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Patoine K, Ta K, Gilbert A, Percuoco M, Gerdon AE. Equilibrium interactions of biomimetic DNA aptamers produce intrafibrillar calcium phosphate mineralization of collagen. Acta Biomater 2024; 179:234-242. [PMID: 38554888 DOI: 10.1016/j.actbio.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/02/2024]
Abstract
Native and biomimetic DNA structures have been demonstrated to impact materials synthesis under a variety of conditions but have only just begun to be explored in this role compared to other biopolymers such as peptides, proteins, polysaccharides, and glycopolymers. One selected DNA aptamer has been explored in calcium phosphate and calcium carbonate mineralization, demonstrating sequence-dependent control of kinetics, morphology, and crystallinity. This aptamer is here applied to a biologically-relevant bone model system that uses collagen hydrogels. In the presence of the aptamer, intrafibrillar collagen mineralization is observed compared to negative controls and a positive control using well-studied poly-aspartic acid. The mechanism of interaction is explored through affinity measurements, kinetics of calcium uptake, and kinetics of aptamer uptake into the forming mineral. There is a marked difference observed between the selected aptamer containing a G-quadruplex secondary structure compared to a control sequence with no G-quadruplex. It is hypothesized that the equilibrium interaction of the aptamer with calcium-phosphate precursors and with the collagen itself leads to slow kinetic mineral formation and a morphology appropriate to bone. This points to new uses for DNA aptamers in biologically-relevant mineralization systems and the possibility of future biomedical applications. STATEMENT OF SIGNIFICANCE: Collagen is the protein structural component that mineralizes with calcium phosphate to form durable bone. Crystalline calcium phosphate must be infused throughout the collagen fiber structure to produce a strong material. This process is assisted by soluble proteins that interact with both calcium phosphate precursors and the collagen protein and has been proposed to follow a polymer-induce liquid precursor (PILP) model. Further understanding of this model and control of the process through synthetic, biomimetic molecules could have significant advantages in biomedical, restorative procedures. For the first time, synthetic DNA aptamers with specific secondary structures are here shown to influence and direct collagen mineralization. The mechanism of this process has been studied to demonstrate an important equilibrium between the DNA aptamer, calcium phosphate precursors, and collagen.
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Affiliation(s)
- Kassidy Patoine
- Department of Chemistry & Physics, Emmanuel College, 400 Fenway, Boston, MA 02115, United States
| | - Kristy Ta
- Department of Chemistry & Physics, Emmanuel College, 400 Fenway, Boston, MA 02115, United States
| | - Amanda Gilbert
- Department of Chemistry & Physics, Emmanuel College, 400 Fenway, Boston, MA 02115, United States
| | - Marielle Percuoco
- Department of Chemistry & Physics, Emmanuel College, 400 Fenway, Boston, MA 02115, United States
| | - Aren E Gerdon
- Department of Chemistry & Physics, Emmanuel College, 400 Fenway, Boston, MA 02115, United States.
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2
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Lei H, Wang H, Wang X, Xiao Z, Tian T, Cui K. Surface-enhanced Raman scattering-based identification of breast cancer progression using extracellular vesicles-derived integrin α6β4. Talanta 2024; 275:126092. [PMID: 38615459 DOI: 10.1016/j.talanta.2024.126092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024]
Abstract
Detection of progression is of great importance to breast cancer treatment and can benefit patients. Limited by current detection technologies and biomarkers, early breast cancer progression diagnosis remains challenging. Researchers have found blood extracellular vesicles (EVs)-derived integrin α6β4 directly facilitate progression in breast cancer, enabling cancer detection. However, EVs size and heterogeneity hinder protein detection, masked by abundant background EVs. Hence, novel tools for efficient detection of EVs with high selectivity and low interference are significantly desired. Here, a new silver-coated gold nanorods SERS probe, termed as Au@Ag@IDA-B/4MSTP, based on DNA aptamer was established for the detection of integrin α6β4 derived from EVs. Validation of the Au@Ag@IDA-B/4MSTP probes using cell-culture-derived EVs revealed a LOD of 23 particles/μL for EVs detection. This tool was further confirmed to mimic the real state of cancer with subcutaneous tumor model and lung metastasis model in mice. With 10 μL of blood plasma and simple Raman analysis process, the test achieved 85.7 % sensitivity and 83.3 % specificity. Moreover, our method achieves a simplified approach that expedites the detection process. These results demonstrate the good detection performance of Au@Ag@IDA-B/4MSTP probes for EVs integrin α6β4, and suggest that this non-invasive approach could be a promising tool for early detection of breast cancer progression.
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Affiliation(s)
- Haozhi Lei
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China; Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Shanghai, 200127, China
| | - Haoze Wang
- Department of Pharmacology and Chemical Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China; College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, 200233, China
| | - Xiqiu Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Zeyu Xiao
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China; Department of Pharmacology and Chemical Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Tian Tian
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Kai Cui
- Department of Pharmacology and Chemical Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
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3
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Wen X, Huang Z, Yang X, He X, Li L, Chen H, Wang K, Guo Q, Liu J. Development of an aptamer capable of multidrug resistance reversal for tumor combination chemotherapy. Proc Natl Acad Sci U S A 2024; 121:e2321116121. [PMID: 38557176 PMCID: PMC11009676 DOI: 10.1073/pnas.2321116121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Multidrug resistance (MDR) is a major factor in the failure of many forms of tumor chemotherapy. Development of a specific ligand for MDR-reversal would enhance the intracellular accumulation of therapeutic agents and effectively improve the tumor treatments. Here, an aptamer was screened against a doxorubicin (DOX)-resistant human hepatocellular carcinoma cell line (HepG2/DOX) via cell-based systematic evolution of ligands by exponential enrichment. A 50 nt truncated sequence termed d3 was obtained with high affinity and specificity for HepG2/DOX cells. Multidrug resistance protein 1 (MDR1) is determined to be a possible recognition target of the selected aptamer. Aptamer d3 binding was revealed to block the MDR of the tumor cells and increase the accumulation of intracellular anticancer drugs, including DOX, vincristine, and paclitaxel, which led to a boost to the cell killing of the anticancer drugs and lowering their survival of the tumor cells. The aptamer d3-mediated MDR-reversal for effective chemotherapy was further verified in an in vivo animal model, and combination of aptamer d3 with DOX significantly improved the suppression of tumor growth by treating a xenograft HepG2/DOX tumor in vivo. This work demonstrates the feasibility of a therapeutic DNA aptamer as a tumor MDR-reversal agent, and combination of the selected aptamer with chemotherapeutic drugs shows great potential for liver cancer treatments.
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Affiliation(s)
- Xiaohong Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha410082, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha410082, China
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha410082, China
| | - Zhixiang Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha410082, China
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha410082, China
- College of Biology, Hunan University, Changsha410082, China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha410082, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha410082, China
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha410082, China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha410082, China
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha410082, China
- College of Biology, Hunan University, Changsha410082, China
| | - Lie Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha410082, China
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha410082, China
- College of Biology, Hunan University, Changsha410082, China
| | - Haiyan Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha410082, China
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha410082, China
- College of Biology, Hunan University, Changsha410082, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha410082, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha410082, China
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha410082, China
| | - Qiuping Guo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha410082, China
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha410082, China
- College of Biology, Hunan University, Changsha410082, China
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha410082, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha410082, China
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha410082, China
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4
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Chen Y, Gong C, Chen K, Wang Z, He M, Wang P, Chen K, Jiao Y, Yang Y. G-quadruplex DNA-based colorimetric biosensor for the ultrasensitive visual detection of strontium ions using MnO 2 nanorods as oxidase mimetics. Mikrochim Acta 2024; 191:213. [PMID: 38512701 DOI: 10.1007/s00604-024-06293-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024]
Abstract
Strontium-90 (90Sr) is a major radioactive component that has attracted great attention, but its detection remains challenging since there are no specific energy rays indicative of its presence. Herein, a biosensor that is capable of rapidly detecting Sr2+ ions is demonstrated. Simple colorimetric method for sensitive detection of Sr2+ with the help of single-stranded DNA was developed by preparing MnO2 nanorods as oxidase mimic catalysis 3,3',5,5'-tetramethylbenzidine (TMB). Under weakly acidic conditions, MnO2 exhibited a strong oxidase-mimicking activity to oxidize colorless TMB into blue oxidation products (oxTMB) with discernible absorbance signals. Nevertheless, the introduction of a guanine-rich DNA aptamer inhibited MnO2-mediated TMB oxidation and reduced oxTMB formation, resulting in blue fading and diminished absorbance. Upon the addition of strontium ions to the system, the aptamers formed a stable G-quadruplex structure with strontium ions, thereby restoring the oxidase-mimicking activity of MnO2. Under the best experimental conditions, the absorbance exhibits a linear relationship with the Sr2+ concentration within the range 0.01-200 μM, with a limit of detection of 0.0028 µM. When the concentration of Sr2+ from 10-8 to 10-6 mol L-1, a distinct color change gradient could be observed in paper-based sensor. We successfully applied this approach to determine Sr2+ in natural water samples, obtaining recoveries ranging from 97.6 to 103% with a relative standard deviation of less than 5%. By providing technical solutions for detection, our work contributed to the effective monitoring of transportation of radioactive Sr in the environment.
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Affiliation(s)
- Yiting Chen
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Chunhui Gong
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Kaiwei Chen
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Ziwei Wang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Manli He
- Department of General Education, Army Engineering University of PLA, Nanjing, 211101, China
| | - Peng Wang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Kai Chen
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Yan Jiao
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Yi Yang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Nanjing University of Information Science & Technology, Nanjing, 210044, China.
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5
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Qiao Y, Shi Y, Ji M, Wang Z, Bai X, Zhang K, Yin K, Zhang Y, Chen X, Zhang Y, Lu J, Zhao J, Liu K, Yuan B. Selection and identification of a prohibitin 2-binding DNA aptamer for tumor tissue imaging and targeted chemotherapy. Int J Biol Macromol 2024; 259:129002. [PMID: 38176501 DOI: 10.1016/j.ijbiomac.2023.129002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024]
Abstract
Tumor cell-targeting molecules play a vital role in cancer diagnosis, targeted therapy, and biomarker discovery. Aptamers are emerging as novel targeting molecules with unique advantages in cancer research. In this work, we have developed several DNA aptamers through cell-based systematic evolution of ligands by exponential enrichment (Cell-SELEX). The selected SYL-6 aptamer can bind to a variety of cancer cells with high signal. Tumor tissue imaging demonstrated that SYL-6-Cy5 fluorescent probe was able to recognize multiple clinical tumor tissues but not the normal tissues, which indicates great potential of SYL-6 for clinical tumor diagnosis. Meanwhile, we identified prohibitin 2 (PHB2) as the molecular target of SYL-6 using mass spectrometry, pull-down and RNA interference assays. Moreover, SYL-6 can be used as a delivery vehicle to carry with doxorubicin (Dox) chemotherapeutic agents for antitumor targeted chemotherapy. The constructed SYL-6-Dox can not only selectively kill tumor cells in vitro, but also inhibit tumor growth with reduced side effects in vivo. This work may provide a general tumor cell-targeting molecule and a potential biomarker for cancer diagnosis and targeted therapy.
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Affiliation(s)
- Yan Qiao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou 450000, Henan, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yanli Shi
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; Department of Pathology, Zhoukou Central Hospital, Zhoukou 466000, Henan, China
| | - Mengmeng Ji
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Zhaoting Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Xue Bai
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Kai Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Kai Yin
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yangyang Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Xinhuan Chen
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou 450000, Henan, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yueteng Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Jing Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou 450000, Henan, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Jimin Zhao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou 450000, Henan, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou 450000, Henan, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou 450001, Henan, China; China-US (Henan) Hormel Cancer Institute, Zhengzhou 450003, Henan, China; Cancer Chemoprevention International Collaboration Laboratory, Zhengzhou 450000, Henan, China.
| | - Baoyin Yuan
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou 450000, Henan, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou 450001, Henan, China.
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6
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Noorizadeh M, Geetha M, Bensaali F, Meskin N, Sadasivuni KK, Zughaier SM, Elgamal M, Ait Hssain A. A Path towards Timely VAP Diagnosis: Proof-of-Concept Study on Pyocyanin Sensing with Cu-Mg Doped Graphene Oxide. Biosensors (Basel) 2024; 14:48. [PMID: 38248425 DOI: 10.3390/bios14010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/09/2024] [Accepted: 01/13/2024] [Indexed: 01/23/2024]
Abstract
In response to the urgent requirement for rapid, precise, and cost-effective detection in intensive care units (ICUs) for ventilated patients, as well as the need to overcome the limitations of traditional detection methods, researchers have turned their attention towards advancing novel technologies. Among these, biosensors have emerged as a reliable platform for achieving accurate and early diagnoses. In this study, we explore the possibility of using Pyocyanin analysis for early detection of pathogens in ventilator-associated pneumonia (VAP) and lower respiratory tract infections in ventilated patients. To achieve this, we developed an electrochemical sensor utilizing a graphene oxide-copper oxide-doped MgO (GO - Cu - Mgo) (GCM) catalyst for Pyocyanin detection. Pyocyanin is a virulence factor in the phenazine group that is produced by Pseudomonas aeruginosa strains, leading to infections such as pneumonia, urinary tract infections, and cystic fibrosis. We additionally investigated the use of DNA aptamers for detecting Pyocyanin as a biomarker of Pseudomonas aeruginosa, a common causative agent of VAP. The results of this study indicated that electrochemical detection of Pyocyanin using a GCM catalyst shows promising potential for various applications, including clinical diagnostics and drug discovery.
