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Sittiwanichai S, Archapraditkul C, Japrung D, Shigeta Y, Mori T, Pongprayoon P. Aggregation of Apo/Glycated Human Serum Albumins and Aptamer-Saturated Graphene Quantum Dot: A Simulation Study. Biochemistry 2024; 63:1697-1707. [PMID: 38889356 DOI: 10.1021/acs.biochem.4c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Human serum albumin (HSA) is a protein carrier that transports a wide range of drugs and nutrients. The amount of glycated HSA (GHSA) is used as a diabetes biomarker. To quantify the GHSA amount, the fluorescent graphene-based aptasensor has been a successful method. In aptasensors, the key mechanism is the adsorption/desorption of albumin from the aptamer-graphene complex. Recently, the graphene quantum dot (GQD) has been reported to be an aptamer sorbent. Due to its comparable size to aptamers, it is attractive enough to explore the possibility of GQD as a part of an albumin aptasensor. Therefore, molecular dynamics (MD) simulations were performed here to reveal the binding mechanism of albumin to an aptamer-GQD complex in molecular detail. GQD saturated by albumin-selective aptamers (GQDA) is studied, and GHSA and HSA are studied in comparison to understand the effect of glycation. Fast and spontaneous albumin-GQDA binding was observed. While no specific GQDA-binding site on both albumins was found, the residues used for binding were confined to domains I and III for HSA and domains II and III for GHSA. Albumins were found to bind preferably to aptamers rather than to GQD. Lysines and arginines were the main contributors to binding. We also found the dissociation of GLC from all GHSA trajectories, which highlights the role of GQDA in interfering with the ligand binding affinity in Sudlow site I. The binding of GQDA appears to impair albumin structure and function. The insights obtained here will be useful for the future design of diabetes aptasensors.
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Affiliation(s)
- Sirin Sittiwanichai
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Chanya Archapraditkul
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Deanpen Japrung
- National Nanotechnology Center, National Science and Technology Development Agency, Thailand Science Park, Pathum Thani 12120, Thailand
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Toshifumi Mori
- Institute for Material Chemistry and Engineering, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
- Interdisciplinary Graduate School of Engineering Science, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
| | - Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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3
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Sittiwanichai S, Niramitranon J, Japrung D, Pongprayoon P. Binding of Apo and Glycated Human Serum Albumins to an Albumin-Selective Aptamer-Bound Graphene Quantum Dot Complex. ACS OMEGA 2023; 8:21862-21870. [PMID: 37360475 PMCID: PMC10286295 DOI: 10.1021/acsomega.3c01595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023]
Abstract
Diabetes mellitus is a chronic metabolic disease involving continued elevated blood glucose levels. It is a leading cause of mortality and reduced life expectancy. Glycated human serum albumin (GHSA) has been reported to be a potential diabetes biomarker. A nanomaterial-based aptasensor is one of the effective techniques to detect GHSA. Graphene quantum dots (GQDs) have been widely used in aptasensors as an aptamer fluorescence quencher due to their high biocompatibility and sensitivity. GHSA-selective fluorescent aptamers are first quenched upon binding to GQDs. The presence of albumin targets results in the release of aptamers to albumin and consequently fluorescence recovery. To date, the molecular details on how GQDs interact with GHSA-selective aptamers and albumin remain limited, especially the interactions of an aptamer-bound GQD (GQDA) with an albumin. Thus, in this work, molecular dynamics simulations were used to reveal the binding mechanism of human serum albumin (HSA) and GHSA to GQDA. The results show the rapid and spontaneous assembly of albumin and GQDA. Multiple sites of albumins can accommodate both aptamers and GQDs. This suggests that the saturation of aptamers on GQDs is required for accurate albumin detection. Guanine and thymine are keys for albumin-aptamer clustering. GHSA gets denatured more than HSA. The presence of bound GQDA on GHSA widens the entrance of drug site I, resulting in the release of open-chain glucose. The insight obtained here will serve as a base for accurate GQD-based aptasensor design and development.
