005, China.
| | - Fang Li
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China.
| | - Shufeng Liu
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai, 264005, China.
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8
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Qu JH, Leirs K, Maes W, Imbrechts M, Callewaert N, Lagrou K, Geukens N, Lammertyn J, Spasic D. Innovative FO-SPR Label-free Strategy for Detecting Anti-RBD Antibodies in COVID-19 Patient Serum and Whole Blood. ACS Sens 2022; 7:477-487. [PMID: 35061357 PMCID: PMC8806028 DOI: 10.1021/acssensors.1c02215] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/12/2022] [Indexed: 12/14/2022]
Abstract
The ongoing COVID-19 pandemic has emphasized the urgent need for rapid, accurate, and large-scale diagnostic tools. Next to this, the significance of serological tests (i.e., detection of SARS-CoV-2 antibodies) also became apparent for studying patients' immune status and past viral infection. In this work, we present a novel approach for not only measuring antibody levels but also profiling of binding kinetics of the complete polyclonal antibody response against the receptor binding domain (RBD) of SARS-CoV-2 spike protein, an aspect not possible to achieve with traditional serological tests. This fiber optic surface plasmon resonance (FO-SPR)-based label-free method was successfully accomplished in COVID-19 patient serum and, for the first time, directly in undiluted whole blood, omitting the need for any sample preparation. Notably, this bioassay (1) was on par with FO-SPR sandwich bioassays (traditionally regarded as more sensitive) in distinguishing COVID-19 from control samples, irrespective of the type of sample matrix, and (2) had a significantly shorter time-to-result of only 30 min compared to >1 or 4 h for the FO-SPR sandwich bioassay and the conventional ELISA, respectively. Finally, the label-free approach revealed that no direct correlation was present between antibody levels and their kinetic profiling in different COVID-19 patients, as another evidence to support previous hypothesis that antibody-binding kinetics against the antigen in patient blood might play a role in the COVID-19 severity. Taking all this into account, the presented work positions the FO-SPR technology at the forefront of other COVID-19 serological tests, with a huge potential toward other applications in need for quantification and kinetic profiling of antibodies.
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Affiliation(s)
- Jia-Huan Qu
- Department of Biosystems, Biosensors Group,
KU Leuven, Willem de Croylaan 42, 3001 Leuven,
Belgium
| | - Karen Leirs
- Department of Biosystems, Biosensors Group,
KU Leuven, Willem de Croylaan 42, 3001 Leuven,
Belgium
| | - Wim Maes
- PharmAbs, KU Leuven,
Herestraat 49, Box 820, 3000 Leuven, Belgium
| | - Maya Imbrechts
- PharmAbs, KU Leuven,
Herestraat 49, Box 820, 3000 Leuven, Belgium
| | | | - Katrien Lagrou
- Department of Microbiology, Immunology and
Transplantation, Laboratory of Clinical Bacteriology and Mycology, KU
Leuven, 3000 Leuven, Belgium
- Department of Laboratory Medicine and National
Reference Centre for Respiratory Pathogens, University Hospitals
Leuven, 3000 Leuven, Belgium
| | - Nick Geukens
- PharmAbs, KU Leuven,
Herestraat 49, Box 820, 3000 Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group,
KU Leuven, Willem de Croylaan 42, 3001 Leuven,
Belgium
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group,
KU Leuven, Willem de Croylaan 42, 3001 Leuven,
Belgium
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9
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Huang Z, Wang X, Wu Z, Jiang JH. Recent Advances on DNAzyme-Based Sensing. Chem Asian J 2022; 17:e202101414. [PMID: 35156764 DOI: 10.1002/asia.202101414] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/09/2022] [Indexed: 11/08/2022]
Abstract
DNAzymes are functional nucleic acid with catalytic activity. Owing to the high sensitivity, excellent programmability, and flexible obtainment through in vitro selection, RNA-cleaving DNAzymes have attracted increasing interest in developing DNAzyme-based sensors. In this review, we summarize the recent advances on DNAzyme-based sensing applications. We initially conclude two general strategies to expand the library of DNAzymes, in vitro selection to discover new DNAzymes towards different targets of interest and chemical modifications to endue the existing DNAzymes with new function or properties. We then discuss the recent applications of DNAzyme-based sensors for the detection of a variety of important biomolecules both in vitro and in vivo . Finally, perspectives on the challenges and future directions in the development of DNAzyme-based sensors are provided.
