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Abdelrazig AO, Rijiravanich P, Suwannarat S, Surareungchai W, Somasundrum M. Detection of DNA using gold nanoparticle-coated silica nanoparticles. Anal Biochem 2024; 686:115411. [PMID: 38070665 DOI: 10.1016/j.ab.2023.115411] [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: 09/22/2023] [Revised: 11/13/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023]
Abstract
We report a sensitive lateral flow assay (LFA) in which the assay colour change originated from reporter labels constructed from silica spheres (radius = 450 nm) coated with approximately 3.9 × 103 gold nanoparticles (radius = 8.5 nm). These reporter labels were modified with DNA and deposited in the conjugation area of an LFA device assembled on wax-patterned Fusion 5 paper. Test and control zones of the device were pre-loaded with capture probe formed by avidin-coated mesoporous silica nanoparticles attached with biotin-tagged DNA sequences. Proof-of-concept was demonstrated by the detection of a partial sequence of the actin gene of Colletotrichum truncatum. The DNA target could be detected with an LOD of 46 pM, which was 5 times lower than a comparative assay using gold nanoparticles alone. The assay showed good selectivity against the Colletotrichum species C. scovillei and C. gloeosporioides, as well as against DNA from the fungal genera Aspergillus niger and Alternaria alternata. There was negligible change in sensor response over storage for one month at room temperature. The LFA was used to detect PCR products following extraction from mycelium.
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Affiliation(s)
- Amir Osman Abdelrazig
- Sensor Technology Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (KMUTT), Bang Khun Thian, Bangkok, 10150, Thailand
| | - Patsamon Rijiravanich
- BioSciences and Systems Biology Research Team, National Center for Genetic Engineering and Biotechnology, National Sciences and Technology Development Agency at KMUTT, Bang Khun Thian, Bangkok, 10150, Thailand.
| | - Sawita Suwannarat
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Werasak Surareungchai
- Analytical Sciences and National Doping Test Institute, Mahidol University, Bangkok, 10400, Thailand; School of Bioresources and Technology, KMUTT, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Mithran Somasundrum
- BioSciences and Systems Biology Research Team, National Center for Genetic Engineering and Biotechnology, National Sciences and Technology Development Agency at KMUTT, Bang Khun Thian, Bangkok, 10150, Thailand.
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Bajaj A, Abutoama M, Isaacs S, Abuleil MJ, Yaniv K, Kushmaro A, Modic M, Cvelbar U, Abdulhalim I. Biofilm growth monitoring using guided wave ultralong-range Surface Plasmon Resonance: A proof of concept. Biosens Bioelectron 2023; 228:115204. [PMID: 36913883 DOI: 10.1016/j.bios.2023.115204] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 03/01/2023] [Accepted: 03/05/2023] [Indexed: 03/15/2023]
Abstract
Unwelcomed biofilms are problematic in food industries, surgical devices, marine applications, and wastewater treatment plants, essentially everywhere where there is moisture. Very recently, label-free advanced sensors such as localized and extended surface plasmon resonance (SPR) have been explored as tools for monitoring biofilm formation. However, conventional noble metal SPR substrates suffer from low penetration depth (100-300 nm) into the dielectric medium above the surface, preventing the reliable detection of large entities of single or multi-layered cell assemblies like biofilms which can grow up to a few micrometers or more. In this study, we propose using a plasmonic insulator-metal-insulator (IMI) structure (SiO2-Ag-SiO2) with a higher penetration depth based on a diverging beam single wavelength format of Kretschmann configuration in a portable SPR device. An SPR line detection algorithm for locating the reflectance minimum of the device helps to view changes in refractive index and accumulation of the biofilm in real-time down to 10-7 RIU precision. The optimized IMI structure exhibits strong penetration dependence on wavelength and incidence angle. Within the plasmonic resonance, different angles penetrate different depths, showing a maximum near the critical angle. At the wavelength of 635 nm, a high penetration depth of more than 4 μm was obtained. Compared to a thin gold film substrate, for which the penetration depth is only ∼200 nm, the IMI substrate provides more reliable results. The average thickness of the biofilm after 24 h of growth was found to be between 6 and 7 μm with ∼63% live cell volume, as estimated from confocal microscopic images using an image processing tool. To explain this saturation thickness, a graded index biofilm structure is proposed in which the refractive index decreases with the distance from the interface. Furthermore, when plasma-assisted degeneration of biofilms was studied in a semi-real-time format, there was almost no effect on the IMI substrate compared to the gold substrate. The growth rate over the SiO2 surface was higher than on gold, possibly due to differences between surface charge effects. On the gold, the excited plasmon generates an oscillating cloud of electrons, while for the SiO2 case, this does not happen. This methodology can be utilized to detect and characterize biofilms with better signal reliability with respect to concentration and size dependence.
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Affiliation(s)
- Aabha Bajaj
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Mohammad Abutoama
- Department of Electro-optics and Photonics Engineering, ECE School, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Sivan Isaacs
- Department of Electro-optics and Photonics Engineering, ECE School, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Marwan J Abuleil
- Department of Electro-optics and Photonics Engineering, ECE School, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Karin Yaniv
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Faculty of Engineering Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Ariel Kushmaro
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel; Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Faculty of Engineering Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel; School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Martina Modic
- Department of Gaseous Electronics (F6), Jožef Stefan Institute, Jamova cesta 39, SI-1000, Ljubljana, Slovenia
| | - Uroš Cvelbar
- Department of Gaseous Electronics (F6), Jožef Stefan Institute, Jamova cesta 39, SI-1000, Ljubljana, Slovenia
| | - Ibrahim Abdulhalim
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel; Department of Electro-optics and Photonics Engineering, ECE School, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel.
