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Srivastava A, Harijan M, Prasad R, Singh M. Dual template (epitope) imprinted electrode for sensing bacterial protein with high selectivity. J Mol Recognit 2024; 37:e3087. [PMID: 38686731 DOI: 10.1002/jmr.3087] [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: 09/25/2023] [Revised: 04/03/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
Epitope imprinting has shown better prospects to synthesize synthetic receptors for proteins. Here, dual epitope imprinted polymer electrode (DEIP) matrix was fabricated on gold surface of electrochemical quartz crystal microbalance (EQCM) for recognition of target epitope sequence in blood samples of patients suffering from brain fever. Epitope sequences from outer membrane protein Por B of Neisseria meningitidis (MC58) bacteria predicted through immunoinformatic tools were chosen for imprinting. Self-assembled monolayers (SAM) of cysteine appended epitope sequences on gold nanoparticles were subjected to polymerization prior to electrodeposition on gold coated EQCM electrode. The polymeric matrix was woven around the cysteine appended epitope SAMs through multiple monomers (3-sulfo propyl methacrylate potassium salt (3-SPMAP), benzyl methacrylate (BMA)) and crosslinker (N, N'-methylene-bis-acrylamide). On extraction of the peptide sequences, imprinted cavities were able to selectively and specifically bind targeted epitope sequences in laboratory samples as well as 'real' samples of patients. Selectivity of sensor was examined through mismatched peptide sequences and certain plasma proteins also. The sensor was able to show specific binding towards the blood samples of infected patients, even in the presence of 'matrix' and other plasma proteins such as albumin and globulin. Even other peptide sequences, similar to epitope sequences only with one or two amino acid mismatches were also unable to show any binding. The analytical performance of DEIP-EQCM sensor was tested through selectivity, specificity, matrix effect, detection limit (0.68-1.01 nM), quantification limit (2.05-3.05 nM) and reproducibility (RSD ~ 5%). Hence, a diagnostic tool for bacterium causing meningitis is successfully fabricated in a facile manner which will broaden the clinical access and make efficient population screening feasible.
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Affiliation(s)
- Akriti Srivastava
- Department of Chemistry, MMV, Banaras Hindu University, Varanasi, India
| | - Manjeet Harijan
- Department of Chemistry, MMV, Banaras Hindu University, Varanasi, India
| | - Rajniti Prasad
- Department of Paediatrics, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Meenakshi Singh
- Department of Chemistry, MMV, Banaras Hindu University, Varanasi, India
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Abdul Rashid JI, Yusof NA, Abdullah J, Shomiad Shueb RH. Strategies in the optimization of DNA hybridization conditions and its role in electrochemical detection of dengue virus (DENV) using response surface methodology (RSM). RSC Adv 2023; 13:18748-18759. [PMID: 37362605 PMCID: PMC10286818 DOI: 10.1039/d3ra00216k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/28/2023] [Indexed: 06/28/2023] Open
Abstract
In recent years, limited research has been conducted on enhancing DNA hybridization-based biosensor approaches using statistical models. This study explores the application of response surface methodology (RSM) to improve the performance of a DNA hybridization biosensor for dengue virus (DENV) detection. The biosensor is based on silicon nanowires decorated with gold nanoparticles (SiNWs/AuNPs) and utilizes methylene blue as a redox indicator. The DNA hybridization process between the immobilized DNA probe and the target DENV gene was monitored using differential pulse voltammetry (DPV) based on the reduction of methylene blue. Fourier-transform infrared spectroscopy (FTIR) and electrochemical impedance spectroscopy (EIS) were employed to confirm successful DNA hybridization events on the modified screen-printed gold electrode (SPGE) surface. Several parameters, including pH buffer, NaCl concentration, temperature, and hybridization time, were simultaneously optimized, with NaCl concentration having the most significant impact on DNA hybridization events. This study enhances the understanding of the role of each parameter in influencing DNA hybridization detection in electrochemical biosensors. The optimized biosensor demonstrated the ability to detect complementary oligonucleotide and amplified DENV gene concentrations as low as 0.0891 ng µL-1 (10 pM) and 2.8 ng µL-1, respectively. The developed biosensor shows promise for rapid clinical diagnosis of dengue virus infection.