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Affiliation(s)
- Mohammad Noorizadeh
- Department of Electrical Engineering, College of Engineering, Qatar University, Doha 2713, Qatar
| | - Mithra Geetha
- Department of Mechanical and Industrial Engineering, Centre for Advanced Materials, Qatar University, Doha 2713, Qatar
| | - Faycal Bensaali
- Department of Electrical Engineering, College of Engineering, Qatar University, Doha 2713, Qatar
| | - Nader Meskin
- Department of Electrical Engineering, College of Engineering, Qatar University, Doha 2713, Qatar
| | - Kishor K Sadasivuni
- Department of Mechanical and Industrial Engineering, Centre for Advanced Materials, Qatar University, Doha 2713, Qatar
| | - Susu M Zughaier
- College of Medicine, QU Health, Qatar University, Doha 2713, Qatar
| | - Mahmoud Elgamal
- College of Medicine, QU Health, Qatar University, Doha 2713, Qatar
| | - Ali Ait Hssain
- Medical Intensive Care Unit, Hamad Medical Corporation, Doha 3050, Qatar
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Lee M, Kim SH, Kim D, Kim HJ. Rapid and Easy Detection of Microcystin-LR Using a Bioactivated Multi-Walled Carbon Nanotube-Based Field-Effect Transistor Sensor. Biosensors (Basel) 2024; 14:37. [PMID: 38248414 PMCID: PMC10813581 DOI: 10.3390/bios14010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
In this study, we developed a multi-walled carbon nanotube (MWCNT)-based field-effect transistor (MWCNT-FET) sensor with high sensitivity and selectivity for microcystin-LR (MC-LR). Carboxylated MWCNTs were activated with an MC-LR-targeting aptamer (MCTA). Subsequently the bioactivated MWCNTs were immobilized between interdigitated drain (D) and source (S) electrodes through self-assembly. The top-gated MWCNT-FET sensor was configured by dropping the sample solution onto the D and S electrodes and immersing a Ag/AgCl electrode in the sample solution as a gate (G) electrode. We believe that the FET sensor's conduction path arises from the interplay between the MCTAs, with the applied gate potential modulating this path. Using standard instruments and a personal computer, the sensor's response was detected in real-time within a 10 min time frame. This label-free FET sensor demonstrated an impressive detection capability for MC-LR in the concentration range of 0.1-0.5 ng/mL, exhibiting a lower detection limit of 0.11 ng/mL. Additionally, the MWCNT-FET sensor displayed consistent reproducibility, a robust selectivity for MC-LR over its congeners, and minimal matrix interferences. Given these attributes, this easily mass-producible FET sensor is a promising tool for rapid, straightforward, and sensitive MC-LR detection in freshwater environments.
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Affiliation(s)
- Myeongsoon Lee
- Department of Chemistry, Pukyong National University, Busan 48513, Republic of Korea; (M.L.); (D.K.)
| | - Seong H. Kim
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA;
| | - Don Kim
- Department of Chemistry, Pukyong National University, Busan 48513, Republic of Korea; (M.L.); (D.K.)
| | - Hak Jun Kim
- Department of Chemistry, Pukyong National University, Busan 48513, Republic of Korea; (M.L.); (D.K.)
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Drobintseva AO, Mironova ES, Zubareva TS, Krylova YS, Kvetnoy IM, Paltsev MA, Yablonsky PK. [Modern approaches to studying the molecular mechanisms of lung functioning in normal and pathological conditions]. Arkh Patol 2024; 86:58-64. [PMID: 38591908 DOI: 10.17116/patol20248602158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Problems with breathing and lung function are caused by the development of various lung diseases associated with lifestyle, harmful environmental factors and genetic predisposition. Knowledge of the molecular mechanisms of the development of the pathological process will allow on time identification of the disease or the development of targeted therapy. The article provides an overview of modern methods that make it possible to most accurately reproduce the structural, functional and mechanical properties of the lung (organ-on-a-chip), to perform non-invasive molecular studies of biomarkers of bronchopulmonary pathology using saliva diagnostics, as well as using DNA and RNA aptamers, verify tumor markers in biological samples of human tissue. Analysis of alterations in the pattern of protein glycosylation using glycodiagnostic methods makes it possible to detect lung cancer in the early stages.
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Affiliation(s)
- A O Drobintseva
- Saint Petersburg State Pediatric Medical University, St. Petersburg, Russia
- Saint Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - E S Mironova
- Saint Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
- Saint Petersburg Institute of Bioregulation and Gerontology, St. Petersburg, Russia
| | - T S Zubareva
- Saint Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
- Saint Petersburg Institute of Bioregulation and Gerontology, St. Petersburg, Russia
| | - Yu S Krylova
- Saint Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
- First Saint Petersburg State Medical University named after. acad. I.P. Pavlov (Pavlov University), St. Petersburg, Russia
| | - I M Kvetnoy
- Saint Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
- Saint Petersburg State University, St. Petersburg, Russia
| | - M A Paltsev
- Lomonosov Moscow State University, Moscow, Russia
| | - P K Yablonsky
- Saint Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
- Saint Petersburg State University, St. Petersburg, Russia
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9
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Suzuki Y. Detailed Protocol for Predicting 3D Structure of DNA Aptamers and Performing In Silico Docking Calculations. Methods Mol Biol 2024; 2766:139-144. [PMID: 38270873 DOI: 10.1007/978-1-0716-3682-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
This paper presents a comprehensive protocol for predicting the three-dimensional (3D) structure of DNA aptamers and performing in silico docking calculations. The protocol includes steps for sequence input, structure prediction, sequence modification, structure minimization, and docking. The procedure is executed on a Mac environment utilizing bioinformatics tools such as mfold, RNA Composer, PyMOL, and Hdock. The protocol is intended to provide a guide for researchers in structural biology and drug design.
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Affiliation(s)
- Yasuyuki Suzuki
- Department of Anaesthesiology, Saiseikai Matsuyama Hospital, Matsuyama, Ehime, Japan
- Department of Pharmacology, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
- Research Division, Saiseikai Research Institute of Health Care and Welfare, Tokyo, Japan
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Sliman YA, Samoylenkova NS, Antipova OM, Brylev VA, Veryutin DA, Sapozhnikova KA, Alekseeva AI, Pronin IN, Kopylov AM, Pavlova GV. [Covalently conjugated DNA aptamer with doxorubicin as in vitro model for effective targeted drug delivery to human glioblastoma tumor cells]. Zh Vopr Neirokhir Im N N Burdenko 2024; 88:48-55. [PMID: 38334730 DOI: 10.17116/neiro20248801148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Targeted delivery of chemotherapeutic agents with aptamers is a very effective method increasing therapeutic index compared to non-targeted drugs. OBJECTIVE To study the effectiveness of in vitro therapeutic effect of covalently conjugated GR20 DNA aptamer with doxorubicin on glioblastoma cells compared to reference culture of human fibroblasts. MATERIAL AND METHODS A Sus/fP2 cell culture was obtained from glioblastoma tissue sample to analyze the effectiveness of conjugate. A linear culture of human dermal fibroblasts (mesenchymal stem cells) DF1 was used as a control. To assess antiproliferative activity of covalently conjugated GR20 aptamer with doxorubicin, we used the MTS test. The Cell Index was measured using the xCelligence S16 cell analyzer assessing viability of cell cultures by recording changes in real time. RESULTS Human glioblastoma Sus/fP2 cells reduce own proliferative potential by 80% when exposed to doxorubicin (0.5 µM, 72 hours, MTS test), by 9% when exposed to GR20 aptamer (10 µM, 72 hours, MTS test) and by 26% when exposed to covalently conjugated DOX-GR20 (0.5 µM, 72 hours, MTS test). A long-term study of proliferative potential of Sus/fP2 cells on the xCelligence S16 analyzer revealed a significant decrease in the number of cells under the effect of doxorubicin and covalently conjugated DOX-GR20. Effectiveness of covalently conjugated DOX-GR20 is halved. GR20 aptamer at a concentration of 10 μM and its conjugate with doxorubicin DOX-GR20 at a concentration of 1 μM have no negative effect on cells of the control culture of DF1 fibroblasts, while doxorubicin is toxic for these cells. MTS test and xCelligence S16 cell analyzer found no decrease in metabolic activity of DF1 cells and their ability to proliferate. CONCLUSION We established obvious antiproliferative effect of covalent conjugate DOX-GR20 on continuous human glioblastoma cell culture Sus/fP2 without toxic effect on the reference culture (dermal fibroblasts DF1).
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Affiliation(s)
- Ya A Sliman
- Burdenko Neurosurgical Center, Moscow, Russia
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | | | - O M Antipova
- Lomonosov Moscow State University, Moscow, Russia
| | - V A Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - D A Veryutin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - K A Sapozhnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - A I Alekseeva
- Avtsyn Research Institute of Human Morphology of federal state budgetary scientific institution «Petrovsky national research centre of surgery», Moscow, Russia
- Institute of Higher Nervous Activity and Neurophysiology, Moscow, Russia
| | - I N Pronin
- Burdenko Neurosurgical Center, Moscow, Russia
| | - A M Kopylov
- Lomonosov Moscow State University, Moscow, Russia
| | - G V Pavlova
- Burdenko Neurosurgical Center, Moscow, Russia
- Institute of Higher Nervous Activity and Neurophysiology, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
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11
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Yuan W, Li S, Ma X, Pang C, Wu Y, Wang M, Li B. MOF@Au NPs/aptamer fluorescent probe for the selective and sensitive detection of thiamethoxam. LUMINESCENCE 2023. [PMID: 38104966 DOI: 10.1002/bio.4651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/20/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023]
Abstract
The luminescence performance of fluorescent reagents plays a crucial role in fluorescence analysis. Therefore, in this study, a novel bi-ligand Zn-based metal-organic framework, Au nanoparticle (NP) fluorescent material was synthesized using a hydrothermal method with Zn as the metal source. Simultaneously, a DNA aptamer was introduced as a molecular recognition element to develop a Zn-based MOF@Au NPs/DNA aptamer fluorescent probe for the ultra-trace detection of thiamethoxam residues in agricultural products. The probe captured different concentrations of the target molecule, thiamethoxam, through the DNA aptamer, causing a conformational change in the DNA aptamer and bursting the fluorescence of the probe, therefore establishing a fluorometric method for thiamethoxam detection. This method is highly sensitive due to the excellent luminescence properties of the Zn-based MOF@Au NPs, and the DNA aptamer can specifically recognize thiamethoxam, offering high selectivity. The linear range of the method was 2.5-6000 × 10-11 mol L-1 , with a detection limit of 8.33 × 10-12 mol L-1 . This method was applied to the determination of actual samples, such as bananas, and the spiked recovery rate was found to be in the range 84.05-109.07%. Overall, the proposed probe has high sensitivity, high selectivity, and easy operation for the detection of thiamethoxam residues in actual samples.
