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Ghadin N, Yusof NAM, Syarul Nataqain B, Raston NHA, Low CF. Selection and characterization of ssDNA aptamer targeting Macrobrachium rosenbergii nodavirus capsid protein: A potential capture agent in gold-nanoparticle-based aptasensor for viral protein detection. JOURNAL OF FISH DISEASES 2024; 47:e13892. [PMID: 38014615 DOI: 10.1111/jfd.13892] [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: 08/23/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
The giant freshwater prawn holds a significant position as a valuable crustacean species cultivated in the aquaculture industry, particularly well-known and demanded among the Southeast Asian countries. Aquaculture production of this species has been impacted by Macrobrachium rosenbergii nodavirus (MrNV) infection, which particularly affects the larvae and post-larvae stages of the prawn. The infection has been recorded to cause mortality rates of up to 100% among the affected prawns. A simple, fast, and easy to deploy on-site detection or diagnostic method is crucial for early detection of MrNV to control the disease outbreak. In the present study, novel single-stranded DNA aptamers targeting the MrNV capsid protein were identified using the systematic evolution of ligands by exponential enrichment (SELEX) approach. The aptamer was then conjugated with the citrate-capped gold nanoparticles (AuNPs), and the sensitivity of this AuNP-based aptasensor for the detection of MrNV capsid protein was evaluated. Findings revealed that the aptamer candidate, APT-MrNV-CP-1 was enriched throughout the SELEX cycle 4, 9, and 12 with the sequence percentage of 1.76%, 9.09%, and 12.42%, respectively. The conjugation of APT-MrNV-CP-1 with citrate-capped AuNPs exhibited the highest sensitivity in detecting the MrNV capsid protein, where the presence of 62.5 nM of the viral capsid protein led to a significant agglomeration of the AuNPs. This study demonstrated the practicality of an AuNP-based aptasensor for disease diagnosis, particularly for detecting MrNV infection in giant freshwater prawns.
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Affiliation(s)
- Norazli Ghadin
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Nur Afiqah Md Yusof
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | | | - Nurul Hanun Ahmad Raston
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Chen Fei Low
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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Chinnappan R, Ramadan Q, Zourob M. Isolation and Detection of Exosomal Mir210 Using Carbon Nanomaterial-Coated Magnetic Beads. J Funct Biomater 2023; 14:441. [PMID: 37754855 PMCID: PMC10531929 DOI: 10.3390/jfb14090441] [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: 06/20/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/28/2023] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that are found in various cellular compartments and play an important role in regulating gene expression. Extracellular miRNAs, such as those found within extracellular vesicles such as exosomes are involved in cell-to-cell communication. The intercellular transfer of miRNAs has been implicated in various diseases' pathogenesis including cancer and has been studied extensively as potential cancer biomarkers. However, the extraction of miRNA from exosomes is still a challenging task. The current nucleic acid extraction assays are expensive and labor-intensive. In this study, we demonstrated a microfluidic device for aptamer-based magnetic separation of the exosomes and subsequent detection of the miRNA using a fluorescence switching assay, which was enabled by carbon nanomaterials coated on magnetic beads. In the OFF state, the fluorophore-labelled cDNA is quenched using carbon nanomaterials. However, when the target miRNA210 is introduced, the cDNA detaches from the bead's surface, which leads to an increase in the fluorescence intensity (ON state). This increment was found to be proportional to miRNA concentration within the dynamic range of 0-100 nM with a detection limit of 5 pM. The assay was validated with spiked miRNA using the standard RT-PCR method. No notable cross-reactivity with other closely related miRNAs was observed. The developed method can be utilized for the minimally invasive detection of cancer biomarkers.
