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El Aamri M, Baachaoui S, Mohammadi H, Raouafi N, Amine A. Smartphone-based device for rapid and single-step detection of piRNA-651 using anti-DNA:RNA hybrid antibody and enzymatic signal amplification. Anal Chim Acta 2024; 1305:342583. [PMID: 38677845 DOI: 10.1016/j.aca.2024.342583] [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: 05/17/2023] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024]
Abstract
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs/piRs) are a class of small noncoding RNAs that play a crucial role in regulating various biological processes, including carcinogenesis. One specific piRNA, piR-651, has been reported to be overexpressed in both human blood serum and solid cancer tissues, that can be used a viable biomarker in cancer diagnosis. Early diagnosis of cancer can help reduce the burden of the disease and improve survival rates. In the present work, we report for the first time a smartphone-based colorimetric biosensor for highly sensitive and specific detection of piR-651 thanks to an enzymatic signal amplification, which yielded high colorimetric intensities. Indeed, a heteroduplex DNA:RNA was formed in the presence of piR-651 with the capture DNA probe immobilized on the magnetic beads for easy magnetic separation. Then, a HRP tethered to anti-DNA:RNA (S9.6) was used to reveal the DNA-RNA heteroduplex formed by catalyzing the oxidation of TMB substrate into colorimetric TMBox, which absorbs at 630 nm. The absorbance is positively proportional to the piR-651 concentrations. On the other hand, the colorimetric product of the assay can be photographed with a smartphone camera and analyzed using ImageJ software. Using a smartphone and under optimal conditions, the biosensor responded linearly to the logarithm of piRNA-651 from 8 fM to 100 pM with a detection limit of 2.3 fM and discriminates against other piRNAs. It was also successfully applied to the determination of piRNA-651 levels in spiked human serum.
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Affiliation(s)
- Maliana El Aamri
- Hassan II University of Casablanca, Faculty of Sciences and Techniques, Laboratory of Process Engineering and Environment, Chemical Analysis and Biosensors Group, P.A 146, Mohammedia, Morocco
| | - Sabrine Baachaoui
- University of Tunis El Manar, Faculty of Science, Chemistry Department, Analytical Chemistry and Electrochemistry Lab (LR99ES15), Sensors and Biosensors Group, Tunis El Manar, 2092, Tunisia
| | - Hasna Mohammadi
- Hassan II University of Casablanca, Faculty of Sciences and Techniques, Laboratory of Process Engineering and Environment, Chemical Analysis and Biosensors Group, P.A 146, Mohammedia, Morocco
| | - Noureddine Raouafi
- University of Tunis El Manar, Faculty of Science, Chemistry Department, Analytical Chemistry and Electrochemistry Lab (LR99ES15), Sensors and Biosensors Group, Tunis El Manar, 2092, Tunisia.
| | - Aziz Amine
- Hassan II University of Casablanca, Faculty of Sciences and Techniques, Laboratory of Process Engineering and Environment, Chemical Analysis and Biosensors Group, P.A 146, Mohammedia, Morocco.
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Kouz S, Raouafi A, Ouhibi A, Lorrain N, Essafi M, Mejri M, Raouafi N, Moadhen A, Guendouz M. Detection of SARS-CoV-2 N protein using AgNPs-modified aligned silicon nanowires BioSERS chip. RSC Adv 2024; 14:12071-12080. [PMID: 38628480 PMCID: PMC11019291 DOI: 10.1039/d4ra00267a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
The SARS-CoV-2 (COVID-19) pandemic had a strong impact on societies and economies worldwide and tests for high-performance detection of SARS-CoV-2 biomarkers are still needed for potential future outbreaks of the disease. In this paper, we present the different steps for the design of an aptamer-based surface-enhanced Raman scattering (BioSERS) sensing chip capable of detecting the coronavirus nucleocapsid protein (N protein) in spiked phosphate-buffered solutions and real samples of human blood serum. Optimization of the preparation steps in terms of the aptamer concentration used for the functionalization of the silver nanoparticles, time for affixing the aptamer, incubation time with target protein, and insulation of the silver active surface with cysteamine, led to a sensitive BioSERS chip, which was able to detect the N protein in the range from 1 to 75 ng mL-1 in spiked phosphate-buffered solutions with a detection limit of 1 ng mL-1 within 30 min. Furthermore, the BioSERS chip was used to detect the target protein in scarcely spiked human serum. This study demonstrates the possibility of a clinical application that can improve the detection limit and accuracy of the currently commercialized SARS-CoV-2 immunodiagnostic kit. Additionally, the system is modular and can be applied to detect other proteins by only changing the aptamer.