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Affiliation(s)
- Weiwei Yuan
- College of Food Science and Technology, and MOE, Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan, China
- Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Hainan Provincial Key Laboratory of Quality and Safety for Tropical Fruits and Vegetables, Key Laboratory of Quality and Safety Control of Subtropical Fruits and Vegetables, Ministry of Agriculture and Rural Affairs, Haikou, China
- Hainan Institute for Food Control, Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, Haikou, China
| | - Shuhuai Li
- Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Hainan Provincial Key Laboratory of Quality and Safety for Tropical Fruits and Vegetables, Key Laboratory of Quality and Safety Control of Subtropical Fruits and Vegetables, Ministry of Agriculture and Rural Affairs, Haikou, China
- Hainan Institute for Food Control, Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, Haikou, China
| | - Xionghui Ma
- Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Hainan Provincial Key Laboratory of Quality and Safety for Tropical Fruits and Vegetables, Key Laboratory of Quality and Safety Control of Subtropical Fruits and Vegetables, Ministry of Agriculture and Rural Affairs, Haikou, China
| | - Chaohai Pang
- Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Hainan Provincial Key Laboratory of Quality and Safety for Tropical Fruits and Vegetables, Key Laboratory of Quality and Safety Control of Subtropical Fruits and Vegetables, Ministry of Agriculture and Rural Affairs, Haikou, China
| | - Yuwei Wu
- Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Hainan Provincial Key Laboratory of Quality and Safety for Tropical Fruits and Vegetables, Key Laboratory of Quality and Safety Control of Subtropical Fruits and Vegetables, Ministry of Agriculture and Rural Affairs, Haikou, China
| | - Mingyue Wang
- College of Food Science and Technology, and MOE, Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan, China
- Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Hainan Provincial Key Laboratory of Quality and Safety for Tropical Fruits and Vegetables, Key Laboratory of Quality and Safety Control of Subtropical Fruits and Vegetables, Ministry of Agriculture and Rural Affairs, Haikou, China
- Hainan Institute for Food Control, Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, Haikou, China
| | - Bei Li
- Hainan Institute for Food Control, Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, Haikou, China
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12
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Mori Y, Ohara M, Terasaki M, Osaka N, Yashima H, Saito T, Otoyama-Kataoka Y, Omachi T, Higashimoto Y, Matsui T, Fukui T, Yamagishi SI. Subcutaneous Infusion of DNA-Aptamer Raised against Advanced Glycation End Products Prevents Loss of Skeletal Muscle Mass and Strength in Accelerated-Aging Mice. Biomedicines 2023; 11:3112. [PMID: 38137333 PMCID: PMC10740860 DOI: 10.3390/biomedicines11123112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
We have developed DNA aptamers that can inhibit the toxic effects of advanced glycation end products (AGE-Apts). We herein evaluated the effects of AGE-Apts on muscle mass and strength in senescence-accelerated mouse prone 8 (SAMP8) mice. Eight-month-old male SAMP8 mice received subcutaneous infusion of control DNA aptamers (CTR-Apts) or AGE-Apts. Mice in an age-matched senescence-accelerated mouse resistant strain 1 (SAMR1) group were treated with CTR-Apts as controls. The soleus muscles were collected after the 8-week intervention for weight measurement and histological, RT-PCR, and immunofluorescence analyses. Grip strength was measured before and after the 8-week intervention. AGE-Apt treatment inhibited the progressive decrease in the grip strength of SAMP8 mice. SAMP8 mice had lower soleus muscle weight and fiber size than SAMR1 mice, which was partly restored by AGE-Apt treatment. Furthermore, AGE-Apt-treated SAMP8 mice had a lower interstitial fibrosis area of the soleus muscle than CTR-Apt-treated SAMP8 mice. The soleus muscle levels of AGEs, oxidative stress, receptor for AGEs, and muscle ring-finger protein-1 were increased in the CTR-Apt-treated mice, all of which, except for AGEs, were inhibited by AGE-Apt treatment. Our present findings suggest that the subcutaneous delivery of AGE-Apts may be a novel therapeutic strategy for aging-related decrease in skeletal muscle mass and strength.
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Affiliation(s)
- Yusaku Mori
- Anti-Glycation Research Section, Division of Diabetes, Metabolism, and Endocrinology, Department of Medicine, Showa University School of Medicine, Shinagawa, Tokyo 142-8555, Japan
| | - Makoto Ohara
- Division of Diabetes, Metabolism, and Endocrinology, Department of Medicine, Showa University School of Medicine, Shinagawa, Tokyo 142-8555, Japan (M.T.); (N.O.); (Y.O.-K.); (T.O.)
| | - Michishige Terasaki
- Division of Diabetes, Metabolism, and Endocrinology, Department of Medicine, Showa University School of Medicine, Shinagawa, Tokyo 142-8555, Japan (M.T.); (N.O.); (Y.O.-K.); (T.O.)
| | - Naoya Osaka
- Division of Diabetes, Metabolism, and Endocrinology, Department of Medicine, Showa University School of Medicine, Shinagawa, Tokyo 142-8555, Japan (M.T.); (N.O.); (Y.O.-K.); (T.O.)
| | - Hironori Yashima
- Division of Diabetes, Metabolism, and Endocrinology, Department of Medicine, Showa University School of Medicine, Shinagawa, Tokyo 142-8555, Japan (M.T.); (N.O.); (Y.O.-K.); (T.O.)
| | - Tomomi Saito
- Division of Diabetes, Metabolism, and Endocrinology, Department of Medicine, Showa University School of Medicine, Shinagawa, Tokyo 142-8555, Japan (M.T.); (N.O.); (Y.O.-K.); (T.O.)
| | - Yurie Otoyama-Kataoka
- Division of Diabetes, Metabolism, and Endocrinology, Department of Medicine, Showa University School of Medicine, Shinagawa, Tokyo 142-8555, Japan (M.T.); (N.O.); (Y.O.-K.); (T.O.)
| | - Takemasa Omachi
- Division of Diabetes, Metabolism, and Endocrinology, Department of Medicine, Showa University School of Medicine, Shinagawa, Tokyo 142-8555, Japan (M.T.); (N.O.); (Y.O.-K.); (T.O.)
| | - Yuichiro Higashimoto
- Department of Chemistry, Kurume University School of Medicine, Kurume 830-0011, Fukuoka, Japan;
| | - Takanori Matsui
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji 910-1195, Fukui, Japan
| | - Tomoyasu Fukui
- Division of Diabetes, Metabolism, and Endocrinology, Department of Medicine, Showa University School of Medicine, Shinagawa, Tokyo 142-8555, Japan (M.T.); (N.O.); (Y.O.-K.); (T.O.)
| | - Sho-ichi Yamagishi
- Division of Diabetes, Metabolism, and Endocrinology, Department of Medicine, Showa University School of Medicine, Shinagawa, Tokyo 142-8555, Japan (M.T.); (N.O.); (Y.O.-K.); (T.O.)
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13
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Manfredini A, Malusà E, Canfora L. Aptamer-based technology for detecting Bacillus subtilis in soil. Appl Microbiol Biotechnol 2023; 107:6963-6972. [PMID: 37698608 DOI: 10.1007/s00253-023-12765-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/12/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
The uncertainty associated with the impact of a bioinoculant on soil microbial community and, as a consequence, on soil quality, as well as the need to define its persistence, has prompted the demand for an accurate detection and tracking of the presence and the quantification of a target microbial inoculant in soil. Although DNA or RNA-based molecular detection are well established and commonly applied in this regard, alternative ligands such as DNA-aptamers have several advantages over them, such as low cost, ease of modification, ease of immobilisation on lab-on-chip or nanosensors, high stability and not thermolability. In this study, we used a toggle-cell SELEX method to isolate, select and characterise ssDNA (single-strand DNA) aptamers to detect a Bacillus subtilis strain which is being tested as a plant growth promoting rhizobacteria (PGPR) formulation. Two ssDNA aptamers (patenting application n.102022000022590) showed strong affinity and specificity for B. subtilis strains, with values of the kinetic parameters Kd (dissociation constant) in the nanomolar range and Bmax (maximum intensity of binding) around 1. Validation of the suitability of the aptamers was validated on three inoculated soils characterised by different chemical-physical features and in soil from a field trial with the formulated B. subtilis PCM/B 00105 strain. These are considered significant features to monitor B. subtilis strains in soil, practical to optimise bioinoculant application methods, support regulatory processes and foster the shift of agricultural production toward more sustainable cropping systems. KEY POINTS: • First DNA aptamers binding a B. subtilis strain included in a bioinoculum formulation. • First DNA aptamer binding B. subtilis in soil. • Aptamer may be a method for microbial inoculant detection in soil.
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Affiliation(s)
| | - Eligio Malusà
- CREA Centro di Ricerca Viticoltura ed Enologia, 31015, Conegliano, Italy
- National Institute of Horticultural Research, 96-100, Skierniewice, Poland
| | - Loredana Canfora
- CREA Centro di Ricerca Agricoltura e Ambiente, 00184, Rome, Italy
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14
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Lee S, Ahn HJ, Park YS, Kim JH, Kim YS, Cho JJ, Park CS. NXP081, DNA Aptamer-Vitamin C Complex Ameliorates DNFB-Induced Atopic Dermatitis in Balb/c Mice. Nutrients 2023; 15:4172. [PMID: 37836456 PMCID: PMC10574402 DOI: 10.3390/nu15194172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Atopic dermatitis (AD) is a chronic inflammatory disease characterized by dry and itchy skin. Recently, it has been reported that oxidative stress is involved in skin diseases, possibly including AD. Vitamin C, also referred to as ascorbic acid, is a vital water-soluble compound that functions as an essential nutrient. It plays a significant role as both an antioxidant and an additive in various pharmaceutical and food products. Despite the fact that vitamin C is easily oxidized, we have developed NXP081, a single-stranded DNA aptamer that selectively binds to vitamin C, thereby inhibiting its oxidation. The objective of the current research was to examine the impact of NXP081, an animal model of AD induced by 2,4-dinitrofluorobenzene (DNFB). The experimental drug NXP081, when taken orally, showed promising results in reducing inflammation and improving the skin conditions caused by DNFB. The administration of NXP081 resulted in a significant reduction in ear swelling and a noticeable improvement in the appearance of skin lesions. In addition, the administration of NXP081 resulted in a significant decrease in the migration of mast cells in the skin lesions induced by DNFB. Moreover, NXP081 inhibited the production of interferon-gamma (IFN-γ) in CD4+ T cells that were activated and derived from the lymph nodes. Our findings provide useful information about the anti-inflammatory effect of NXP081 on AD.
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Affiliation(s)
- Sanggon Lee
- Department of Microbiology, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (S.L.); (H.-J.A.); (Y.S.P.); (J.-J.C.)
| | - Hyun-Jong Ahn
- Department of Microbiology, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (S.L.); (H.-J.A.); (Y.S.P.); (J.-J.C.)
| | - Yong Seek Park
- Department of Microbiology, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (S.L.); (H.-J.A.); (Y.S.P.); (J.-J.C.)
| | - Ji-Hyun Kim
- Nexmos Co., Ltd., U-Tower, 767, Sinsu-ro, Yongin-si 16827, Republic of Korea; (J.-H.K.); (Y.-S.K.)
| | - Yoon-Seong Kim
- Nexmos Co., Ltd., U-Tower, 767, Sinsu-ro, Yongin-si 16827, Republic of Korea; (J.-H.K.); (Y.-S.K.)
| | - Jeong-Je Cho
- Department of Microbiology, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (S.L.); (H.-J.A.); (Y.S.P.); (J.-J.C.)
| | - Cheung-Seog Park
- Department of Microbiology, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (S.L.); (H.-J.A.); (Y.S.P.); (J.-J.C.)
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15
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Zhang Y, Xing H, Bolotnikov G, Krämer M, Gotzmann N, Knippschild U, Kissmann AK, Rosenau F. Enriched Aptamer Libraries in Fluorescence-Based Assays for Rikenella microfusus-Specific Gut Microbiome Analyses. Microorganisms 2023; 11:2266. [PMID: 37764110 PMCID: PMC10535755 DOI: 10.3390/microorganisms11092266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/29/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Rikenella microfusus is an essential intestinal probiotic with great potential. The latest research shows that imbalance in the intestinal flora are related to the occurrence of various diseases, such as intestinal diseases, immune diseases, and metabolic diseases. Rikenella may be a target or biomarker for some diseases, providing a new possibility for preventing and treating these diseases by monitoring and optimizing the abundance of Rikenella in the intestine. However, the current monitoring methods have disadvantages, such as long detection times, complicated operations, and high costs, which seriously limit the possibility of clinical application of microbiome-based treatment options. Therefore, the intention of this study was to evolve an enriched aptamer library to be used for specific labeling of R. microfusus, allowing rapid and low-cost detection methods and, ultimately the construction of aptamer-based biosensors. In this study, we used Rikenella as the target bacterium for an in vitro whole Cell-SELEX (Systematic Evolution of Ligands by EXponential Enrichment) to evolve and enrich specific DNA oligonucleotide aptamers. Five other prominent anaerobic gut bacteria were included in this process for counterselection and served as control cells. The aptamer library R.m-R13 was evolved with high specificity and strong affinity (Kd = 9.597 nM after 13 rounds of selection). With this enriched aptamer library, R. microfusus could efficiently be discriminated from the control bacteria in complex mixtures using different analysis techniques, including fluorescence microscopy or fluorometric suspension assays, and even in human stool samples. These preliminary results open new avenues toward the development of aptamer-based microbiome bio-sensing applications for fast and reliable monitoring of R. microfusus.
