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Rokutani S, Hiraka K, Saitoh H, Saito T, Nonaka Y, Ueno K, Tsukakoshi K, Ohnishi N, Ikebukuro K. Aptamer-enhanced particle aggregation inhibition assay for simple homogeneous protein detection using DNA aptamer and thermo-responsive magnetic nanoparticles. Biosens Bioelectron 2024; 245:115827. [PMID: 37979546 DOI: 10.1016/j.bios.2023.115827] [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: 08/18/2023] [Revised: 10/24/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
A simple and sensitive homogeneous protein detection system is required for the early detection of biomarkers. Thermo-responsive magnetic particles (TM) have already been developed to achieve easy bound/free separation at the homogeneous protein detection system, but they are still limited owing to the requirement of secondary antibodies and negatively charged polymers, and it is challenging to control the TM aggregation behavior because of the size of the TM. Therefore, at new method to control TM aggregation behavior that is simple, easy, and highly sensitive is required. In this study, we developed a DNA aptamer-based TM assay as a simple protein detection system without additional secondary molecular recognition elements or negatively charged polymer. In the first attempt, a DNA aptamer was modified on the TM surface, and its aggregation behavior was monitored depending on the target molecule concentration. The TM aggregation rate during the heating process decreased depending on the amount of the DNA aptamer and increased depending on the target protein level. This suggests that the DNA aptamer prevented TM aggregation owing to its negative charge and achieved target protein detection owing to the cancellation of repulsion. Capturable aptamers were used in the TM assay to improve the sensitivity and limit of detection. The designed Capture DNA was modified on the TM surface, and the aptamer was captured in the presence of the target protein through a conformational change. Eventually, Capturable aptamer-based TM assay achieved a sub-nanomolar limit of detection and higher sensitivity than that of our initial investigation. Through this study and the ease of the DNA aptamer design, it was shown that the DNA aptamer-modified TM assay enabled the development of a simple and sensitive homogeneous protein detection system.
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Affiliation(s)
- Shunsuke Rokutani
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kentaro Hiraka
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan; College of Science, Engineering and Technology, Grand Canyon University, 3300 W Camelback Rd, Phoenix, AZ, 85017, USA; National Institute for Physiological Sciences, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Hiroshi Saitoh
- JNC Petrochemical Corporation, Goi Research Center, 5-1 Goi-kaigan, Ichihara, Chiba, 290-8551, Japan
| | - Taiki Saito
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Yoshihiko Nonaka
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kinuko Ueno
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Noriyuki Ohnishi
- JNC Petrochemical Corporation, Goi Research Center, 5-1 Goi-kaigan, Ichihara, Chiba, 290-8551, Japan.
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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Şahin S, Caglayan MO, Üstündağ Z. Recent advances in aptamer-based sensors for breast cancer diagnosis: special cases for nanomaterial-based VEGF, HER2, and MUC1 aptasensors. Mikrochim Acta 2020; 187:549. [PMID: 32888061 DOI: 10.1007/s00604-020-04526-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/20/2020] [Indexed: 02/07/2023]
Abstract
Cancer is one of the most common and important diseases with a high mortality rate. Breast cancer is among the three most common types of cancer in women, and the mortality rate has reached 0.024% in some countries. For early-stage preclinical diagnosis of breast cancer, sensitive and reliable tools are needed. Today, there are many types of biomarkers that have been identified for cancer diagnosis. A wide variety of detection strategies have also been developed for the detection of these biomarkers from serum or other body fluids at physiological concentrations. Aptamers are single-stranded DNA or RNA oligonucleotides and promising in the production of more sensitive and reliable biosensor platforms in combination with a wide range of nanomaterials. Conformational changes triggered by the target analyte have been successfully applied in fluorometric, colorimetric, plasmonic, and electrochemical-based detection strategies. This review article presents aptasensor approaches used in the detection of vascular endothelial growth factor (VEGF), human epidermal growth factor receptor 2 (HER2), and mucin-1 glycoprotein (MUC1) biomarkers, which are frequently studied in the diagnosis of breast cancer. The focus of this review article is on developments of the last decade for detecting these biomarkers using various sensitivity enhancement techniques and nanomaterials.