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Affiliation(s)
- Zhimei Huang
- Hunan University, College of Chemistry and Chemical Engineering, CHINA
| | - Xiangnan Wang
- Hunan University of Technology and Business, College of Science, CHINA
| | - Zhenkun Wu
- Hunan University, State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics and College of Chemistry and Chemical Engineering, South of Lushan Road, 410082, Changsha, CHINA
| | - Jian-Hui Jiang
- Hunan University, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Chemistry and Chemical Engineering, CHINA
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10
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Ni H, Zhang L, Ping A, Krasavin AV, Ali H, Ni B, Chang J. Dual-mode independent detection of pressure and refractive index by miniature grating-coupled surface plasmon sensor. OPTICS EXPRESS 2022; 30:5758-5768. [PMID: 35209531 DOI: 10.1364/oe.446766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Multiple parameters need to be monitored to analyze the kinetics of biological progresses. Surface plasmon polariton resonance sensors offer a non-invasive approach to continuously detect the local change of refractive index of molecules with high sensitivity. However, the fabrication of miniaturized, compact, and low-cost sensors is still challenging. In this paper, we propose and demonstrate a grating-coupled SPR sensor platform featuring dual mode operation for simultaneous sensing of pressure and refractive index, which can be fabricated using a highly-efficient low-cost method, allowing large-scale production. Both sensing functionalities are realized by optical means via monitoring the spectral positions of a surface plasmon polariton mode (for refractive index sensing) and Fabry-Perot or metal-insulator-metal modes (for pressure sensing), which are supported by the structure. Simultaneous measurement of refractive index with the sensitivity of 494 nm/RIU and pressure was demonstrated experimentally. The proposed platform is promising for biomonitoring that requires both high refractive index sensitivity and local pressure detection.
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11
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Dillen A, Mohrbacher A, Lammertyn J. A Versatile One-Step Competitive Fiber Optic Surface Plasmon Resonance Bioassay Enabled by DNA Nanotechnology. ACS Sens 2021; 6:3677-3684. [PMID: 34633181 DOI: 10.1021/acssensors.1c01447] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fiber optic surface plasmon resonance (FO-SPR)-based biosensors have emerged as powerful tools for biomarker detection due to their ability for real-time analysis of biomolecular interactions, cost-effectiveness, and user-friendliness. However, as (FO-)SPR signals are determined by the mass of the target molecules, the detection of low-molecular-weight targets remains challenging and currently requires tedious labeling and preparation steps. Therefore, in this work, we established a new concept for low-molecular-weight target detection by implementing duplexed aptamers on an FO-SPR sensor. In this manner, we enabled one-step competitive detection and could achieve significant signals, independent of the weight of the target molecules, without requiring labeling or preprocessing steps. This was demonstrated for the detection of a small molecule (ATP), protein (thrombin), and ssDNA target, thereby reaching detection limits of 72 μM, 36 nM, and 30 nM respectively and proving the generalizability of the proposed bioassay. Furthermore, target detection was successfully achieved in 10-fold diluted plasma, which demonstrated the applicability of the assay in biologically relevant matrices. Altogether, the developed one-step competitive FO-SPR bioassay opens up possibilities for the detection of low-molecular-weight targets in a fast and straightforward manner.