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Affiliation(s)
- Yiting Zhang
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Hu Xing
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Grigory Bolotnikov
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Nina Gotzmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Surgery Center, Ulm University, Albert-Einstein-Allee 23, 89081 Ulm, Germany;
| | - Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
- Max-Planck-Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
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Garaiová Z, Gašperová M, Šubjaková V, Hianik T. Interaction of G-quadruplex Forming DNA Aptamers with PAMAM Dendrimers Studied by Dynamic Light Scattering and UV-VIS Spectrophotometry. Chemphyschem 2023; 24:e202300264. [PMID: 37318900 DOI: 10.1002/cphc.202300264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
The complexes of G-quadruplex forming DNA thrombin binding aptamers (TBA) and polyamidoamine dendrimers (PAMAM) were studied with the aim to form a model targeted drug delivery system. Hydrodynamic diameter, zeta potential and melting temperature (Tm ) were investigated by dynamic light scattering and UV-VIS spectrophotometry. Non-covalent adsorption by means of electrostatic interaction between positively charged amino groups of dendrimers (+) and negatively charged phosphate groups of aptamers (-) has driven the formation of aggregates. The size of complexes was in the range of 0.2-2 μm and depended on the type of dispersant, charge ratio (+/-) and temperature. Raising the temperature increased the polydispersity, new smaller size distributions were observed indicating the G-quadruplex unfolding. The melting transition temperature of TBA aptamer was affected by the presence of amino-terminated PAMAM rather than carboxylated succinic acid PAMAM-SAH dendrimer, thus supporting the electrostatic nature of interaction that disturbed denaturation of target-specific quadruplex aptamer structure.
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Affiliation(s)
- Zuzana Garaiová
- Department of Nuclear Physics and Biophysics Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 842 48, Bratislava, Slovakia
| | - Martina Gašperová
- Department of Nuclear Physics and Biophysics Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 842 48, Bratislava, Slovakia
| | - Veronika Šubjaková
- Department of Nuclear Physics and Biophysics Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 842 48, Bratislava, Slovakia
| | - Tibor Hianik
- Department of Nuclear Physics and Biophysics Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 842 48, Bratislava, Slovakia
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Liu Y, Hu B, Pei X, Li J, Qi D, Xu Y, Ou H, Wu Y, Xue L, Huang JH, Wu E, Hu X. A Non-G-Quadruplex DNA Aptamer Targeting NCL for Diagnosis and Therapy in Bladder Cancer. Adv Healthc Mater 2023; 12:e2300791. [PMID: 37262080 DOI: 10.1002/adhm.202300791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Indexed: 06/03/2023]
Abstract
Bladder cancer (BC) is a highly aggressive malignant tumor affecting the urinary system, characterized by metastasis and a poor prognosis that often leads to limited therapeutic success. This study aims to develop a novel DNA aptamer for the diagnosis and treatment of BC using a tissue-based systematic evolution of ligands by an exponential enrichment (SELEX) process. By using SELEX, this work successfully generates a new aptamer named TB-5, which demonstrates a remarkable and specific affinity for nucleolin (NCL) in BC tissues and displays marked biocompatibility both in vitro and in vivo. Additionally, this work shows that NCL is a reliable tissue-specific biomarker in BC. Moreover, according to circular dichroism spectroscopy, TB-5 forms a non-G-quadruplex structure, distinguishing it from the current NCL-targeting aptamer AS1411, and exhibits a distinct binding region on NCL compared to AS1411. Notably, this study further reveals that TB-5 activates NCL function by promoting autophagy and suppressing the migration and invasion of BC cells, which occurs by disrupting mRNA transcription processes. These findings highlight the critical role of NCL in the pathological examination of BC and warrant more comprehensive investigations on anti-NCL aptamers in BC imaging and treatment.
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Affiliation(s)
- Yunyi Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Bei Hu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Xiaming Pei
- Department of Urology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine. Changsha, Hunan, 410013, China
| | - Juan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Dan Qi
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA
| | - Yuxi Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Hailong Ou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Yatao Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Lei Xue
- Department of Pathology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine. Changsha, Hunan, 410013, China
| | - Jason H Huang
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA
- Department of Medical Education, Texas A&M University School of Medicine, College Station, TX, 77843, USA
| | - Erxi Wu
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA
- Department of Medical Education, Texas A&M University School of Medicine, College Station, TX, 77843, USA
- Department of Pharmaceutical Sciences, Texas A&M University School of Pharmacy, College Station, TX, 77843, USA
- LIVESTRONG Cancer Institutes and Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Xiaoxiao Hu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Research Institute of Hunan University in Chongqing, Chongqing, 401120, China
- Shenzhen Research Institute, Hunan University, Shenzhen, Guangdong, 518000, China
- Hunan Yonghe-sun Biotechnology Co. Ltd., Changsha, Hunan, 410082, China
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18
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Mizunuma M, Suzuki M, Kobayashi T, Hara Y, Kaneko A, Furukawa K, Chuman Y. Development of Mn 2+-Specific Biosensor Using G-Quadruplex-Based DNA. Int J Mol Sci 2023; 24:11556. [PMID: 37511324 PMCID: PMC10380348 DOI: 10.3390/ijms241411556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Metal ions are used in various situations in living organisms and as a part of functional materials. Since the excessive intake of metal ions can cause health hazards and environmental pollution, the development of new molecules that can monitor metal ion concentrations with high sensitivity and selectivity is strongly desired. DNA can form various structures, and these structures and their properties have been used in a wide range of fields, including materials, sensors, and drugs. Guanine-rich sequences respond to metal ions and form G-quadruplex structures and G-wires, which are the self-assembling macromolecules of G-quadruplex structures. Therefore, guanine-rich DNA can be applied to a metal ion-detection sensor and functional materials. In this study, the IRDAptamer library originally designed based on G-quadruplex structures was used to screen for Mn2+, which is known to induce neurodegenerative diseases. Circular dichroism and fluorescence analysis using Thioflavin T showed that the identified IRDAptamer sequence designated MnG4C1 forms a non-canonical G-quadruplex structure in response to low concentrations of Mn2+. A serum resistance and thermostability analysis revealed that MnG4C1 acquired stability in a Mn2+-dependent manner. A Förster resonance energy transfer (FRET) system using fluorescent molecules attached to the termini of MnG4C1 showed that FRET was effectively induced based on Mn2+-dependent conformational changes, and the limit of detection (LOD) was 0.76 µM for Mn2+. These results suggested that MnG4C1 can be used as a novel DNA-based Mn2+-detecting molecule.
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Affiliation(s)
- Masataka Mizunuma
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Mirai Suzuki
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Tamaki Kobayashi
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Yuki Hara
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Atsushi Kaneko
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Kazuhiro Furukawa
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Yoshiro Chuman
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
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19
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Lin YD, Zida SI, Yang CC, Khung YL. VEGF Detection via Impedance Spectroscopy on Surface Functionalized Interdigitated Biosensor. J Funct Biomater 2023; 14:365. [PMID: 37504860 PMCID: PMC10381268 DOI: 10.3390/jfb14070365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023] Open
Abstract
Vascular endothelial growth factor (VEGF), a clinically important biomarker, often plays a key role in angiogenesis, would healing, tumor growth, lung development, and in retinal diseases. Hence, detecting and quantifying VEGF is deemed medically important in clinical diagnosis for many diseases. In this report, a simple yet highly cost-effective platform was proposed for VEGF protein detection using commercially available interdigitated sensors that are surface modified to present DNA optimally for VEGF capture. The dielectric characteristics between the fingers of the sensor were modulated by the negatively charged aptamer-VEGF capture, and the impedance was estimated using an impedance analyzer. Impedance-spectra tests were compared among pristine unmodified surfaces, functionalized monolayer surfaces, and aptamer-grafted surfaces in order to evaluate the efficacy of VEGF detection. From our results, the sensitivity experiments as conducted showed the ability of the interdigitated sensor to detect VEGF at a low concentration of 5 pM (200 pg/mL). The specificity of the functionalized sensor in detecting VEGF was further examined by comparing the impedance to platelet-derived growth factor, and the results confirm the specificity of the sensor. Finally, the Nyquist plot of impedance spectra was also presented to help data visualization and the overall performance of the device was found to be a highly suitable template for a smart biosensor for the detection of VEGF.
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Affiliation(s)
- Yue-Der Lin
- Ph.D. Program of Electrical and Communications Engineering, Feng Chia University, No. 100, Wenhwa Road, Seatwen, Taichung 40724, Taiwan
- Master's Program of Biomedical Informatics and Biomedical Engineering, Feng Chia University, No. 100, Wenhwa Road, Seatwen, Taichung 40724, Taiwan
- Department of Automatic Control Engineering, Feng Chia University, No. 100, Wenhwa Road, Seatwen, Taichung 40724, Taiwan
| | - Serge Ismael Zida
- Ph.D. Program of Electrical and Communications Engineering, Feng Chia University, No. 100, Wenhwa Road, Seatwen, Taichung 40724, Taiwan
| | - Chu-Chun Yang
- Master's Program of Biomedical Informatics and Biomedical Engineering, Feng Chia University, No. 100, Wenhwa Road, Seatwen, Taichung 40724, Taiwan
| | - Yit Lung Khung
- Department of Biological Science and Technology, China Medical University, No. 100, Section 1, Jingmao Road, Beitun District, Taichung 406040, Taiwan
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20
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Spagnolo S, Davoudian K, De La Franier B, Hianik T, Thompson M. Staphylococcus aureus Detection in Milk Using a Thickness Shear Mode Acoustic Aptasensor with an Antifouling Probe Linker. Biosensors (Basel) 2023; 13:614. [PMID: 37366979 DOI: 10.3390/bios13060614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023]
Abstract
Contamination of food by pathogens can pose a serious risk to health. Therefore, monitoring for the presence of pathogens is critical to identify and regulate microbiological contamination of food. In this work, an aptasensor based on a thickness shear mode acoustic method (TSM) with dissipation monitoring was developed to detect and quantify Staphylococcus aureus directly in whole UHT cow's milk. The frequency variation and dissipation data demonstrated the correct immobilization of the components. The analysis of viscoelastic properties suggests that DNA aptamers bind to the surface in a non-dense manner, which favors the binding with bacteria. The aptasensor demonstrated high sensitivity and was able to detect S. aureus in milk with a 33 CFU/mL limit of detection. Analysis was successful in milk due to the sensor's antifouling properties, which is based on 3-dithiothreitol propanoic acid (DTTCOOH) antifouling thiol linker. Compared to bare and modified (dithiothreitol (DTT), 11-mercaptoundecanoic acid (MUA), and 1-undecanethiol (UDT)) quartz crystals, the sensitivity of the sensor's antifouling in milk improved by about 82-96%. The excellent sensitivity and ability to detect and quantify S. aureus in whole UHT cow's milk demonstrates that the system is applicable for rapid and efficient analysis of milk safety.
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Affiliation(s)
- Sandro Spagnolo
- Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská Dolina F1, 84248 Bratislava, Slovakia
| | - Katharina Davoudian
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S3H6, Canada
| | - Brian De La Franier
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S3H6, Canada
| | - Tibor Hianik
- Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská Dolina F1, 84248 Bratislava, Slovakia
| | - Michael Thompson
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S3H6, Canada
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21
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Gao Z, Wang Y, Wang H, Li X, Xu Y, Qiu J. Recent Aptamer-Based Biosensors for Cd 2+ Detection. Biosensors (Basel) 2023; 13:612. [PMID: 37366977 DOI: 10.3390/bios13060612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023]
Abstract
Cd2+, a major environmental pollutant, is heavily toxic to human health. Many traditional techniques are high-cost and complicated; thus, developing a simple, sensitive, convenient, and cheap monitoring approach is necessary. The aptamer can be obtained from a novel method called SELEX, which is widely used as a DNA biosensor for its easy acquisition and high affinity of the target, especially for heavy metal ions detection, such as Cd2+. In recent years, highly stable Cd2+ aptamer oligonucleotides (CAOs) were observed, and electrochemical, fluorescent, and colorimetric biosensors based on aptamers have been designed to monitor Cd2+. In addition, the monitoring sensitivity of aptamer-based biosensors is improved with signal amplification mechanisms such as hybridization chain reactions and enzyme-free methods. This paper reviews approaches to building biosensors for inspecting Cd2+ by electrochemical, fluorescent, and colorimetric methods. Finally, many practical applications of sensors and their implications for humans and the environment are discussed.
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Affiliation(s)
- Zihan Gao
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yin Wang
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Haijian Wang
- Hangzhou Alltest Biotech Co., Ltd., Hangzhou 310000, China
| | - Xiangxiang Li
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Youyang Xu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jieqiong Qiu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
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22
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Won A, Choi S, Kim A, Hong J. Effect of DNA aptamer through blocking of negative regulation of Wnt/β-catenin signaling in human hair follicle dermal papilla cells. Skin Res Technol 2023; 29:e13326. [PMID: 37231925 PMCID: PMC10182398 DOI: 10.1111/srt.13326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/03/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND When Wnt binds to the N-terminal of Frizzled, a conformational change occurs in the C-terminal of Frizzled, which binds to Dishevelled1 (Dvl1), a Wnt signaling component protein. When Dvl1 binds to the C-terminal of Frizzled, the concentration of β-catenin increases and it enters the nucleus to transmit cell proliferation signals. CXXC-type zinc finger protein 5 (CXXC5) binds to the Frizzled binding site of Dvl1 and interferes with Dvl1-Frizzled binding. Therefore, blocking CXXC5-Dvl1 binding may induce Wnt signal transduction. MATERIALS AND METHODS We used WD-aptamer, a DNA aptamer that specifically binds to Dvl1 and interferes with CXXC5-Dvl1 interaction. We confirmed the penetration of WD-aptamer into human hair follicle dermal papilla cells (HFDPCs) and measured β-catenin expression following treatment with WD-aptamer in HFDPCs, wherein Wnt signaling was activated by Wnt3a. In addition, MTT assay was performed to investigate the effect of WD-aptamer on cell proliferation. RESULTS WD-aptamer penetrated the cell, affected Wnt signaling, and increased β-catenin expression, which plays an important role in signaling. Additionally, WD-aptamer induced HFDPC proliferation. CONCLUSION CXXC5-associated negative feedback of Wnt/β-catenin signaling can be regulated by interfering with CXXC5-Dvl1 interaction.