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Affiliation(s)
- Sadok Kouz
- Faculty of Sciences of Tunis, Laboratory of Nanomaterials Nanotechnology and Energy (L2NE), University of Tunis El Manar 2092 Tunis El Manar Tunisia
- UMR FOTON, CNRS, University of Rennes Enssat, BP 80518, 6 rue Kerampont F22305 Lannion France
| | - Amal Raouafi
- Faculty of Sciences of Tunis, Laboratory of Analytical Chemistry and Electrochemistry (LR99ES15), Sensor and Biosensors Group, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Awatef Ouhibi
- Faculty of Sciences of Tunis, Laboratory of Nanomaterials Nanotechnology and Energy (L2NE), University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Nathalie Lorrain
- UMR FOTON, CNRS, University of Rennes Enssat, BP 80518, 6 rue Kerampont F22305 Lannion France
| | - Makram Essafi
- Pasteur Institute of Tunis, University of Tunis El Manar LTCII LR11 IPT02 Tunis Tunisia
| | - Manel Mejri
- Pasteur Institute of Tunis, University of Tunis El Manar LTCII LR11 IPT02 Tunis Tunisia
| | - Noureddine Raouafi
- Faculty of Sciences of Tunis, Laboratory of Analytical Chemistry and Electrochemistry (LR99ES15), Sensor and Biosensors Group, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Adel Moadhen
- Faculty of Sciences of Tunis, Laboratory of Nanomaterials Nanotechnology and Energy (L2NE), University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Mohammed Guendouz
- UMR FOTON, CNRS, University of Rennes Enssat, BP 80518, 6 rue Kerampont F22305 Lannion France
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Argoubi W, Algethami FK, Raouafi N. Enhanced sensitivity in electrochemical detection of ochratoxin A within food samples using ferrocene- and aptamer-tethered gold nanoparticles on disposable electrodes. RSC Adv 2024; 14:8007-8015. [PMID: 38454949 PMCID: PMC10918640 DOI: 10.1039/d3ra08567h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/01/2024] [Indexed: 03/09/2024] Open
Abstract
Ensuring food security is crucial for public health, and the presence of mycotoxins, produced by fungi in improperly stored processed or unprocessed food, poses a significant threat. This research introduces a novel approach - a disposable aptasensing platform designed for the detection of ochratoxin A (OTA). The platform employs gold-nanostructured screen-printed carbon electrodes functionalized with a ferrocene derivative, serving as an integrated faradaic transducing system, and an anti-OTA aptamer as a bioreceptor site. Detection relies on the ferrocene electrochemical signal changes induced by the aptamer folding in the presence of the target molecule. Remarkably sensitive, the platform detects OTA within the range of 0.5 to 70 ng mL-1 and a detection limit of 11 pg mL-1. This limit is approximately 200 times below the levels stipulated by the European Commission for agricultural commodities. Notably, the sensing device exhibits efficacy in detecting OTA in complex media, such as roasted coffee beans and wine, without the need for sample pretreatment, yielding accurate recoveries. Furthermore, while label-free electrochemical aptasensors have proliferated, this study addresses a gap in understanding the binding mechanisms of some aptasensors. To enhance the experimental findings, a theoretical study was conducted to underscore the specificity of the anti-OTA aptamer as a donor for OTA detection. The molecular docking technique was employed to unveil the key binding region of the aptamer, providing valuable insights into the aptasensor specificity.