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Affiliation(s)
- Jahwarhar Izuan Abdul Rashid
- Department of Chemistry and Biology, Centre for Defence Foundation Studies, National Defence University of Malaysia Sungai Besi Camp 57000 Kuala Lumpur Malaysia
| | - Nor Azah Yusof
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Jaafar Abdullah
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Rafidah Hanim Shomiad Shueb
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia 16150 Kubang Kerian Kelantan Malaysia
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Garcia-Melo LF, Morales-Rodríguez M, Madrigal-Bujaidar E, Madrigal-Santillán EO, Morales-González JA, Pineda Cruces RN, Campoy Ramírez JA, Damian-Matsumura P, Tellez-Plancarte A, Batina N, Álvarez-González I. Development of a Nanostructured Electrochemical Genosensor for the Detection of the K-ras Gene. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2022; 2022:6575140. [PMID: 36299712 PMCID: PMC9592225 DOI: 10.1155/2022/6575140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 09/06/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
In the scientific literature, it has been documented that electrochemical genosensors are novel analytical tools with proven clinical diagnostic potential for the identification of carcinogenic processes due to genetic and epigenetic alterations, as well as infectious diseases due to viruses or bacteria. In the present work, we describe the construction of an electrochemical genosensor for the identification of the k12p.1 mutation; it was based on use of Screen-Printed Gold Electrode (SPGE), Cyclic Voltammetry (CV), and Atomic Force Microscopy (AFM), for the monitoring the electron transfer trough the functionalized nanostructured surface and corresponding morphological changes. The sensitivity of the genosensor showed a linear response for the identification of the k12p.1 mutation of the K-ras gene in the concentration range of 10 fM to 1 μM with a detection limit of 7.96 fM in the presence of doxorubicin (Dox) as DNA intercalating agent and indicator of the hybridization reaction. Thus, the electrochemical genosensor developed could be useful for the identification of diseases related with the K-ras oncogene.
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Affiliation(s)
- Luis Fernando Garcia-Melo
- Division de Ingeniería en Nanotecnología, Universidad Politécnica del Valle de México, Av. Mexiquense s/n esquina Av. Universidad Politécnica, Tultitlan Estado de México, CP 54910, Mexico
- Laboratorio de Nanotecnología e Ingeniería Molecular Área Electroquímica, Departamento de Química, CBI, Universidad Autónoma Metropolitana-Iztapalapa (UAM-I), Av. San Rafael Atlixco 186, Iztapalapa, CP 09340, México City, Mexico
| | - Miguel Morales-Rodríguez
- Division de Ingeniería en Nanotecnología, Universidad Politécnica del Valle de México, Av. Mexiquense s/n esquina Av. Universidad Politécnica, Tultitlan Estado de México, CP 54910, Mexico
| | - Eduardo Madrigal-Bujaidar
- Laboratorio de Genética, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Avenida Wilfrido Massieu s/n Col. Zacatenco Del. Gustavo A. Madero, CP 07738, Ciudad de México, Mexico
| | - Eduardo O. Madrigal-Santillán
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Unidad Casco de Santo Tomás, Plan de San Luis y Díaz Mirón, Ciudad de México, CP 11340, Mexico
| | - José Antonio Morales-González
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Unidad Casco de Santo Tomás, Plan de San Luis y Díaz Mirón, Ciudad de México, CP 11340, Mexico
| | - Rosa Natali Pineda Cruces
- Laboratorio de Nanotecnología e Ingeniería Molecular Área Electroquímica, Departamento de Química, CBI, Universidad Autónoma Metropolitana-Iztapalapa (UAM-I), Av. San Rafael Atlixco 186, Iztapalapa, CP 09340, México City, Mexico
| | - Jorge Alfredo Campoy Ramírez
- Laboratorio de Nanotecnología e Ingeniería Molecular Área Electroquímica, Departamento de Química, CBI, Universidad Autónoma Metropolitana-Iztapalapa (UAM-I), Av. San Rafael Atlixco 186, Iztapalapa, CP 09340, México City, Mexico
| | - Pablo Damian-Matsumura
- Laboratorio de Endocrinología Molecular, Departamento de Biología de la Reproducción, CBS, Universidad Autónoma Metropolitana-Iztapalapa (UAM-I), México City, Mexico