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Affiliation(s)
- Areum Won
- Nexmos, Inc.Sinsu‐ro, Suji‐guYongin‐siGyeonggi‐doRepublic of Korea
| | - Sooho Choi
- Nexmos, Inc.Sinsu‐ro, Suji‐guYongin‐siGyeonggi‐doRepublic of Korea
| | - A‐Ru Kim
- Nexmos, Inc.Sinsu‐ro, Suji‐guYongin‐siGyeonggi‐doRepublic of Korea
| | - Junkee Hong
- Nexmos, Inc.Sinsu‐ro, Suji‐guYongin‐siGyeonggi‐doRepublic of Korea
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23
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Gao S, Yang G, Zhang X, Shi R, Chen R, Zhang X, Peng Y, Yang H, Lu Y, Song C. β-Cyclodextrin Polymer-Based Fluorescence Enhancement Strategy via Host-Guest Interaction for Sensitive Assay of SARS-CoV-2. Int J Mol Sci 2023; 24:ijms24087174. [PMID: 37108336 PMCID: PMC10139410 DOI: 10.3390/ijms24087174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/01/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Nucleocapsid protein (N protein) is an appropriate target for early determination of viral antigen-based severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We have found that β-cyclodextrin polymer (β-CDP) has shown a significant fluorescence enhancement effect for fluorophore pyrene via host-guest interaction. Herein, we developed a sensitive and selective N protein-sensing method that combined the host-guest interaction fluorescence enhancement strategy with high recognition of aptamer. The DNA aptamer of N protein modified with pyrene at its 3' terminal was designed as the sensing probe. The added exonuclease I (Exo I) could digest the probe, and the obtained free pyrene as a guest could easily enter into the hydrophobic cavity of host β-CDP, thus inducing outstanding luminescent enhancement. While in the presence of N protein, the probe could combine with it to form a complex owing to the high affinity between the aptamer and the target, which prevented the digestion of Exo I. The steric hindrance of the complex prevented pyrene from entering the cavity of β-CDP, resulting in a tiny fluorescence change. N protein has been selectively analyzed with a low detection limit (11.27 nM) through the detection of the fluorescence intensity. Moreover, the sensing of spiked N protein from human serum and throat swabs samples of three volunteers has been achieved. These results indicated that our proposed method has broad application prospects for early diagnosis of coronavirus disease 2019.
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Affiliation(s)
- Shanshan Gao
- Department of Applied Chemistry, School of Science, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Hefei 230036, China
| | - Gege Yang
- Department of Applied Chemistry, School of Science, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Hefei 230036, China
| | - Xiaohui Zhang
- Department of Applied Chemistry, School of Science, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
| | - Rui Shi
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Rongrong Chen
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Xin Zhang
- Department of Applied Chemistry, School of Science, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
| | - Yuancheng Peng
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Hua Yang
- Department of Applied Chemistry, School of Science, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Hefei 230036, China
| | - Ying Lu
- Department of Applied Chemistry, School of Science, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
| | - Chunxia Song
- Department of Applied Chemistry, School of Science, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Hefei 230036, China
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24
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Kim HR, Kim BC. Development of multi-reactive aptamers for Cronobacter spp. using the sequential partitioning method to detect them in powdered infant formula. Anal Chim Acta 2023; 1249:340935. [PMID: 36868770 DOI: 10.1016/j.aca.2023.340935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Cronobacter spp. are opportunistic foodborne pathogens typically detected in contaminated powdered infant formula (PIF). Thus, the rapid detection and control of Cronobacter spp. are required to prevent outbreaks, necessitating the development of specific aptamers. In this study, we isolated aptamers specific to all seven species of Cronobacter (C. sakazakii, C. malonaticus, C. turicensis, C. muytjensii, C. dublinensis, C. condimenti, and C. universalis) using a newly proposed sequential partitioning method. This method avoids the repeated enrichment steps, reducing the total aptamer selection time compared with the conventional systematic evolution of ligands by the exponential enrichment (SELEX) process. We isolated four aptamers showing high affinity and specificity for all seven species of Cronobacter, with dissociation constants of 3.7-86.6 nM. This represents the first successful isolation of aptamers for multiple targets using the sequential partitioning method. Further, the selected aptamers could effectively detect Cronobacter spp. in contaminated PIF.
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Affiliation(s)
- Hye Ri Kim
- Center for Sustainable Environment Research, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Byoung Chan Kim
- Center for Sustainable Environment Research, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea.
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25
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Kakkar S, Chauhan S, Bharti, Rohit M, Bhalla V. Conformational switching of aptamer biointerfacing graphene-gold nanohybrid for ultrasensitive label-free sensing of cardiac Troponin I. Bioelectrochemistry 2023; 150:108348. [PMID: 36521370 DOI: 10.1016/j.bioelechem.2022.108348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
The development of hybrid biofunctionalized nanomaterials has emerged as an attractive substitute for development of advanced biosensing platforms with superior synergistic properties. Herein, we report a label-free ultrasensitive electrochemical aptasensor comprising nanohybrid of graphene oxide (GO) and aptamer conjugated gold nanoparticles (GNP-A) for detection of cardiac biomarker Troponin I (TnI). The GNP-A are homogenously arranged by self-assembly on GO sheet to construct nanohybrid (GO@GNP-A) onto which the biomarker protein is analysed. TnI interactions at the aptamer biointerfaced nanohybrid surface causes electrochemical signal enhancement probed by using a redox active molecule. The consecutive increase in current signal is strongly attributed to conformational switching of aptamer and charge neutralization at the interface induced by TnI binding. The sensitivity of the nanohybrid aptasensor platform was found to be 0.001 pg/mL. The study has been further substantiated in Acute Myocardial Infarction (AMI) clinical samples for usage towards early, sensitive and efficient point-of-care detection of TnI.
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26
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Molejon NA, Lapada CM, Skouridou V, Rollon AP, El-Shahawi M, Bashammakh A, O'Sullivan CK. Selection of G-rich ss DNA aptamers for the detection of enterotoxins of the cholera toxin family. Anal Biochem 2023; 669:115118. [PMID: 36963555 DOI: 10.1016/j.ab.2023.115118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/26/2023]
Abstract
Cholera and milder diarrheal disease are caused by Vibrio cholerae and enterotoxigenic Escherichia coli and are still a prominent public health concern. Evaluation of suspicious isolates is essential for the rapid containment of acute diarrhea outbreaks or prevention of epidemic cholera. Existing detection techniques require expensive equipment, trained personnel and are time-consuming. Antibody-based methods are also available, but cost and stability issues can limit their applications for point-of-care testing. This study focused on the selection of single stranded DNA aptamers as simpler, more stable and more cost-effective alternatives to antibodies for the co-detection of AB5 toxins secreted by enterobacteria causing acute diarrheal infections. Cholera toxin and Escherichia coli heat-labile enterotoxin, the key toxigenicity biomarkers of these bacteria, were immobilized on magnetic beads and were used in a SELEX-based selection strategy. This led to the enrichment of sequences with a high % GC content and a dominant G-rich motif as revealed by Next Generation Sequencing. Enriched sequences were confirmed to fold into G-quadruplex structures and the binding of one of the most abundant candidates to the two enterotoxins was confirmed. Ongoing work is focused on the development of monitoring tools for potential environmental surveillance of epidemic choleraand milder diarrheal disease.
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Affiliation(s)
- Nerissa A Molejon
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Catherine M Lapada
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Vasso Skouridou
- Interfibio Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007, Tarragona, Spain.
| | - Analiza P Rollon
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Mohammed El-Shahawi
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Abdulaziz Bashammakh
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Ciara K O'Sullivan
- Interfibio Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007, Tarragona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010, Barcelona, Spain.
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27
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Kim ST, Kim HG, Kim YM, Han HS, Cho JH, Lim SC, Lee T, Jahng GH. An aptamer-based magnetic resonance imaging contrast agent for detecting oligomeric amyloid-β in the brain of an Alzheimer's disease mouse model. NMR Biomed 2023; 36:e4862. [PMID: 36308279 DOI: 10.1002/nbm.4862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
The oligomeric amyloid-β (oAβ) is a reliable feature for an early diagnosis of Alzheimer's disease (AD). Therefore, the objective of this study was to demonstrate imaging of oAβ deposits using our developed DNA aptamer called ob5 conjugated with gadolinium (Gd)-dodecane tetraacetic acid (DOTA) as a contrast agent for early diagnosis of AD using MRI. An oAβ-specific aptamer was developed by amide bond formation and conjugated to Gd-DOTA MRI contrast agent and/or cyanine5 (cy5). We verified the performance of our new contrast agent with an AD mouse model using in vivo and ex vivo fluorescent imaging and animal MRI experiments. The presence of soluble Aβ in 3xTg AD mice was detected using GdDOTA-ob5-cy5 probe ex vivo. Fluorescence intensities of the GdDOTA-ob5-cy5 contrast agent were high in the brains of 3xTg-AD mice, but relatively low in the brains of control mice. The GdDOTA-ob5 contrast agent had higher relaxivity than a clinically available contrast agent. T1-weighted MRI signals in 5-month-old 3xTg AD mice increased at 5 min, were prolonged until 10 min, then decreased 15 min after injecting the GdDOTA-ob5 contrast agent. Our targeted DNA aptamer GdDOTA-ob5 contrast agent could be potentially useful for validating the efficacy of a novel diagnostic contrast agent for selectively targeting neurotoxic oAβ. It could ultimately be used for early diagnosis of AD.
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Affiliation(s)
- Sang-Tae Kim
- Neuroscience of Lab., Biomedical Research Institute, Seoul National University College of Medicine, Seongnam City, Geonggido, Republic of Korea
| | - Hyug-Gi Kim
- Department of Radiology, Kyung Hee University Hospital, Seoul, Republic of Korea
| | - Yu Mi Kim
- Neuroscience of Lab., Biomedical Research Institute, Seoul National University College of Medicine, Seongnam City, Geonggido, Republic of Korea
| | - Ho-Seong Han
- Department of Surgery, Bundang Hospital of Seoul National University, Seongnam City, Kyunggeedo, Republic of Korea
| | - Jee-Hyun Cho
- Research Equipment Operations Division, Korea Basic Science Institute, Cheongju-si, Chungcheongbuk-do, Republic of Korea
| | - Sung-Chul Lim
- Department of Pathology, Chosun University Medical School, Gwangju, Republic of Korea
- Department of Education & Research, Chosun University Hospital, Gwangju, Republic of Korea
| | - Taekwan Lee
- Brain Research Core Facility, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Geon-Ho Jahng
- Department of Radiology, Kyung Hee University Hospital at Gangdong, Seoul, Republic of Korea
- Department of Medicine, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
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Yeoh TS, Tang TH, Citartan M. Isolation of a novel DNA aptamer against LipL32 as a potential diagnostic agent for the detection of pathogenic Leptospira. Biotechnol J 2023; 18:e2200418. [PMID: 36426669 DOI: 10.1002/biot.202200418] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022]
Abstract
Leptospirosis is a potentially life-threatening zoonosis caused by pathogenic Leptospira and for rapid diagnostics, direct detection is desirable. LipL32 protein is the most suitable biomarker for direct detection. DNA aptamers are sought to be generated against LipL32 by Systemic Evolution of Ligands via Exponential Enrichment (SELEX). LepDapt-5a is the most potent aptamer candidate among all the candidates, as determined by direct Enzyme-linked Aptasorbent Assay (ELASA). LepDapt-5a was predicted to form a G-quadruplex structure as predicted by QGRS Mapper and validated experimentally by direct ELASA. The diagnostic potential of the aptamer was further tested on a direct and sandwich ELASA platform. A LOD of 106 mL-1 and 105 mL-1 were estimated by direct and sandwich ELASA platforms, respectively, which are within the range associated with leptospiremia levels. The dot blot assay developed was able to attain a LOD of 104 CFU mL-1 against pathogenic Leptospira, which is also within the leptospiremia level. This is the first-ever DNA aptamer and hybrid-heterodimeric aptamer constructed against LipL32. The diagnostic potentiality of the LepDapt-5a DNA aptamer was proven on three major diagnostic platforms, which are direct ELASA, sandwich ELASA, and aptamer-based dot assay.