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Affiliation(s)
- Wicem Argoubi
- Sensors and Biosensors Group, ACE-Lab (LR99ES15), Faculty of Science, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Faisal K Algethami
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU) P.O. Box 90950 Riyadh 11623 Saudi Arabia
| | - Noureddine Raouafi
- Sensors and Biosensors Group, ACE-Lab (LR99ES15), Faculty of Science, University of Tunis El Manar 2092 Tunis El Manar Tunisia
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El Aamri M, Mohammadi H, Amine A. A highly sensitive colorimetric DNA sensor for MicroRNA-155 detection: leveraging the peroxidase-like activity of copper nanoparticles in a double amplification strategy. Mikrochim Acta 2023; 191:32. [PMID: 38102528 DOI: 10.1007/s00604-023-06087-1] [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] [Accepted: 11/06/2023] [Indexed: 12/17/2023]
Abstract
A novel and highly sensitive colorimetric DNA sensor for determination of miRNA-155 at attomolar levelsis presented that combines the peroxidase-like activity of copper nanoparticles (CuNPs) with the hybridization chain reaction (HCR) . The utilization of CuNPs offers advantages such as strong interaction with double-stranded DNA, excellent molecular recognition, and mimic catalytic activity. Herein, a capture probe DNA (P1) was immobilized on carboxylated magnetic beads (MBs), allowing for amplified immobilization due to the 3D surface. Subsequently, the presence of the target microRNA-155 led to the formation of a sandwich structure (P2/microRNA-155/P1/MBs) when P2 was introduced to the modified P1/MBs. The HCR reaction was then triggered by adding H1 and H2 to create a super sandwich (H1/H2)n. Following this, Cu2+ ions were attracted to the negatively charged phosphate groups of the (H1/H2)n and reduced by ascorbic acid, resulting in the formation of CuNPs, which were embedded into the grooves of the (H1/H2)n. The peroxidase-like activity of CuNPs catalyzed the oxidation reaction of 3,3',5,5'-Tetramethylbenzidine (TMB), resulting in a distinct blue color measured at 630 nm. Under optimal conditions, the colorimetric biosensor exhibited a linear response to microRNA-155 concentrations ranging from 80 to 500 aM, with a detection limit of 22 aM, and discriminate against other microRNAs. It was also successfully applied to the determination of microRNA-155 levels in spiked human serum.
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Affiliation(s)
- Maliana El Aamri
- Faculty of Sciences and Techniques, Laboratory of Process Engineering and Environment, Chemical Analysis and Biosensors Group, Hassan II University of Casablanca, P.A 146, Mohammedia, Morocco
| | - Hasna Mohammadi
- Faculty of Sciences and Techniques, Laboratory of Process Engineering and Environment, Chemical Analysis and Biosensors Group, Hassan II University of Casablanca, P.A 146, Mohammedia, Morocco
| | - Aziz Amine
- Faculty of Sciences and Techniques, Laboratory of Process Engineering and Environment, Chemical Analysis and Biosensors Group, Hassan II University of Casablanca, P.A 146, Mohammedia, Morocco.
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Aldulaijan S. In-silico selection of peptides for the recognition of imidacloprid. PLoS One 2023; 18:e0295619. [PMID: 38085733 PMCID: PMC10715655 DOI: 10.1371/journal.pone.0295619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
The sensitive detection of pesticides using low-cost receptors designed from peptides can widen their uses in the environmental surveillance for emerging pollutants. In-silico selection of peptides can help accelerate the design of receptor sequence banks for a given target of interest. In this work, we started from Lymnaea stagnalis acetylcholine-binding protein Q55R mutant receptor-imidacloprid complex, available in the PDB databank, to select three primary short peptides (YSP09, DMR12, WQW13 respectively having 9, 12 and 13 amino acids (AA) in length) from the pesticide interacting zones with the A, B and C chains of the nicotinic receptor. Using molecular docking and molecular dynamics (MD) simulations, we showed that the three peptides can form complexes with the target imidacloprid, having energies close to that obtained from a reference RNR12 peptide. Combination of these peptides allowed preparing a new set of longer peptides (YSM21, PSM22, PSW31 and WQA34) that have higher stability and affinity as shown by the MM-PBSA calculations. In particular, the WQA34 peptide displayed an average binding free energy of -6.44±0.27 kcal/mol, which is three times higher than that of the reference RNR12 peptide (-2.29±0.25 kcal/mol) and formed a stable complex with imidacloprid. Furthermore, the dissociation constants (Kd), calculated from the binding free energy, showed that WQA32 (40 μM) has three orders of magnitude lower Kd than the reference RNR12 peptide (3.4 × 104 μM). Docking and RMSD scores showed that the WQA34 peptide is potentially selective to the target imidacloprid with respect to acetamiprid and clothianidin. Therefore, this peptide can be used in wet-lab experiments to prepare a biosensor to selectively detect imidacloprid.