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Affiliation(s)
| | - Qasem Ramadan
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia;
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia;
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Peng K, Liu X, Yuan H, Li M, Wu X, Wang Z, Hao L, Xu F. A novel fluorescent biosensor based on affinity-enhanced aptamer-peptide conjugate for sensitive detection of lead(II) in aquatic products. Anal Bioanal Chem 2023:10.1007/s00216-023-04735-2. [PMID: 37199793 DOI: 10.1007/s00216-023-04735-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/30/2023] [Accepted: 05/04/2023] [Indexed: 05/19/2023]
Abstract
Lead contamination is a major concern in food safety and, as such, many lead detection methods have been developed, especially aptamer-based biosensors. However, the sensitivity and environmental tolerance of these sensors require improvement. A combination of different types of recognition elements is an effective way to improve the detection sensitivity and environmental tolerance of biosensors. Here, we provide a novel recognition element, an aptamer-peptide conjugate (APC), to achieve enhanced affinity of Pb2+. The APC was synthesized from Pb2+ aptamers and peptides through clicking chemistry. The binding performance and environmental tolerance of APC with Pb2+ was studied through isothermal titration calorimetry (ITC); the binding constant (Ka) was 1.76*106 M-1, indicating that the APC's affinity was increased by 62.96% and 802.56% compared with the aptamers and peptides, respectively. Besides, APC demonstrated better anti-interference (K+) than aptamer and peptide. Through the molecular dynamics (MD) simulation, we found that more binding sites and stronger binding energy between APC with Pb2+are the reasons for higher affinity between APC with Pb2+. Finally, a carboxyfluorescein (FAM)-labeled APC fluorescent probe was synthesized and a fluorescent detection method for Pb2+ was established. The limit of detection of the FAM-APC probe was calculated to be 12.45 nM. This detection method was also applied to the swimming crab and showed great potential in real food matrix detection.
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Affiliation(s)
- Kaimin Peng
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai Engineering Research Center for Food Rapid Detection, Shanghai, 200093, China
| | - Xinna Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai Engineering Research Center for Food Rapid Detection, Shanghai, 200093, China
| | - Hongen Yuan
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai Engineering Research Center for Food Rapid Detection, Shanghai, 200093, China
| | - Mengqiu Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai Engineering Research Center for Food Rapid Detection, Shanghai, 200093, China
| | - Xiuxiu Wu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai Engineering Research Center for Food Rapid Detection, Shanghai, 200093, China
| | - Zhouping Wang
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liling Hao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai Engineering Research Center for Food Rapid Detection, Shanghai, 200093, China.
| | - Fei Xu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai Engineering Research Center for Food Rapid Detection, Shanghai, 200093, China.
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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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Bilibana MP, Citartan M, Fuku X, Jijana AN, Mathumba P, Iwuoha E. Aptamers functionalized hybrid nanomaterials for algal toxins detection and decontamination in aquatic system: Current progress, opportunities, and challenges. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 232:113249. [PMID: 35104779 DOI: 10.1016/j.ecoenv.2022.113249] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Purification and detection of algal toxins is the most effective technique to ensure that people have clean and safe drinking water. To achieve these objectives, various state-of-the-art technologies were designed and fabricated to decontaminate and detect algal toxins in aquatic environments. Amongst these technologies, aptamer-functionalized hybrid nanomaterials conjugates have received significant consideration as a result of their several benefits over other methods, such as good controllable selectivity, low immunogenicity, and biocompatibility. Because of their excellent properties, aptamer-functionalized hybrid nanomaterials conjugates are one of several remarkable agents. Several isolated aptamer sequences for algal toxins are addressed in this review, as well as aptasensor and decontamination aptamer functionalized metal nanoparticle-derived hybrid nanocomposites applications. In addition, we present diverse aptamer-functionalized hybrid nanomaterial conjugates designs and their applications for sensing and decontamination.