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Affiliation(s)
- Tzi Shien Yeoh
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia
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Kimoto M, Tan HP, Tan YS, Mislan NABM, Hirao I. Success probability of high-affinity DNA aptamer generation by genetic alphabet expansion. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220031. [PMID: 36633272 PMCID: PMC9835594 DOI: 10.1098/rstb.2022.0031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Nucleic acid aptamers as antibody alternatives bind specifically to target molecules. These aptamers are generated by isolating candidates from libraries with random sequence fragments, through an evolutionary engineering system. We recently reported a high-affinity DNA aptamer generation method that introduces unnatural bases (UBs) as a fifth letter into the library, by genetic alphabet expansion. By incorporating hydrophobic UBs, the affinities of DNA aptamers to target proteins are increased over 100-fold, as compared with those of conventional aptamers with only the natural four letters. However, there is still plenty of room for improvement of the methods for routinely generating high-affinity UB-containing DNA (UB-DNA) aptamers. The success probabilities of the high-affinity aptamer generation depend on the existence of the aptamer candidate sequences in the initial library. We estimated the success probabilities by analysing several UB-DNA aptamers that we generated, as examples. In addition, we investigated the possible improvement of conventional aptamer affinities by introducing one UB at specific positions. Our data revealed that UB-DNA aptamers adopt specific tertiary structures, in which many bases including UBs interact with target proteins for high affinity, suggesting the importance of the UB-DNA library design. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Michiko Kimoto
- Xenolis Pte Ltd, 79 Science Park Drive, #06-01/08, Cintech IV, Singapore 118264, Singapore,Institute of Bioengineering and Bioimaging, Agency for Science, Technologyand Research (A*STAR), 31 Biopolis Way, #07-01 Nanos, Singapore 138669, Singapore
| | - Hui Pen Tan
- Xenolis Pte Ltd, 79 Science Park Drive, #06-01/08, Cintech IV, Singapore 118264, Singapore,Institute of Bioengineering and Bioimaging, Agency for Science, Technologyand Research (A*STAR), 31 Biopolis Way, #07-01 Nanos, Singapore 138669, Singapore
| | - Yaw Sing Tan
- Xenolis Pte Ltd, 79 Science Park Drive, #06-01/08, Cintech IV, Singapore 118264, Singapore,Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Nur Afiqah Binte Mohd Mislan
- Xenolis Pte Ltd, 79 Science Park Drive, #06-01/08, Cintech IV, Singapore 118264, Singapore,Institute of Bioengineering and Bioimaging, Agency for Science, Technologyand Research (A*STAR), 31 Biopolis Way, #07-01 Nanos, Singapore 138669, Singapore
| | - Ichiro Hirao
- Xenolis Pte Ltd, 79 Science Park Drive, #06-01/08, Cintech IV, Singapore 118264, Singapore,Institute of Bioengineering and Bioimaging, Agency for Science, Technologyand Research (A*STAR), 31 Biopolis Way, #07-01 Nanos, Singapore 138669, Singapore
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30
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Cao M, Vial A, Minder L, Guédin A, Fribourg S, Azéma L, Feuillie C, Molinari M, Di Primo C, Barthélémy P, Jeanne LC. Aptamer-based nanotrains and nanoflowers as quinine delivery systems. Int J Pharm X 2023; 5:100172. [PMID: 36861067 PMCID: PMC9969250 DOI: 10.1016/j.ijpx.2023.100172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
In this study, we designed aptamer-based self-assemblies for the delivery of quinine. Two different architectures were designed by hybridizing quinine binding aptamers and aptamers targeting Plasmodium falciparum lactate dehydrogenase (PfLDH): nanotrains and nanoflowers. Nanotrains consisted in controlled assembly of quinine binding aptamers through base-pairing linkers. Nanoflowers were larger assemblies obtained by Rolling Cycle Amplification of a quinine binding aptamer template. Self-assembly was confirmed by PAGE, AFM and cryoSEM. The nanotrains preserved their affinity for quinine and exhibited a higher drug selectivity than nanoflowers. Both demonstrated serum stability, hemocompatibility, low cytotoxicity or caspase activity but nanotrains were better tolerated than nanoflowers in the presence of quinine. Flanked with locomotive aptamers, the nanotrains maintained their targeting ability to the protein PfLDH as analyzed by EMSA and SPR experiments. To summarize, nanoflowers were large assemblies with high drug loading ability, but their gelating and aggregating properties prevent from precise characterization and impaired the cell viability in the presence of quinine. On the other hand, nanotrains were assembled in a selective way. They retain their affinity and specificity for the drug quinine, and their safety profile as well as their targeting ability hold promise for their use as drug delivery systems.
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Affiliation(s)
- Mengyuan Cao
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France,Corresponding authors.
| | - Anthony Vial
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Laetitia Minder
- Univ. Bordeaux, INSERM, CNRS, IECB, US001, UAR 3033, Pessac, France
| | - Aurore Guédin
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Sébastien Fribourg
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Laurent Azéma
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Cécile Feuillie
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Michael Molinari
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Carmelo Di Primo
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Philippe Barthélémy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Leblond Chain Jeanne
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France,Corresponding authors.
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Zhang Y, Wang J, Luo R, Guo F, Wang X, Chu X, Zhao Y, Sun P. Stimulus-responsive and dual-target DNA nanodrugs for rheumatoid arthritis treatment. Int J Pharm 2023; 632:122543. [PMID: 36572263 DOI: 10.1016/j.ijpharm.2022.122543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 12/08/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Tumor necrosis factor receptor-1 (TNFR1) and DEK are closely associated with the development of rheumatoid arthritis (RA). Taking advantage of the high adenosine triphosphate (ATP) in RA microenvironment and the interactions of DNA aptamers with their targets, an ATP-responsive DNA nanodrug was constructed that simultaneously targets TNFR1 and DEK for RA therapy. To this end, DEK target aptamer DTA and TNFR1 target aptamer Apt1-67 were equipped with sticky ends to hybridize with ATP aptamer (AptATP) and fabricated DNA nanodrug DAT. Our results showed that DAT was successfully prepared with good stability. In the presence of ATP, DAT was disassembled, resulting in the release of DTA and Apt1-67. In vitro studies demonstrated that DAT was superior to the non-responsive DNA nanodrug TD-3A3T in terms of anti-inflammation activity and ATP was inevitable to maximize the anti-inflammation ability of DAT. The superior efficacy of DAT is attributed to the more potent inhibition of caspase-3 and NETs formation. In vivo results further confirmed the anti-RA efficacy of DAT, whereas the administration routes (intravenous injection and transdermal administration via microneedles) did not cause significant differences. Overall, the present study supplies an intelligent strategy for RA therapy and explores a promising administration route for future clinical medication of RA patients.
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Hou Y, Wang J, Liu S, Sun Y, Dai Y, Luo C, Wang X. A novel flower-shaped Ag@ZIF-67 chemiluminescence sensor for sensitive detection of CEA. Talanta 2023; 253:123938. [PMID: 36150338 DOI: 10.1016/j.talanta.2022.123938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/07/2022] [Accepted: 09/11/2022] [Indexed: 12/13/2022]
Abstract
In this work, a chemiluminescence (CL) aptasensor for sensitive carcinoembryonic antigen (CEA) detection was constructed based on the CL system of luminol-H2O2-NaOH. Magnetic carbon nanotubes (MCNTs), as the base material, was modified with CEA-aptamer and DNA1, and was combined with the novel flower-shaped Ag@ZIF-67 of modified with DNA2 through the principle of base complementary pairing. CEA combined with aptamer when it existed in the solution. At the same time, MCNTs was adsorbed at the bottom of the container under the influence of external magnetic field, and Ag@ZIF-67 enhanced the CL signal. The CL aptasensor demonstrated high selectivity and sensitivity for CEA in human serum sample with (1-4): a detection limit of 4.53 × 10-3 ng/mL in case the detection range was 0.05-500 ng/mL. Furthermore, the proposed method had been shown great potential in cancer diagnosis.
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Affiliation(s)
- Yanan Hou
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Jingdao Wang
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Shantian Liu
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Yuanling Sun
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Yuxue Dai
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Chuannan Luo
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China.
| | - Xueying Wang
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China.
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Abstract
The concentrations of specific macromolecular species can be quantified using diagnostic tools that rely on molecular recognition by nucleic acid aptamers. One such approach involves the formation of osmium tetroxide 2,2'-bipyridine protein adducts, followed by electrochemical detection of analytes that bind specifically to electrode-tethered aptamers. In conjunction with a 27-mer DNA aptamer that binds specifically to exosite II on human alpha thrombin, this technique permits, in theory, a highly sensitive diagnostic tool for the quantification of serum thrombin levels. However, thrombin's aptamer binding site is lined by two tryptophan residues and the conjugation of bulky osmium groups to these residues weakens aptamer binding by an estimated 4 to 12 kcal/mol, undermining detection sensitivity. Therefore, we have rationally modified this DNA aptamer to strengthen its thrombin binding in the presence of conjugated osmium. Specifically, aptamers carrying long hydrophobic thymine derivatives in place of guanine 21 have binding affinities for osmium-conjugated thrombin that are enhanced by 10 to 15 kcal/mol, suggesting that these modified aptamers may be effective in a highly sensitive electrochemical sensor for the quantification of low concentrations of thrombin. Our approach of using molecular simulation to subtly re-engineer a DNA aptamer may be generally applicable for the optimization of other macromolecular binding interfaces.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Loan Huynh
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, USA
| | - Alan Chen
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, USA
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Gao H, Bai Y, He B, Tan CS. A Simple Label-Free Aptamer-Based Electrochemical Biosensor for the Sensitive Detection of C-Reactive Proteins. Biosensors (Basel) 2022; 12:1180. [PMID: 36551147 PMCID: PMC9775280 DOI: 10.3390/bios12121180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
The level of C-reactive protein (CRP) in the human body is closely associated with cardiovascular diseases and inflammation. In this study, a label-free functionalized aptamer sensor was attached to an electrode trimmed with in-gold nanoparticles and carboxylated graphene oxide (AuNPs/GO-COOH) to achieve sensitive measurements relative to CRP. Gold nanoparticles were selected for this study due to super stability, remarkably high electrical conductivity, and biocompatibility. In addition, carboxylated graphene oxide was utilized to promote the anchorage of inducer molecules and to increase detection accuracies. The sensing signal was recorded using differential pulse voltammetry (DPV), and it produced a conspicuous peak current obtained at approximately -0.4 V. Furthermore, the adapted sensor manifested a broad linear span from 0.001 ng/mL to 100 ng/mL. The results also demonstrated that this aptamer sensor had superior stability, specificity, and reproducibility. This aptamer-based electrochemical sensor has enormous potential in complex application situations with interfering substances.
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Affiliation(s)
- Huilin Gao
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Yongchang Bai
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Baixun He
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Cherie S. Tan
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
- Tianjin Key Laboratory of Brain Science and Neuroengineering, Tianjin 300072, China
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35
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Zhang Z, Wang Y, Mei Z, Wang Y, Li H, Li S, Xia F. Incorporating Hydrophobic Moieties into Self-Assembled Monolayers to Enable Electrochemical Aptamer-Based Sensors Deployed Directly in a Complex Matrix. ACS Sens 2022; 7:2615-2624. [PMID: 35998663 DOI: 10.1021/acssensors.2c00995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Continuous real-time measurement of specific targets in complex biological samples is of great significance for early diagnosis and treatment of diseases and thus enables achievement of personalized medicine. Electrochemical aptamer-based (E-AB) sensors are good candidates to fill this role due to their high specificity, sensitivity, rapid detection, and simple preparation. However, this sensor class suffers from severe baseline drift in the complex matrix probably due to the nonspecific adsorption of components. Here, we introduce a series of self-assembled monolayers with a variety of hydrophobic functional groups into an E-AB sensor platform, achieving enhancement of the antifouling performance and thus the detection performance (e.g., stability, sensitivity, and specificity). We reveal that the antifouling performance enhanced by such hydrophobic SAMs is probably due to its instant adsorption of components onto the surface, rather than the repelling of these components by hydrophilic SAMs in previous reports.