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Affiliation(s)
- Sarah Aldulaijan
- Chemistry Department, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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Algethami FK, Rabti A, Mastouri M, Ben Aoun S, Alqarni LS, Elamin MR, Raouafi N. Sub-femtomolar capacitance-based biosensing of kanamycin using screen-printed electrodes coated with redox-active polymeric films. Mikrochim Acta 2023; 190:434. [PMID: 37821740 DOI: 10.1007/s00604-023-06003-7] [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: 08/15/2023] [Accepted: 09/16/2023] [Indexed: 10/13/2023]
Abstract
An ultrasensitive capacitance-based biosensor has been developed capable of detecting the kanamycin (KAN) antibiotic at sub-femtomolar levels. The biosensor was constructed using a potential-pulse-assisted method, allowing for the layer-by-layer deposition of a melanin-like polymeric film (MLPF) on an electrode surface modified with gold nanoparticles (AuNPs). The MLPF was formed through the electrochemical polymerization of dopamine and the specific kanamycin aptamer. By optimizing the operating parameters, we achieved a label-free detection of kanamycin by monitoring the variation of pseudocapacitive properties of the MLPF-modified electrode using electrochemical impedance spectroscopy. The developed biosensor demonstrated a wide linear response ranging from 1 fM to 100 pM, with a remarkable limit of detection of 0.3 fM (S/N = 3) for kanamycin. Furthermore, the biosensor was successfully applied to detect kanamycin in milk samples, exhibiting good recovery. These findings highlight the promising potential of the aptasensor for determination of antibiotic residues and ensuring food safety. In conclusion, our ultrasensitive capacitance-based biosensor provides a reliable and efficient method for detecting trace amounts of kanamycin in dairy products. This technology can contribute to safeguarding consumer health and maintaining high food safety standards.
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Affiliation(s)
- Faisal K Algethami
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), P.O. Box 90950, 11623, Riyadh, Saudi Arabia.
| | - Amal Rabti
- Laboratory of Materials, Treatment, and Analysis (LMTA), National Institute of Research and Physicochemical Analysis (INRAP), Biotechpole Sidi Thabet, 2020, Sidi Thabet, Tunisia
- Sensors and Biosensors Group, Analytical Chemistry and Electrochemistry Lab (LR99ES15), University of Tunis El Manar, Tunis El Manar, 2092, Tunis, Tunisia
| | - Mohamed Mastouri
- Sensors and Biosensors Group, Analytical Chemistry and Electrochemistry Lab (LR99ES15), University of Tunis El Manar, Tunis El Manar, 2092, Tunis, Tunisia
| | - Sami Ben Aoun
- Department of Chemistry, Faculty of Science, Taibah University, P.O Box 30002, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Laila S Alqarni
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), P.O. Box 90950, 11623, Riyadh, Saudi Arabia
| | - Mohamed R Elamin
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), P.O. Box 90950, 11623, Riyadh, Saudi Arabia
| | - Noureddine Raouafi
- Sensors and Biosensors Group, Analytical Chemistry and Electrochemistry Lab (LR99ES15), University of Tunis El Manar, Tunis El Manar, 2092, Tunis, Tunisia.
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