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Jaric S, Bajaj A, Vukic V, Gadjanski I, Abdulhalim I, Bobrinetskiy I. Label-Free Direct Detection of Cylindrospermopsin via Graphene-Enhanced Surface Plasmon Resonance Aptasensor. Toxins (Basel) 2023; 15:toxins15050326. [PMID: 37235360 DOI: 10.3390/toxins15050326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
In this work, we report a novel method for the label-free detection of cyanotoxin molecules based on a direct assay utilizing a graphene-modified surface plasmon resonance (SPR) aptasensor. Molecular dynamic simulation of the aptamer's interaction with cylindrospermopsin (CYN) reveals the strongest binding sites between C18-C26 pairs. To modify the SPR sensor, the wet transfer method of CVD monolayer graphene was used. For the first time, we report the use of graphene functionalized by an aptamer as a bioreceptor in conjunction with SPR for the detection of CYN. In a direct assay with an anti-CYN aptamer, we demonstrated a noticeable change in the optical signal in response to the concentrations far below the maximum tolerable level of 1 µg/L and high specificity.
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Affiliation(s)
- Stefan Jaric
- BioSense Institute-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Aabha Bajaj
- Department of Electro-Optics and Photonics Engineering, School of Electrical and Computer Engineering, Ilse-Katz Institute for Nano-Scale Science and Technology, Ben Gurion University, Beer Sheva 84105, Israel
| | - Vladimir Vukic
- Faculty of Technology Novi Sad, University of Novi Sad, Bulevar Cara Lazara 1, 21000 Novi Sad, Serbia
| | - Ivana Gadjanski
- BioSense Institute-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Ibrahim Abdulhalim
- Department of Electro-Optics and Photonics Engineering, School of Electrical and Computer Engineering, Ilse-Katz Institute for Nano-Scale Science and Technology, Ben Gurion University, Beer Sheva 84105, Israel
- Photonicsys Ltd., 54 Wahat Alsalam-Neveh Shalom, Ibrahim 9976100, Israel
| | - Ivan Bobrinetskiy
- BioSense Institute-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia
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Xu Z, Jiang X, Li Y, Ma X, Tang Y, Li H, Yi K, Li J, Liu Z. Antifungal activity of montmorillonite/peptide aptamer nanocomposite against Colletotrichum gloeosporioides on Stylosanthes. Int J Biol Macromol 2022; 217:282-290. [PMID: 35835303 DOI: 10.1016/j.ijbiomac.2022.07.034] [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: 04/01/2022] [Revised: 06/20/2022] [Accepted: 07/05/2022] [Indexed: 11/30/2022]
Abstract
Chemical agents are effective treatment methods for anthracnose induced by pathogenic Colletotrichum gloeosporioides on Stylosanthes. However, excess consumption of chemical agents destroys the environment, synthetic biology was capable of conquering the issue. The antifungal agent is developed by enclosing a bio-synthesized peptide aptamer with layered montmorillonite via electrostatic interaction. Compared with free peptide aptamer, the nanocomposite exhibits higher antifungal activity against Colletotrichum gloeosporioides, further improving the utilization of peptide aptamer. The nanocomposite killed Colletotrichum gloeosporioides by releasing peptide aptamer after they entered the spore. Moreover, montmorillonite enhances the adhesion ability of peptide aptamer via hydrophobic interactions between nanomaterials and leaves, prolonging the extension time of nanocomposite on leaves. Consequently, 0.1 mg of nanocomposite demonstrates a comparable effect to commercial carbendazim (1 %) to prevent anthracnose on leaves of Stylosanthes induced by HK-04 at room temperature. This work demonstrates an alternative to commercial antifungal agents and proposes a versatile approach to preparing environmental-friendly antifungal agents to inhibit fungal infections on crops.
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Affiliation(s)
- Zhenfei Xu
- School of Life Sciences, Hainan University, Haikou 570228, China; One Health Insititute, Hainan University, Haikou 570228, China
| | - Xiaoli Jiang
- School of Life Sciences, Hainan University, Haikou 570228, China; One Health Insititute, Hainan University, Haikou 570228, China
| | - Ye Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiang Ma
- School of Life Sciences, Hainan University, Haikou 570228, China; One Health Insititute, Hainan University, Haikou 570228, China
| | - Yanqiong Tang
- School of Life Sciences, Hainan University, Haikou 570228, China; One Health Insititute, Hainan University, Haikou 570228, China
| | - Hong Li
- School of Life Sciences, Hainan University, Haikou 570228, China; One Health Insititute, Hainan University, Haikou 570228, China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Juanjuan Li
- School of Life Sciences, Hainan University, Haikou 570228, China; One Health Insititute, Hainan University, Haikou 570228, China.
| | - Zhu Liu
- School of Life Sciences, Hainan University, Haikou 570228, China; One Health Insititute, Hainan University, Haikou 570228, China.
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Integration of a multichannel surface plasmon resonance sensor chip and refractive index matching film array for protein detection in human urine. Talanta 2022; 246:123533. [DOI: 10.1016/j.talanta.2022.123533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/30/2022] [Accepted: 05/05/2022] [Indexed: 11/22/2022]
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