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Affiliation(s)
- Samet Şahin
- Department of Bioengineering, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey.
| | | | - Zafer Üstündağ
- Department of Chemistry, Kütahya Dumlupınar University, 43100, Kütahya, Turkey
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Highly sensitive electrochemiluminescence biosensor for VEGF165 detection based on a g-C3N4/PDDA/CdSe nanocomposite. Anal Bioanal Chem 2020; 412:3073-3081. [DOI: 10.1007/s00216-020-02552-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/14/2020] [Accepted: 02/26/2020] [Indexed: 02/05/2023]
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Dehghani S, Nosrati R, Yousefi M, Nezami A, Soltani F, Taghdisi SM, Abnous K, Alibolandi M, Ramezani M. Aptamer-based biosensors and nanosensors for the detection of vascular endothelial growth factor (VEGF): A review. Biosens Bioelectron 2018; 110:23-37. [PMID: 29579646 DOI: 10.1016/j.bios.2018.03.037] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/06/2018] [Accepted: 03/16/2018] [Indexed: 02/06/2023]
Abstract
Vascular endothelial growth factor (VEGF) is a key regulator of vascular formation and a predominant protein biomarker in cancer angiogenesis. Owing to its crucial roles in the cancer metastasis, VEGF detection and quantification is of great importance in clinical diagnostics. Today, there exist a wide variety of detection strategies for identifying many types of disease biomarkers, especially for VEGF. As artificial single-stranded DNA or RNA oligonucleotides with catalytic and receptor properties, aptamers have drawn lots of attention to be applied in biosensing platforms due to their target-induced conformational changes as well as high stability and target versatility. So far, various sensitivity-enhancement techniques in combination with a broad range of smart nanomaterials have integrated into the design of novel aptasensors to improve detection limit and sensitivity of analyte detection. This review article provides a brief classification and description of the research progresses of aptamer-based biosensors and nanobiosensors for the detection and quantitative determination of VEGF based on optical and electrochemical platforms.
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Affiliation(s)
- Sadegh Dehghani
- Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahim Nosrati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Yousefi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Nezami
- Department of Pharmacodynamy and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Soltani
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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Hydrogel-based suspension array for biomarker detection using horseradish peroxidase-mediated silver precipitation. Anal Chim Acta 2017; 999:132-138. [PMID: 29254564 DOI: 10.1016/j.aca.2017.10.033] [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: 08/04/2017] [Revised: 10/18/2017] [Accepted: 10/26/2017] [Indexed: 01/25/2023]
Abstract
Advances in medical diagnostics and personalized therapy require robust, sensitive yet cost-effective diagnostic tools for rapid measurement of biomolecules including proteins in body fluids. State-of-the-art technologies are complex and rely on expensive or custom made detection system, and therefore, cannot be readily adapted for point-of-care (POC) analysis. The development of a novel detection platform, which leverages horseradish peroxidase (HRP)-mediated silver precipitation within antibody immobilized porosity tuned poly (ethylene) glycol diacrylate (PEGDA) hydrogel microparticles with the operational advantages of suspension arrays for sensitive quantification of biomarkers, is described. In this study, vascular endothelial growth factor (VEGF) has been used as a model protein. The silver deposition corresponded to the concentration of VEGF in solution. The detection limit of 5.2 ± 1.0 pg/mL and assay time of 2 h highlights that this assay exceeds the conventional technologies in terms of sensitivity and speed. The practical applicability of the hydrogel microparticle based detection system has been established by demonstrating the ability of the system to quantify the production of VEGF by highly aggressive (MDA-MB-231) and non-aggressive (MCF-7) breast cancer cells. The reliance on simple instrument for quantification of clinically relevant markers bolsters the adaptability of the detection platform/method in POC settings.