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Affiliation(s)
- Zishuo Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Yuanyuan Wang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Ziyin Mei
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Yiming Wang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hui Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Shaoguang Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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36
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Gu P, Lu Y, Li S, Ma C. A Label-Free Fluorescence Aptasensor Based on G-Quadruplex/Thioflavin T Complex for the Detection of Trypsin. Molecules 2022; 27:molecules27186093. [PMID: 36144829 PMCID: PMC9503660 DOI: 10.3390/molecules27186093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022]
Abstract
A novel, label-free fluorescent assay has been developed for the detection of trypsin by using thioflavin T as a fluorescent probe. A specific DNA aptamer can be combined by adding cytochrome c. Trypsin hydrolyzes the cytochrome c into small peptide fragments, exposing the G-quadruplex part of DNA aptamer, which has a high affinity for thioflavin T, which then enhances the fluorescence intensity. In the absence of trypsin, the fluorescence intensity was inhibited as the combination of cytochrome c and the DNA aptamer impeded thioflavin T’s binding. Thus, the fluorescent biosensor showed a linear relationship from 0.2 to 60 μg/mL with a detection limit of 0.2 μg/mL. Furthermore, the proposed method was also successfully employed for determining trypsin in biological samples. This method is simple, rapid, cheap, and selective and possesses great potential for the detection of trypsin in bioanalytical and biological samples and medical diagnoses.
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Budiarto BR, Mustopa AZ, Ningrum RA, Amilia N, Saepudin E. Gold nanoparticles (AuNP)-based aptasensor for enteropathogenic Escherichia coli detection. Mol Biol Rep 2022; 49:9355-9363. [PMID: 35896842 DOI: 10.1007/s11033-022-07786-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Diarrhea is a major cause of severe gastrointestinal illness in the infant especially in many developing countries. Although this molecular technique has been accepted as standard technique to detect Diarrhea-causing EPEC, the practical aspect of this technique for in-site rapid screening purposes is still facing a major challenge. In this study, we characterized EPEC specific aptamers and applied it as an AuNP-based aptasensor for point of care (POC) diagnosis purpose. METHODS As many as six selected DNA aptamers was screened using target bacteria and the bound aptamer was measured by qPCR technique. Moreover, Kd value for each optimal bound aptamer was measured by using the same technique. Colorimetry assay was applied to test specificity and LOD of AuNP-based aptasensor. RESULTS Two DNA aptamers have been successfully obtained to detect Enteropathogenic Escherichia coli K.1.1. DNA aptamer S8-7 exhibited constant dissociation (Kd) value of 17.08 nM, while DNA aptamer S10-5 exhibited Kd value of 34.14 nM. AuNP-based aptasensor showed high selectivity and specificity for EPEC K.1.1 with a limit of detection (LOD) value of 105 CFU/mL. Truncation study on DNA aptamer S8-7 showed that elimination of primer binding sequence only slightly increased both performance of detection and LOD value of AuNP-based aptasensor. CONCLUSION Further study is necessary to improve AuNP-aptasensor performance such as through mutagenesis approach on targeted DNA aptamers before AuNP-based aptasensor can be applied as a biosensor in point of care (POC) diagnosis.
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Affiliation(s)
- Bugi Ratno Budiarto
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Raya Bogor Street KM.46, Cibinong, Bogor, West Java, 16911, Indonesia
| | - Apon Zaenal Mustopa
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Raya Bogor Street KM.46, Cibinong, Bogor, West Java, 16911, Indonesia.
| | - Ratih Asmana Ningrum
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Raya Bogor Street KM.46, Cibinong, Bogor, West Java, 16911, Indonesia
| | - Nurul Amilia
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Indonesia, Depok, 16424, Indonesia.,Department of Chemistry, Faculty of Science and Technology, UIN Syarif Hidayatullah Jakarta, South Tangerang, 15412, Indonesia
| | - Endang Saepudin
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Indonesia, Depok, 16424, Indonesia
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Song M, Li Y, Gao R, Liu J, Huang Q. De novo design of DNA aptamers that target okadaic acid (OA) by docking-then-assembling of single nucleotides. Biosens Bioelectron 2022; 215:114562. [PMID: 35870338 DOI: 10.1016/j.bios.2022.114562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/24/2022] [Accepted: 07/07/2022] [Indexed: 11/15/2022]
Abstract
Okadaic acid (OA) is a diarrhetic shellfish poison widespread in ocean, so its detection is of great significance to seafood safety. Because of good sensitivity and low cost, biosensors using nucleic-acid aptamers as the recognition molecules are emerging as an important detection tool. However, the traditional SELEX screening method for acquiring OA high-affinity aptamers is time- and resource-intensive. Alternatively, here we developed a de novo design method based on the 3D structure of a target molecule, such as OA. Without experimental screening, this method designs OA aptamers by a computational approach of docking-then-assembling (DTA) of single nucleotides (A, C, G and T) as: (1) determining the high-affinity nucleotide binding sites of the target molecule via saturated molecular docking; (2) assembling the bound nucleotides into binding units to the target molecule; (3) constructing full-length aptamers by introducing stabilizing units to connect these binding units. In this way, five OA aptamers were designed, and microscale thermophoresis (MST) experiments verified that their Kd values are in the range of 100-600 nM; and one of them (named 9CGAT_4_a) could specifically bind to OA with low affinities for the other three marine biotoxins. Therefore, this study provides high-affinity and specific aptamers for the development of OA biosensors, and presents a promising de novo design method applicable to other target molecules.
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Affiliation(s)
- Menghua Song
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yuanyuan Li
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ruihua Gao
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200438, China
| | - Jianping Liu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China; Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, 201203, China.
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39
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Silwal AP, Thennakoon SKS, Arya SP, Postema RM, Jahan R, Phuoc CMT, Tan X. DNA aptamers inhibit SARS-CoV-2 spike-protein binding to hACE2 by an RBD- independent or dependent approach. Theranostics 2022; 12:5522-5536. [PMID: 35910791 PMCID: PMC9330529 DOI: 10.7150/thno.74428] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022] Open
Abstract
Objective: Nobody knows when the COVID-19 pandemic will end or when and where the next coronavirus will outbreak. Therefore, it is still necessary to develop SARS-CoV-2 inhibitors for different variants or even the new coronavirus. Since SARS-CoV-2 uses its surface spike-protein to recognize hACE2, mediating its entry into cells, ligands that can specifically recognize the spike-protein have the potential to prevent infection. Methods: We have recently discovered DNA aptamers against the S2-domain of the WT spike-protein by exploiting the selection process called SELEX. After optimization, among all candidates, the aptamer S2A2C1 has the shortest sequence and the best binding affinity toward the S2-protein. More importantly, the S2A2C1 aptamer does not bind to the RBD of the spike-protein, but it efficiently blocks the spike-protein/hACE2 interaction, suggesting an RBD-independent inhibition approach. To further improve its performance, we conjugated the S2A2C1 aptamer with a reported anti-RBD aptamer, S1B6C3, using various linkers and constructed hetero-bivalent fusion aptamers. Binding affinities of mono and fusion aptamers against the spike-proteins were measured. The inhibition efficacies of mono and fusion aptamers to prevent the hACE2/spike-protein interaction were determined using ELISA. Results: Anti-spike-protein aptamers, including S2A2C1 and S1B6C3-A5-S2A2C1, maintained high binding affinity toward the WT, Delta, and Omicron spike-proteins and high inhibition efficacies to prevent them from binding to hACE2, rendering them well-suited as diagnostic and therapeutic molecular tools to target SARS-CoV-2 and its variants. Conclusions: Overall, we discovered the anti-S2 aptamer, S2A2C1, which inhibits the hACE2/spike-protein interaction via an RBD-independent approach. The anti-S2 and anti-RBD aptamers were conjugated to obtain the fusion aptamer, S1B6C3-A5-S2A2C1, which recognizes the spike-protein by an RBD-dependent approach. Our strategies, which discovered aptamer inhibitors targeting the highly conserved S2-protein, as well as the design of fusion aptamers, can be used to target new coronaviruses as they emerge.
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Affiliation(s)
| | | | | | | | | | | | - Xiaohong Tan
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
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Kusumawati A, Mustopa AZ, Wibawan IWT, Setiyono A, Sudarwanto MB. A sequential toggle cell-SELEX DNA aptamer for targeting Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli bacteria. J Genet Eng Biotechnol 2022; 20:95. [PMID: 35776386 DOI: 10.1186/s43141-022-00374-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/02/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND Mastitis is an inflammation of the mammary glands caused by a microbial infection. The common bacteria causing this infection in dairy farms are Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli. The aptamer is a new biosensor platform for detecting pathogens; however, its use for simultaneous detection of S. aureus, S. agalactiae, and E. coli bacteria has not been reported. This study's objective is to isolate and characterize polyclonal DNA aptamer with broad reactivity to the mastitis bacteria S. aureus, S. agalactiae, and E. coli using a sequential toggle cell-SELEX. METHODS AND RESULTS The DNA aptamer pool from SELEX 15 was inserted into the pGEM-T easy plasmid. Furthermore, the transformant clones were selected by PCR colony, plasmid isolation, and sequencing. Six DNA aptamers, consisting of S15K3, S15K4, S15K6, S15K13, S15K15, and S15K20 with a constant region and the right size of 81 bp were derived from the sequencing analysis. The secondary structure of the DNA was predicted using Mfold software. The DNA was analyzed with binding characteristics, including binding capacity and affinity (Kd), using qPCR. The results indicated aptamer S15K15 has the highest binding ability into S. agalactiae, while S15K13 performed binding capacity most to E. coli EPEC 4, and S15K3 has the highest capacity of binding to S. aureus BPA-12. CONCLUSION Aptamer S15K3 has the best binding characteristics on all three bacterial targets.
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Ji C, Yu C, Song M, Pei H, Fu P, Lin Y, Wang J. Construction of Molecular Transporter Based on DNA Structure Regulation. ACS Appl Bio Mater 2022; 5:2122-2129. [PMID: 35481744 DOI: 10.1021/acsabm.2c00222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study aims to build a molecular transporter machine that is based on the microstructure regulation of DNA triplets, which can automatically search, load, target delivery, and unload target protein molecules. The design of the molecular transporter includes: (1) a DNA triplet, which can recognize and load of the target protein; (2) a similar DNA triplet realizing the target transport; and (3) the signal-indicating DNA, which is connected at the target destination to achieve fixation of the target protein at the target destination. The molecular transporter machine would provide research practice and theoretical guidance for the development of DNA-based molecular machines.
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Affiliation(s)
- Chengdong Ji
- Zybio Inc, Chongqing, 400082, China.,Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Chunchun Yu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570311, China
| | - Min Song
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Hua Pei
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570311, China
| | | | | | - Jing Wang
- Zybio Inc, Chongqing, 400082, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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Curti F, Fortunati S, Knoll W, Giannetto M, Corradini R, Bertucci A, Careri M. A Folding-Based Electrochemical Aptasensor for the Single-Step Detection of the SARS-CoV-2 Spike Protein. ACS Appl Mater Interfaces 2022; 14:19204-19211. [PMID: 35446532 PMCID: PMC9045037 DOI: 10.1021/acsami.2c02405] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Efficient and timely testing has taken center stage in the management, control, and monitoring of the current COVID-19 pandemic. Simple, rapid, cost-effective diagnostics are needed that can complement current polymerase chain reaction-based methods and lateral flow immunoassays. Here, we report the development of an electrochemical sensing platform based on single-walled carbon nanotube screen-printed electrodes (SWCNT-SPEs) functionalized with a redox-tagged DNA aptamer that specifically binds to the receptor binding domain of the SARS-CoV-2 spike protein S1 subunit. Single-step, reagentless detection of the S1 protein is achieved through a binding-induced, concentration-dependent folding of the DNA aptamer that reduces the efficiency of the electron transfer process between the redox tag and the electrode surface and causes a suppression of the resulting amperometric signal. This aptasensor is specific for the target S1 protein with a dissociation constant (KD) value of 43 ± 4 nM and a limit of detection of 7 nM. We demonstrate that the target S1 protein can be detected both in a buffer solution and in an artificial viral transport medium widely used for the collection of nasopharyngeal swabs, and that no cross-reactivity is observed in the presence of different, non-target viral proteins. We expect that this SWCNT-SPE-based format of electrochemical aptasensor will prove useful for the detection of other protein targets for which nucleic acid aptamer ligands are made available.
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Affiliation(s)
- Federica Curti
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße
24, 3430 Tulln an
der Donau, Austria
| | - Simone Fortunati
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Wolfgang Knoll
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße
24, 3430 Tulln an
der Donau, Austria
- Department
of Scientific Coordination and Management, Danube Private University, A-3500 Krems, Austria
| | - Marco Giannetto
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Roberto Corradini
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Alessandro Bertucci
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Maria Careri
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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Wang J, Hou Y, Sun Y, Fang F, Luo C, Wang X. A chemiluminescence aptasensor for sensitive detection of alpha-fetoprotein based on hemin@ZIF-67. Anal Bioanal Chem 2022; 414:4757-4765. [PMID: 35508645 DOI: 10.1007/s00216-022-04099-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/17/2022] [Accepted: 04/22/2022] [Indexed: 02/07/2023]
Abstract
In this work, hemin@ZIF-67 composites were prepared and were used to construct a chemiluminescence (CL) aptasensor for alpha-fetoprotein (AFP) detection. Hemin is a catalytic porphyrin with two carboxylate groups that can covalently bond to metal ions. A hemin/ZIF-67 composite was prepared via covalent bonding between the carboxyl groups of hemin and the cobalt ion of ZIF-67, and these materials were characterized by scanning electron microscopy (SEM), infrared spectroscopy (IR), and X-ray diffraction (XRD). Hemin@ZIF-67 was used as the peroxidase material, and the aptamer of alpha-fetoprotein was modified on its surface by electrostatic adsorption. Then a simple CL aptasensor was constructed based on the CL system of luminol-H2O2-NaOH. Under the optimal conditions, the CL intensity value was linearly proportional to the concentration of AFP in the range of 4 × 10-10 to 200 × 10-10 mg/mL. The detection limit was 1.3 × 10-10 mg/mL. Thus the aptasensor enables highly sensitive and selective detection of AFP.