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Affiliation(s)
- Mawethu Pascoe Bilibana
- Department of Chemistry, School of Physical and Chemical Sciences, Faculty of Natural and Agricultural Sciences, Mafikeng Campus, North-West University, Private Bag X2046, Mmabatho 2735, South Africa; Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Natural and Agricultural Sciences, Mafikeng Campus, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
| | - Marimuthu Citartan
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas 13200, Pulau Pinang, Malaysia
| | - Xolile Fuku
- Institute for Nanotechnology and Water Sustainability (iNanoWS), Florida Campus, College of Science, Engineering and Technology, University of South Africa, Johannesburg 1710, South Africa
| | - Abongile Nwabisa Jijana
- National Innovation Centre, Advanced Material Division, Mintek, 200 Malibongwe Drive, Private Bag x 3015, Johannesburg, Gauteng, South Africa
| | - Penny Mathumba
- National Innovation Centre, Advanced Material Division, Mintek, 200 Malibongwe Drive, Private Bag x 3015, Johannesburg, Gauteng, South Africa
| | - Emmanuel Iwuoha
- SensorLab (University of Western Cape Sensor Laboratories), Chemical Sciences Building, University of the Western Cape, Bellville, 7535 Cape Town, South Africa
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Screening and application of a broad-spectrum aptamer for acyclic guanosine analogues. Anal Bioanal Chem 2021; 413:4855-4863. [PMID: 34110440 DOI: 10.1007/s00216-021-03446-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/16/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
Acyclic guanosine analogues, a class of widely used antiviral drugs, can cause chronic toxicity and virus resistance. Therefore, it is essential to establish rapid and accurate methods to detect acyclic guanosine analogues. In this study, five acyclic guanosine analogues (acyclovir, famciclovir, ganciclovir, penciclovir, and valaciclovir) were used as positive targets to obtain broad-spectrum aptamers through Capture-SELEX technology. Real-time quantitative PCR (Q-PCR) was used to monitor the aptamer SELEX process. After the sixteen rounds of selection against mixed targets, sequences were obtained by high-throughput sequencing (HTS). Furthermore, a broad-spectrum aptamer, named CIV6, was found as the higher performance aptamer that was suitable for five acyclic guanosine analogues by graphene oxide (GO) polarization and fluorescence assay. Finally, the aptamer CIV6 was used to construct GO fluorescence assay to detect five acyclic guanosine analogues. The limits of detection (LOD) of acyclovir, famciclovir, ganciclovir, penciclovir, and valaciclovir were 0.48 ng·mL-1, 0.53 ng·mL-1, 0.50 ng·mL-1, 0.56 ng·mL-1, and 0.38 ng·mL-1, respectively.
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Dillon M, Zaczek-Moczydlowska MA, Edwards C, Turner AD, Miller PI, Moore H, McKinney A, Lawton L, Campbell K. Current Trends and Challenges for Rapid SMART Diagnostics at Point-of-Site Testing for Marine Toxins. SENSORS (BASEL, SWITZERLAND) 2021; 21:2499. [PMID: 33916687 PMCID: PMC8038394 DOI: 10.3390/s21072499] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 12/26/2022]
Abstract
In the past twenty years marine biotoxin analysis in routine regulatory monitoring has advanced significantly in Europe (EU) and other regions from the use of the mouse bioassay (MBA) towards the high-end analytical techniques such as high-performance liquid chromatography (HPLC) with tandem mass spectrometry (MS). Previously, acceptance of these advanced methods, in progressing away from the MBA, was hindered by a lack of commercial certified analytical standards for method development and validation. This has now been addressed whereby the availability of a wide range of analytical standards from several companies in the EU, North America and Asia has enhanced the development and validation of methods to the required regulatory standards. However, the cost of the high-end analytical equipment, lengthy procedures and the need for qualified personnel to perform analysis can still be a challenge for routine monitoring laboratories. In developing regions, aquaculture production is increasing and alternative inexpensive Sensitive, Measurable, Accurate and Real-Time (SMART) rapid point-of-site testing (POST) methods suitable for novice end users that can be validated and internationally accepted remain an objective for both regulators and the industry. The range of commercial testing kits on the market for marine toxin analysis remains limited and even more so those meeting the requirements for use in regulatory control. Individual assays include enzyme-linked immunosorbent assays (ELISA) and lateral flow membrane-based immunoassays (LFIA) for EU-regulated toxins, such as okadaic acid (OA) and dinophysistoxins (DTXs), saxitoxin (STX) and its analogues and domoic acid (DA) in the form of three separate tests offering varying costs and benefits for the industry. It can be observed from the literature that not only are developments and improvements ongoing for these assays, but there are also novel assays being developed using upcoming state-of-the-art biosensor technology. This review focuses on both currently available methods and recent advances in innovative methods for marine biotoxin testing and the end-user practicalities that need to be observed. Furthermore, it highlights trends that are influencing assay developments such as multiplexing capabilities and rapid POST, indicating potential detection methods that will shape the future market.
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Affiliation(s)
- Michael Dillon
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK; (M.D.); (M.A.Z.-M.)