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Development of an electrochemical detection system for measuring DNA methylation levels using methyl CpG-binding protein and glucose dehydrogenase-fused zinc finger protein. Biosens Bioelectron 2016; 93:118-123. [PMID: 27666367 DOI: 10.1016/j.bios.2016.09.060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/30/2016] [Accepted: 09/16/2016] [Indexed: 11/22/2022]
Abstract
DNA methylation level at a certain gene region is considered as a new type of biomarker for diagnosis and its miniaturized and rapid detection system is required for diagnosis. Here we have developed a simple electrochemical detection system for DNA methylation using methyl CpG-binding domain (MBD) and a glucose dehydrogenase (GDH)-fused zinc finger protein. This analytical system consists of three steps: (1) methylated DNA collection by MBD, (2) PCR amplification of a target genomic region among collected methylated DNA, and (3) electrochemical detection of the PCR products using a GDH-fused zinc finger protein. With this system, we have successfully measured the methylation levels at the promoter region of the androgen receptor gene in 106 copies of genomic DNA extracted from PC3 and TSU-PR1 cancer cell lines. Since no sequence analysis or enzymatic digestion is required for this detection system, DNA methylation levels can be measured within 3h with a simple procedure.
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Methods for Improving Aptamer Binding Affinity. Molecules 2016; 21:421. [PMID: 27043498 PMCID: PMC6273865 DOI: 10.3390/molecules21040421] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/06/2016] [Accepted: 03/22/2016] [Indexed: 12/11/2022] Open
Abstract
Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to achieve desired binding affinities. The optimization of primary sequences and stabilization of aptamer conformations are the main approaches to refining the binding properties of aptamers. In particular, sequence optimization using combined in silico sequence recombinations and in vitro functional evaluations is effective for the improvement of binding affinities, however, the binding affinities of aptamers are limited by the low hydrophobicity of nucleic acids. Accordingly, introduction of hydrophobic moieties into aptamers expands the diversity of interactions between aptamers and targets. Moreover, construction of multivalent aptamers by connecting aptamers that recognize distinct epitopes is an attractive approach to substantial increases in binding affinity. In addition, binding affinities can be tuned by optimizing the scaffolds of multivalent constructs. In this review, we summarize the various techniques for improving the binding affinities of aptamers.
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G-quadruplex DNAzyme-based electrochemiluminescence biosensing strategy for VEGF165 detection: Combination of aptamer-target recognition and T7 exonuclease-assisted cycling signal amplification. Biosens Bioelectron 2015; 74:98-103. [PMID: 26120816 DOI: 10.1016/j.bios.2015.05.069] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/19/2015] [Accepted: 05/29/2015] [Indexed: 01/05/2023]
Abstract
The expression profile of vascular endothelial growth factor (VEGF) is highly correlated with the occurrence and development of cancer. This work reports an electrochemiluminescence (ECL) approach for highly sensitive detection of VEGF165. This approach comprises aptamer-target recognition, T7 exonuclease (T7 Exo)-assisted cycling signal amplification and efficient quenching of ECL of CdS:Eu nanocrystals (NCs) by using DNAzyme. In this assay, CdS:Eu NCs were used as the ECL substrate, A guanine (G)-rich single-stranded DNA (ssDNA) sequence and VEGF165 aptamer were co-immobilized on the surface of the CdS:Eu NCs modified glassy carbon electrode. After recognition and binding to VEGF165, the aptamer moved away from the electrode surface and induced the proposed cyclic cleavage of the target DNA with T7 Exo. A large amount of G-rich ssDNA was released on the CdS:Eu film and folded into G-quadruplex/hemin DNAzyme in the presence of hemin and K(+), consequently decreasing the ECL intensity of CdS:Eu. A good linearity was obtained for VEGF165 detection within the range of 1 pM to 20 nM with a detection limit of 0.2 pM. This assay could be a universal and promising protocol for detection of various biomarkers for early clinical diagnosis.