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Affiliation(s)
- Annelies Dillen
- KU Leuven, Department of Biosystems − Biosensors Group, Willem de Croylaan 42, Box 2428, Leuven 3001, Belgium
| | - Aurélie Mohrbacher
- KU Leuven, Department of Biosystems − Biosensors Group, Willem de Croylaan 42, Box 2428, Leuven 3001, Belgium
| | - Jeroen Lammertyn
- KU Leuven, Department of Biosystems − Biosensors Group, Willem de Croylaan 42, Box 2428, Leuven 3001, Belgium
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RNA-cleaving DNAzymes as a diagnostic and therapeutic agent against antimicrobial resistant bacteria. Curr Genet 2021; 68:27-38. [PMID: 34505182 DOI: 10.1007/s00294-021-01212-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/12/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
The development of nucleic-acid-based antimicrobials such as RNA-cleaving DNAzyme (RCD), a short catalytically active nucleic acid, is a promising alternative to the current antibiotics. The current rapid spread of antimicrobial resistance (AMR) in bacteria renders some antibiotics useless against bacterial infection, thus creating the need for alternative antimicrobials such as DNAzymes. This review summarizes recent advances in the use of RCD as a diagnostic and therapeutic agent against AMR. Firstly, the recent diagnostic application of RCD for the detection of bacterial cells and the associated resistant gene(s) is discussed. The next section summarises the therapeutic application of RCD in AMR bacterial infections which includes direct targeting of the resistant genes and indirect targeting of AMR-associated genes. Finally, this review extends the discussion to challenges of utilizing RCD in real-life applications, and the potential of combining both diagnostic and therapeutic applications of RCD into a single agent as a theranostic agent.
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Loyez M, Wells M, Hambÿe S, Hubinon F, Blankert B, Wattiez R, Caucheteur C. PfHRP2 detection using plasmonic optrodes: performance analysis. Malar J 2021; 20:332. [PMID: 34320995 PMCID: PMC8320217 DOI: 10.1186/s12936-021-03863-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/23/2021] [Indexed: 12/11/2022] Open
Abstract
Background Early malaria diagnosis and its profiling require the development of new sensing platforms enabling rapid and early analysis of parasites in blood or saliva, aside the widespread rapid diagnostic tests (RDTs). Methods This study shows the performance of a cost-effective optical fiber-based solution to target the presence of Plasmodium falciparum histidine-rich protein 2 (PfHRP2). Unclad multimode optical fiber probes are coated with a thin gold film to excite Surface Plasmon Resonance (SPR) yielding high sensitivity to bio-interactions between targets and bioreceptors grafted on the metal surface. Results Their performances are presented in laboratory conditions using PBS spiked with growing concentrations of purified target proteins and within in vitro cultures. Two probe configurations are studied through label-free detection and amplification using secondary antibodies to show the possibility to lower the intrisic limit of detection. Conclusions As malaria hits millions of people worldwide, the improvement and multiplexing of this optical fiber technique can be of great interest, especially for a future purpose of using multiple receptors on the fiber surface or several coated-nanoparticles as amplifiers. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-03863-3.
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Affiliation(s)
- Médéric Loyez
- Proteomics and Microbiology Department, University of Mons, Champ de Mars 6, 7000, Mons, Belgium. .,Electromagnetism and Telecommunications Department, University of Mons, Bld. Dolez 31, 7000, Mons, Belgium.
| | - Mathilde Wells
- Laboratory of Pharmaceutical Analysis, University of Mons, Avenue Maistriau 15, 7000, Mons, Belgium
| | - Stéphanie Hambÿe
- Laboratory of Pharmaceutical Analysis, University of Mons, Avenue Maistriau 15, 7000, Mons, Belgium
| | - François Hubinon
- Electromagnetism and Telecommunications Department, University of Mons, Bld. Dolez 31, 7000, Mons, Belgium
| | - Bertrand Blankert
- Laboratory of Pharmaceutical Analysis, University of Mons, Avenue Maistriau 15, 7000, Mons, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, Champ de Mars 6, 7000, Mons, Belgium
| | - Christophe Caucheteur
- Electromagnetism and Telecommunications Department, University of Mons, Bld. Dolez 31, 7000, Mons, Belgium