- Faculty of Health, Peninsula Medical School, University of Plymouth, Plymouth PL4 8AA, UK
| | - Maja A. Zaczek-Moczydlowska
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK; (M.D.); (M.A.Z.-M.)
| | - Christine Edwards
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen AB10 7GJ, UK; (C.E.); (L.L.)
| | - Andrew D. Turner
- Centre for Environment, Fisheries and Aquaculture Science, The Nothe, Barrack Road, Weymouth, Dorset DT4 8UB, UK;
| | - Peter I. Miller
- Plymouth Marine Laboratory, Remote Sensing Group, Prospect Place, Plymouth PL1 3DH, UK;
| | - Heather Moore
- Agri-Food and Biosciences Institute, 18a Newforge Lane, Belfast, Northern Ireland BT9 5PX, UK; (H.M.); (A.M.)
| | - April McKinney
- Agri-Food and Biosciences Institute, 18a Newforge Lane, Belfast, Northern Ireland BT9 5PX, UK; (H.M.); (A.M.)
| | - Linda Lawton
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen AB10 7GJ, UK; (C.E.); (L.L.)
| | - Katrina Campbell
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK; (M.D.); (M.A.Z.-M.)
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Yang Y, Yu G, Chen Y, Jia N, Li R. Four decades of progress in cylindrospermopsin research: The ins and outs of a potent cyanotoxin. JOURNAL OF HAZARDOUS MATERIALS 2021; 406:124653. [PMID: 33321325 DOI: 10.1016/j.jhazmat.2020.124653] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 06/12/2023]
Abstract
The cyanotoxin cylindrospermopsin (CYN), a toxic metabolite from cyanobacteria, is of particular concern due to its cosmopolitan occurrence, aquatic bioaccumulation, and multi-organ toxicity. CYN is the second most often recorded cyanotoxin worldwide, and cases of human morbidity and animal mortality are associated with ingestion of CYN contaminated water. The toxin poses a great challenge for drinking water treatment plants and public health authorities. CYN, with the major toxicity manifested in the liver, is cytotoxic, genotoxic, immunotoxic, neurotoxic and may be carcinogenic. Adverse effects are also reported for endocrine and developmental processes. We present a comprehensive review of CYN over the past four decades since its first reported poisoning event, highlighting its global occurrence, biosynthesis, toxicology, removal, and monitoring. In addition, current data gaps are identified, and future directions for CYN research are outlined. This review is beneficial for understanding the ins and outs of this environmental pollutant, and for robustly assessing health hazards posed by CYN exposure to humans and other organisms.
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Affiliation(s)
- Yiming Yang
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, Guangdong 510182, China
| | - Gongliang Yu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Youxin Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Nannan Jia
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Renhui Li
- College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang 325035, China.
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Aptamer selection and aptasensor construction for bone density biomarkers. Talanta 2020; 224:121818. [PMID: 33379043 DOI: 10.1016/j.talanta.2020.121818] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 01/22/2023]
Abstract
Osteoporosis (OP) is a bone disease involved in dysregulation of one of the bone metabolism arms, formation, or desorption cause a porous bone. Osteocalcin (OC) and beta-crosslap (BC), are the well-known markers for OP, which are connected to bone formation and desorption, respectively. In addition to the OP biomarker, BC is also used as an estrogen replacement therapeutic monitoring. ELISA and other antibody-based detection methods are routinely used for measuring OC and BC. These methods have limitations that include thermostability, sensitivity, sacrificing animals, and cost of production. However, aptamer-based-assays are of interest to overcome these drawbacks and achieve the most specific and robust application. Herein, specific aptamers for OC and BC were selected by the systematic evolution of ligands by exponential enrichment (SELEX) method from the pool of ssDNA library with 60 random sequences. The binding affinity (Kd) of the selected aptamers were evaluated against the respective biomarkers. The high-affinity aptamers of OC and BC showed the Kd values of 59 and 55 nM respectively. A graphene oxide-based aptasensors were fabricated from the high-affinity aptamers, and the detection limits of OC and BC were found to be 0.4 pg/ml and 0.21 pg/ml, respectively. These aptasensors have been tested with OC and BC spiked buffer samples and validated using serum samples collected from osteoporotic rats.
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