| | - Alexandro Tellez-Plancarte
- Laboratorio de Genética, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Avenida Wilfrido Massieu s/n Col. Zacatenco Del. Gustavo A. Madero, CP 07738, Ciudad de México, Mexico
| | - Nikola Batina
- Laboratorio de Nanotecnología e Ingeniería Molecular Área Electroquímica, Departamento de Química, CBI, Universidad Autónoma Metropolitana-Iztapalapa (UAM-I), Av. San Rafael Atlixco 186, Iztapalapa, CP 09340, México City, Mexico
| | - Isela Álvarez-González
- Laboratorio de Genética, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Avenida Wilfrido Massieu s/n Col. Zacatenco Del. Gustavo A. Madero, CP 07738, Ciudad de México, Mexico
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A sensitive gold-nanorods-based nanobiosensor for specific detection of Campylobacter jejuni and Campylobacter coli. J Nanobiotechnology 2019; 17:43. [PMID: 30914053 PMCID: PMC6434641 DOI: 10.1186/s12951-019-0476-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/13/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Campylobacteriosis is a zoonotic infectious disease that can be mostly undiagnosed or unreported due to fastidious Campylobacter species. The aim of this study was to develop a simple, sensitive, and quick assay for the detection of Campylobacter spp. and taking advantage of the great sensitivity of gold nanorods (GNRs) to trace changes in the local environment and interparticle distance. METHODS Characterized GNRs were modified by specific ssDNA probes of cadF gene. First, the biosensor was evaluated using recombinant plasmid (pTG19-T/cadF) and synthetic single-stranded 95 bp gene, followed by a collection of the extracted DNAs of the stool samples. The sensing strategy was compared by culture, PCR, and real-time PCR. RESULTS AND DISCUSSION Analysis of 283 specimens showed successful detection of Campylobacter spp. in 44 cases (16%), which was comparable to culture (7%), PCR (15%), and real-time PCR (18%). In comparison with real-time PCR, the sensitivity of the biosensor was reported 88%, while the specificity test for all assays was the same (100%). However, it was not able to detect Campylobacter in 6 positive clinical samples, as compared to real-time PCR. The limit of detection was calculated to be the same for the biosensor and real-time PCR (102 copy number/mL). CONCLUSIONS Taking high speed and simplicity of this assay into consideration, the plasmonic nanobiosensor could pave the way in designing a new generation of diagnostic kits for detection of C. jejuni and C. coli species in clinical laboratories.
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de Castro ACH, Kochi LT, Moço ACR, Coimbra RS, Oliveira GC, Cuadros-Orellana S, Madurro JM, Brito-Madurro AG. A new genosensor for meningococcal meningitis diagnosis using biological samples. J Solid State Electrochem 2018. [DOI: 10.1007/s10008-018-3940-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Datta M, Desai D, Kumar A. Gene Specific DNA Sensors for Diagnosis of Pathogenic Infections. Indian J Microbiol 2017; 57:139-147. [PMID: 28611490 DOI: 10.1007/s12088-017-0650-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/13/2017] [Indexed: 11/24/2022] Open
Abstract
Gene specific DNA based sensors have potential applications for rapid and real time monitoring of hybridization signal with the target nucleic acid of pathogens. Different types of DNA based sensors and their applications have been studied for rapid and accurate detection of pathogens causing human diseases. These sensors are based on surface plasmon resonance, quantum-dots, molecular beacons, piezoelectric and electrochemical etc. Curbing epidemics at an early stage is one of the massive challenges in healthcare systems. Timely detection of the causative organism may provide a solution to restrain mortality caused by the disease. With the advent of interdisciplinary sciences, bioelectronics has emerged as an effective alternative for disease diagnostics. Gene specific DNA sensors present themselves as cost-effective, sensitive and specific platforms for detection of disease causing pathogens. The mini review explores different transducer based sensors and their potential in diagnosis of acute and chronic diseases.