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Zhao S, Ma W, Xu L, Wu X, Kuang H, Wang L, Xu C. Ultrasensitive SERS detection of VEGF based on a self-assembled Ag ornamented–AU pyramid superstructure. Biosens Bioelectron 2015; 68:593-597. [DOI: 10.1016/j.bios.2015.01.056] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/13/2015] [Accepted: 01/23/2015] [Indexed: 10/24/2022]
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Vascular Endothelial Growth Factor (VEGF) Detection Using an Aptamer and PNA-Based Bound/Free Separation System. MATERIALS 2014; 7:1046-1054. [PMID: 28788498 PMCID: PMC5453099 DOI: 10.3390/ma7021046] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 01/15/2014] [Accepted: 01/28/2014] [Indexed: 11/16/2022]
Abstract
We have developed a bound/free separation system using a vascular endothelial growth factor (VEGF) aptamer and a peptide nucleic acid (PNA) to detect VEGF. In this system, we designed capture PNA (CaPNA), which hybridizes with the aptamer in the absence of the target protein, but does not hybridize with the aptamer in the presence of the target protein due to steric hindrance and/or stabilization of the aptamer's structure. By removing the aptamers not bound to the target protein using CaPNA immobilized beads, we can detect the target protein by measuring signals labeled with the aptamer in the supernatant. In this study, we detected VEGF using CaPNA-immobilized beads without the time-consuming washing step. This simple and rapid system can detect 25 nM of VEGF in 15 min.
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Yoshida W, Abe K, Ikebukuro K. Emerging techniques employed in aptamer-based diagnostic tests. Expert Rev Mol Diagn 2014; 14:143-51. [PMID: 24400930 DOI: 10.1586/14737159.2014.868307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Since aptamers were reported in 1990, research into the applications of aptamers, particularly diagnostic applications, has been growing. Aptamers can act as recognition elements instead of antibodies. In this regard, aptamers have unique characteristics because they are composed of nucleic acids. Intra- and intermolecular interactions of nucleic acids can be easily tailored following straightforward hybridization rules. Nucleic acids can be enzymatically replicated and their sequences can be determined using high-throughput methods. Using these properties, ligand-induced structural change-based aptamer sensors for homogeneous assays, polymerase- and/or nuclease-combined aptamer sensors for ultrasensitive assays, and microarray/next-generation sequencing-based aptamer sensors for multiplexed assays have been developed. This article reviews these unique aptamer sensors, demonstrating their great potential for diagnostic applications.
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Affiliation(s)
- Wataru Yoshida
- Department of Biotechnology and Life Science, Tokyo University of Agriculture & Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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Al-Ameen MA, Ghosh G. Sensitive quantification of vascular endothelial growth factor (VEGF) using porosity induced hydrogel microspheres. Biosens Bioelectron 2013; 49:105-10. [DOI: 10.1016/j.bios.2013.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/26/2013] [Accepted: 05/02/2013] [Indexed: 12/13/2022]
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Electrochemical biosensors using aptamers for theranostics. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 140:183-202. [PMID: 23873093 DOI: 10.1007/10_2013_226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Theranostics, a new term consisting of the words "therapy" and "diagnostics," represents the concept of selecting specific patients for appropriate drug administration using diagnostics. For the development of a molecular targeting drug, the theranostics approach is effective. Therefore, the market for molecular diagnostics is likely to grow at an extraordinary rate over the next 10 years. In this review, we focus on aptamer-based electrochemical biosensors for theranostics. Aptamers are molecular recognition elements that can bind to various target molecules from small compounds to proteins with affinities and specificities comparable to those of antibodies. Inasmuch as various molecules would be targeted for analysis using theranostics, aptamer-based biosensors would be an attractive format because they can be developed for various molecules using the same sensing format. Although a diverse sensing system can be constructed, we focus on electrochemical biosensors in this review because they can measure biomarkers rapidly in a miniaturized sensing system with low cost, such as blood glucose sensors. We summarize the sensing systems of aptamer-based electrochemical biosensors and discuss their advantages for theranostics.
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