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Affiliation(s)
- Jingdao Wang
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Yanan Hou
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Yuanling Sun
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Fang Fang
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Chuannan Luo
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China.
| | - Xueying Wang
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China.
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Dreymann N, Wuensche J, Sabrowski W, Moeller A, Czepluch D, Vu Van D, Fuessel S, Menger MM. Inhibition of Human Urokinase-Type Plasminogen Activator (uPA) Enzyme Activity and Receptor Binding by DNA Aptamers as Potential Therapeutics through Binding to the Different Forms of uPA. Int J Mol Sci 2022; 23:4890. [PMID: 35563278 DOI: 10.3390/ijms23094890] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 02/06/2023] Open
Abstract
Urokinase-type plasminogen activator is widely discussed as a marker for cancer prognosis and diagnosis and as a target for cancer therapies. Together with its receptor, uPA plays an important role in tumorigenesis, tumor progression and metastasis. In the present study, systematic evolution of ligands by exponential enrichment (SELEX) was used to select single-stranded DNA aptamers targeting different forms of human uPA. Selected aptamers allowed the distinction between HMW-uPA and LMW-uPA, and therefore, presumably, have different binding regions. Here, uPAapt-02-FR showed highly affine binding with a KD of 0.7 nM for HMW-uPA and 21 nM for LMW-uPA and was also able to bind to pro-uPA with a KD of 14 nM. Furthermore, no cross-reactivity to mouse uPA or tissue-type plasminogen activator (tPA) was measured, demonstrating high specificity. Suppression of the catalytic activity of uPA and inhibition of uPAR-binding could be demonstrated through binding with different aptamers and several of their truncated variants. Since RNA aptamers are already known to inhibit uPA-uPAR binding and other pathological functions of the uPA system, these aptamers represent a novel, promising tool not only for detection of uPA but also for interfering with the pathological functions of the uPA system by additionally inhibiting uPA activity.
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Biyani M, Yasuda K, Isogai Y, Okamoto Y, Weilin W, Kodera N, Flechsig H, Sakaki T, Nakajima M, Biyani M. Novel DNA Aptamer for CYP24A1 Inhibition with Enhanced Antiproliferative Activity in Cancer Cells. ACS Appl Mater Interfaces 2022; 14:18064-18078. [PMID: 35436103 DOI: 10.1021/acsami.1c22965] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Overexpression of the vitamin D3-inactivating enzyme CYP24A1 (cytochrome P450 family 24 subfamily and hereafter referred to as CYP24) can cause chronic kidney diseases, osteoporosis, and several types of cancers. Therefore, CYP24 inhibition has been considered a potential therapeutic approach. Vitamin D3 mimetics and small molecule inhibitors have been shown to be effective, but nonspecific binding, drug resistance, and potential toxicity limit their effectiveness. We have identified a novel 70-nt DNA aptamer-based inhibitor of CYP24 by utilizing the competition-based aptamer selection strategy, taking CYP24 as the positive target protein and CYP27B1 (the enzyme catalyzing active vitamin D3 production) as the countertarget protein. One of the identified aptamers, Apt-7, showed a 5.8-fold higher binding affinity with CYP24 than the similar competitor CYP27B1. Interestingly, Apt-7 selectively inhibited CYP24 (the relative CYP24 activity decreased by 39.1 ± 3% and showed almost no inhibition of CYP27B1). Furthermore, Apt-7 showed cellular internalization in CYP24-overexpressing A549 lung adenocarcinoma cells via endocytosis and induced endogenous CYP24 inhibition-based antiproliferative activity in cancer cells. We also employed high-speed atomic force microscopy experiments and molecular docking simulations to provide a single-molecule explanation of the aptamer-based CYP24 inhibition mechanism. The novel aptamer identified in this study presents an opportunity to generate a new probe for the recognition and inhibition of CYP24 for biomedical research and could assist in the diagnosis and treatment of cancer.
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Affiliation(s)
- Madhu Biyani
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Kaori Yasuda
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhiro Isogai
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yuki Okamoto
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Wei Weilin
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Noriyuki Kodera
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Holger Flechsig
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Toshiyuki Sakaki
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Miki Nakajima
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Manish Biyani
- BioSeeds Corporation, JAIST venture business laboratory, Ishikawa Create Labo, Asahidai 2-13, Nomi City, Ishikawa 923-1211, Japan
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Yang X, Liang X, Nandi R, Tian Y, Zhang Y, Li Y, Zhou J, Dong Y, Liu D, Zhong Z, Yang Z. DNA-Modified Liquid Crystal Droplets. Biosensors (Basel) 2022; 12:275. [PMID: 35624576 PMCID: PMC9138460 DOI: 10.3390/bios12050275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
In this work, we have combined the advantages of sequence programmability of DNA nanotechnology and optical birefringence of liquid crystals (LCs). Herein, DNA amphiphiles were adsorbed onto LC droplets. A unique phenomenon of LC droplet aggregation was demonstrated, using DNA-modified LC droplets, through complementary DNA hybridization. Further functionalization of DNA-modified LC droplets with a desired DNA sequence was used to detect a wide range of chemicals and biomolecules, such as Hg2+, thrombin, and enzymes, through LC droplet aggregation and vice versa, which can be seen through the naked eye. These DNA-modified LC droplets can be printed onto a desired patterned surface with temperature-induced responsiveness and reversibility. Overall, our work is the first to report DNA-modified LC droplet, which provides a general detection platform based on the development of DNA aptamers. Additionally, this work inspires the exploration of surface information visualization combined with microcontact printing.
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Affiliation(s)
- Xiuxiu Yang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Xiao Liang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Rajib Nandi
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Yi Tian
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Yiyang Zhang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Yan Li
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Jingsheng Zhou
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Yuanchen Dong
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Zhengwei Zhong
- Department of Chemical Engineering, Hebei Petroleum University of Technology, Chengde 067000, China
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
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Yang X, Yang L, Yang D, Li M, Wang P. In Situ DNA Self-Assembly on the Cell Surface Drives Unidirectional Clustering of Membrane Proteins for the Modulation of Cell Behaviors. Nano Lett 2022; 22:3410-3416. [PMID: 35389660 DOI: 10.1021/acs.nanolett.2c00680] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cell membrane proteins play a pivotal role in regulating intracellular signal transductions and cell behaviors. Many membrane proteins form clusters in order to initiate downstream signaling pathways for the modulation of cell behaviors. Developing rational methods to program the in situ clustering of designated membrane proteins on the cell surface to form large assemblies remains challenging. Here we use the membrane-anchored DNA hybridization chain reaction (HCR) to induce DNA self-assembly on the live cell surface and drive the unidirectional clustering of membrane proteins for the modulation of cell behaviors. Reactive DNA strands are specifically anchored onto the membrane proteins of interest by using DNA aptamers. Upon activation, the chain reaction between the protein-anchored DNA strands drives the assembly of membrane proteins forming one-dimensional clusters. We demonstrate both homogeneous and heterogeneous clustering of membrane proteins on multiple cell types that exhibit a potent capability for modulating cell behaviors including migration, proliferation, and survival.
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Affiliation(s)
- Xueqin Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lijiao Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Min Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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Hua Y, Ma J, Li D, Wang R. DNA-Based Biosensors for the Biochemical Analysis: A Review. Biosensors (Basel) 2022; 12:bios12030183. [PMID: 35323453 PMCID: PMC8945906 DOI: 10.3390/bios12030183] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 05/21/2023]
Abstract
In recent years, DNA-based biosensors have shown great potential as the candidate of the next generation biomedical detection device due to their robust chemical properties and customizable biosensing functions. Compared with the conventional biosensors, the DNA-based biosensors have advantages such as wider detection targets, more durable lifetime, and lower production cost. Additionally, the ingenious DNA structures can control the signal conduction near the biosensor surface, which could significantly improve the performance of biosensors. In order to show a big picture of the DNA biosensor's advantages, this article reviews the background knowledge and recent advances of DNA-based biosensors, including the functional DNA strands-based biosensors, DNA hybridization-based biosensors, and DNA templated biosensors. Then, the challenges and future directions of DNA-based biosensors are discussed and proposed.
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Nguyen DK, Jang CH. Ultrasensitive colorimetric detection of amoxicillin based on Tris-HCl-induced aggregation of gold nanoparticles. Anal Biochem 2022; 645:114634. [PMID: 35271807 DOI: 10.1016/j.ab.2022.114634] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/15/2022] [Accepted: 02/28/2022] [Indexed: 11/26/2022]
Abstract
An ultrasensitive colorimetric aptasensor for the detection of amoxicillin (AMO) based on the Tris-HCl buffer-induced aggregation of gold nanoparticles (AuNPs) was developed. The AuNPs were aggregated by the addition of Tris-HCl buffer. The adsorption of the aptamer on the AuNP surface increased its negative charge density, leading to the enhancement of the electrostatic repulsion between the nanoparticles, thus protecting AuNPs from aggregation in the Tris-HCl buffer. However, the specific binding of the aptamer with AMO induced conformational changes in the aptamer, which reduced the adsorption of the aptamer on the AuNP surface, diminishing the protective effect of the aptamer. This resulted in the aggregation of AuNPs by Tris-HCl buffer, and consequently, color change of the solution containing AuNPs from red to blue. Under optimized conditions, a linear relationship between the absorbance ratio variation (ΔA680/A520) and the AMO concentration was observed in the concentration range of 0.1-125 nM, with a detection limit of 67 pM. The developed biosensor exhibited high selectivity toward AMO. Moreover, this strategy was successfully applied to the detection of AMO in lake water samples. Thus, the present aptasensor is a promising alternative for the simple and ultrasensitive detection of AMO in the environment.
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Affiliation(s)
- Duy Khiem Nguyen
- Department of Chemistry, Gachon University, Seongnam-daero 1342, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea
| | - Chang-Hyun Jang
- Department of Chemistry, Gachon University, Seongnam-daero 1342, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea.
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Saito T, Shimizu Y, Tsukakoshi K, Abe K, Lee J, Ueno K, Asano R, Jones BV, Yamada T, Nakano T, Tong J, Hishiki A, Hara K, Hashimoto H, Sode K, Toyo'oka T, Todoroki K, Ikebukuro K. Development of a DNA aptamer that binds to the complementarity-determining region of therapeutic monoclonal antibody and affinity improvement induced by pH-change for sensitive detection. Biosens Bioelectron 2022; 203:114027. [PMID: 35114463 DOI: 10.1016/j.bios.2022.114027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 11/26/2022]
Abstract
Therapeutic monoclonal antibodies (mAbs) are successful biomedicines; however, evaluation of their pharmacokinetics and pharmacodynamics demands highly specific discrimination from human immunoglobulin G naturally present in the blood. Here, we developed a novel anti-idiotype aptamer (termed A14#1) with extraordinary specificity against the anti-vascular endothelial growth factor therapeutic mAb, bevacizumab. Structural analysis of the antibody-aptamer complex showed that several bases of A14#1 recognized only the complementarity determining region (CDR) of bevacizumab, thereby contributing to its extraordinary specificity. As the CDR of bevacizumab is predicted to be highly positively charged under mildly acidic conditions and that DNA is negatively charged, the affinity of A14#1 to bevacizumab markedly increased at pH 4.7 (KD = 44 pM) than at pH 7.4 (KD = 12 nM). A14#1-based electrochemical detection method capable of detecting 31 pM of bevacizumab at pH 4.7 was thus developed. A14#1 could be potentially useful for therapeutic drug measurement as a novel ligand of bevacizumab.
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Affiliation(s)
- Taro Saito
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Yutaka Shimizu
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Koichi Abe
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Jinhee Lee
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA
| | - Kinuko Ueno
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Ryutaro Asano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Brian V Jones
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Tomohiro Yamada
- Department of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Tatsuki Nakano
- Department of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Jiaxing Tong
- Department of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Asami Hishiki
- Department of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Kodai Hara
- Department of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Hiroshi Hashimoto
- Department of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Koji Sode
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA
| | - Toshimasa Toyo'oka
- Department of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Kenichiro Todoroki
- Department of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan.
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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