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Affiliation(s)
- Manali Datta
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan 302007 India
| | - Dignya Desai
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan 302007 India
| | - Ashok Kumar
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007 India
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Singh S, Kaushal A, Khare S, Kumar P, Kumar A. Gold-mercaptopropionic acid-polyethylenimine composite based DNA sensor for early detection of rheumatic heart disease. Analyst 2015; 139:3600-6. [PMID: 24875529 DOI: 10.1039/c4an00324a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The first gold-mercaptopropionic acid-polyethylenimine composite based electrochemical DNA biosensor was fabricated for the early detection of Streptococcus pyogenes infection in humans causing rheumatic heart disease (heart valve damage). No biosensor is available for the detection of rheumatic heart disease (RHD). Therefore, the mga gene based sensor was developed by the covalent immobilization of a 5'-carboxyl modified single stranded DNA probe onto the gold composite electrode. The immobilized probe was hybridized with the genomic DNA (G-DNA) of S. pyogenes from throat swabs and the electrochemical response was measured by cyclic voltammetry (CV), differential pulse voltammetry (DPV) and electrochemical impedance (EI). Covalent immobilization of the probe onto the gold composite and its hybridization with G-DNA was characterized by FTIR and SEM. The sensitivity of the sensor was 110.25 μA cm(-2) ng(-1) with DPV and the lower limit of detection was 10 pg per 6 μL. The sensor was validated with patient throat swab samples and results were compared with available methods. The sensor is highly specific to S. pyogenes and can prevent damage to heart valves by the early detection of the infection in only 30 min.
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Affiliation(s)
- Swati Singh
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India.
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Ahirwar R, Tanwar S, Parween S, Kumar A, Nahar P. Image-based detection of oligonucleotides--a low cost alternative to spectrophotometric or fluorometric methods. Analyst 2015; 139:2186-92. [PMID: 24653995 DOI: 10.1039/c3an02402d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we report a sensitive and low cost image-based (photocolorimetric) method for the detection of oligonucleotides on an activated polypropylene microtest plate (APPμTP). The assay was developed on the APPμTP by covalently immobilising 20-mer amino-modified oligonucleotides. Biotin-tagged complementary target sequences were then hybridised with the immobilised oligonucleotides. Colour was developed by streptavidin-HRP conjugate and the image of the coloured assay solution was taken by a desktop scanner and analysed using colour saturation. The developed method was analysed for its detection limit, accuracy, sensitivity and interference. The linearity range was found to be 1.7-170 ng mL(-1) while the lower limit of detection and limit of quantification were 1.7 and 5.6 ng mL(-1) respectively. The method showed comparable sensitivity to fluorometric methods, and was found to be correlated to fluorescence (R(2) = 0.8081, p-value < 0.0001) and absorbance (R(2) = 0.9394, p-value < 0.0001)-based quantification. It discriminates mismatched base sequences from perfectly matched sequences efficiently. Validation of the method was carried out by detecting por A DNA of Neisseria meningitidis in bacterial meningitis samples. The por A-specific probe having a 6-carbon spacer at its 5'-NH2 terminus was immobilised covalently to the APPμTP and hybridised with different samples of biotinylated single-stranded por A DNA.
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Affiliation(s)
- Rajesh Ahirwar
- Department of Chemical and Systems Biology, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.
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