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Gong P, Wang Y, Zhou X, Wang S, Zhang Y, Zhao Y, Nguyen LV, Ebendorff-Heidepriem H, Peng L, Warren-Smith SC, Li X. In Situ Temperature-Compensated DNA Hybridization Detection Using a Dual-Channel Optical Fiber Sensor. Anal Chem 2021; 93:10561-10567. [PMID: 34291916 DOI: 10.1021/acs.analchem.1c01660] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A multifunction, high-sensitivity, and temperature-compensated optical fiber DNA hybridization sensor combining surface plasmon resonance (SPR) and Mach-Zehnder interference (MZI) has been designed and implemented. We demonstrate, for the first time to our knowledge, the dual-parameter measurement of temperature and refractive index (RI) by simultaneously using SPR and MZI in a simple single-mode fiber (SMF)-no-core fiber (NCF)-SMF structure. The experimental results show RI sensitivities of 930 and 1899 nm/RIU and temperature sensitivities of 0.4 and -1.4 nm/°C for the MZI and SPR, respectively. We demonstrate a sensitivity matrix used to simultaneously detect both parameters, solving the problem of temperature interference of RI variation-based biosensors. In addition, the sensor can also distinguish biological binding events by detecting the localized RI changes at the fiber's surface. We realize label-free sensing of DNA hybridization detection by immobilizing probe DNA (pDNA) onto the fiber as the probe to capture complementary DNA (cDNA). The experimental results show that the sensor can qualitatively detect cDNA after temperature compensation, and the limit of detection (LOD) of the sensor reaches 80 nM. The proposed sensor has advantages of high sensitivity, real time, low cost, temperature compensation, and low detection limit and is suitable for in situ monitoring, high-precision sensing of DNA molecules, and other related fields, such as gene diagnosis, kinship judgment, environmental monitoring, and so on.
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Affiliation(s)
- Pengqi Gong
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China
| | - Yiming Wang
- No. 120 High School of Shenyang, Shenyang, Liaoning 110031, China
| | - Xue Zhou
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China
| | - Shankun Wang
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China
| | - Yanan Zhang
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China
| | - Yong Zhao
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China.,Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, Hebei 066004, China
| | - Linh Viet Nguyen
- Institute for Photonics and Advanced Sensing and School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Heike Ebendorff-Heidepriem
- Institute for Photonics and Advanced Sensing and School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Lu Peng
- Institute for Photonics and Advanced Sensing and School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephen C Warren-Smith
- Institute for Photonics and Advanced Sensing and School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia.,Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Xuegang Li
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China
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Dillen A, Vandezande W, Daems D, Lammertyn J. Unraveling the effect of the aptamer complementary element on the performance of duplexed aptamers: a thermodynamic study. Anal Bioanal Chem 2021; 413:4739-4750. [PMID: 34109445 DOI: 10.1007/s00216-021-03444-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022]
Abstract
Duplexed aptamers (DAs) are widespread aptasensor formats that simultaneously recognize and signal the concentration of target molecules. They are composed of an aptamer and aptamer complementary element (ACE) which consists of a short oligonucleotide that partially inhibits the aptamer sequence. Although the design principles to engineer DAs are straightforward, the tailored development of DAs for a particular target is currently based on trial and error due to limited knowledge of how the ACE sequence affects the final performance of DA biosensors. Therefore, we have established a thermodynamic model describing the influence of the ACE on the performance of DAs applied in equilibrium assays and demonstrated that this relationship can be described by the binding strength between the aptamer and ACE. To validate our theoretical findings, the model was applied to the 29-mer anti-thrombin aptamer as a case study, and an experimental relation between the aptamer-ACE binding strength and performance of DAs was established. The obtained results indicated that our proposed model could accurately describe the effect of the ACE sequence on the performance of the established DAs for thrombin detection, applied for equilibrium assays. Furthermore, to characterize the binding strength between the aptamer and ACEs evaluated in this work, a set of fitting equations was derived which enables thermodynamic characterization of DNA-based interactions through thermal denaturation experiments, thereby overcoming the limitations of current predictive software and chemical denaturation experiments. Altogether, this work encourages the development, characterization, and use of DAs in the field of biosensing.
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Affiliation(s)
- Annelies Dillen
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
| | - Wouter Vandezande
- Department of Microbial and Molecular Systems - Centre for Membrane Separations, Adsorption, Catalysis and Spectroscopy for Sustainable Solutions, KU Leuven, Celestijnenlaan 200F, Box 2454, 3001, Leuven, Belgium
| | - Devin Daems
- Department of Chemistry - AXES research group, University of Antwerp, Groenenborgerlaan 171, 2010, Antwerpen, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium.
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