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Affiliation(s)
- Sirin Sittiwanichai
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Chatuchak, Bangkok 10900, Thailand
| | - Jitti Niramitranon
- Department
of Computer Engineering, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Deanpen Japrung
- National
Science and Technology Development Agency, National Nanotechnology Center, Thailand Science Park, Pathumthani 12120, Thailand
| | - Prapasiri Pongprayoon
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Chatuchak, Bangkok 10900, Thailand
- Center
for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural
Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
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Sun D, Xie J, Chen CJ, Liu JT. Analyzation of the binding mechanism and the isoelectric point of glycated albumin with self-assembled, aptamer-conjugated films by using surface plasmon resonance. Colloids Surf B Biointerfaces 2022; 214:112445. [PMID: 35290823 DOI: 10.1016/j.colsurfb.2022.112445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/24/2022] [Accepted: 03/03/2022] [Indexed: 10/18/2022]
Abstract
Glycated albumin(GA), a biomarker which has great potential to replace glycated hemoglobin in the diagnosis and treatment of diabetes, is being extensively studied by scientists, especially in preventive medicine. Aptamers, as novel probes, have attracted much attention due to their high specificity, wide storage conditions, and simple preparation. However, the interaction mechanism between GA and its aptamer is still unclear, hindering the progress of diabetic aptamer sensors into clinical testing. In this study, the interaction mechanism between GA and its aptamer was evaluated for the first time using surface plasmon resonance by changing the pH value, salt concentration and temperature. The successful preparation of the sensor chip is proved by the water contact angle, Atomic Force Microscope, and the X-ray photoelectron spectroscopy. This study shows that the pH can greatly affect the formation of a complex from the interaction between the aptamer and GA. The interaction mechanism between GA aptamer and GA was caused by electrostatic force. Otherwise, this is the first time to detect protein isoelectric point (pI) using SPR. This study provides an important reference for researchers of aptamer sensors from the perspective of detection environment, and promotes the use of aptamer sensors to the clinic.
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Affiliation(s)
- Dapeng Sun
- Institute of Microelectronics of Chinese Academy of Sciences, Beijing 100029, China; University of Chinese Academy of Sciences, No.19 A Yuquan Road, Beijing 100049, China; Research Center for Materials Science and Opti-Electronic Technology, College of Materials Science and Opti-Electronic Technology, University of Chinese Academy of Sciences, No.19 A Yuquan Road, Beijing 100049, China
| | - Jing Xie
- Institute of Microelectronics of Chinese Academy of Sciences, Beijing 100029, China; University of Chinese Academy of Sciences, No.19 A Yuquan Road, Beijing 100049, China
| | - Ching-Jung Chen
- University of Chinese Academy of Sciences, No.19 A Yuquan Road, Beijing 100049, China; School of Opto-Electronic Technology, University of Chinese Academy of Sciences, China.
| | - Jen-Tsai Liu
- University of Chinese Academy of Sciences, No.19 A Yuquan Road, Beijing 100049, China; Research Center for Materials Science and Opti-Electronic Technology, College of Materials Science and Opti-Electronic Technology, University of Chinese Academy of Sciences, No.19 A Yuquan Road, Beijing 100049, China.
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Electrochemical aptamer-based nanobiosensors for diagnosing Alzheimer's disease: A review. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2022; 135:112689. [DOI: 10.1016/j.msec.2022.112689] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 12/22/2022]
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Feng XQ, Ju Y, Dou WT, Li Q, Jin ZG, He XP, James TD, Ye BC. Ferrocene-Labelled Electroactive Aptamer-Based Sensors (Aptasensors) for Glycated Haemoglobin. Molecules 2021; 26:7077. [PMID: 34885660 PMCID: PMC8659020 DOI: 10.3390/molecules26237077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/14/2021] [Accepted: 11/19/2021] [Indexed: 11/30/2022] Open
Abstract
Glycated haemoglobin (HbA1c) is a diagnostic biomarker for type 2 diabetes. Traditional analytical methods for haemoglobin (Hb) detection rely on chromatography, which requires significant instrumentation and is labour-intensive; consequently, miniaturized devices that can rapidly sense HbA1c are urgently required. With this research, we report on an aptamer-based sensor (aptasensor) for the rapid and selective electrochemical detection of HbA1c. Aptamers that specifically bind HbA1c and Hb were modified with a sulfhydryl and ferrocene group at the 3' and 5'-end, respectively. The modified aptamers were coated through sulfhydryl-gold self-assembly onto screen printed electrodes, producing aptasensors with built in electroactivity. When haemoglobin was added to the electrodes, the current intensity of the ferrocene in the sensor system was reduced in a concentration-dependent manner as determined by differential pulse voltammetry. In addition, electrochemical impedance spectroscopy confirmed selective binding of the analytes to the aptamer-coated electrode. This research offers new insight into the development of portable electrochemical sensors for the detection of HbA1c.
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Affiliation(s)
- Xue-Qing Feng
- Laboratory of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.-Q.F.); (Y.J.)
- Shanghai Center for Clinical Laboratory, Shanghai 200237, China; (Q.L.); (Z.-G.J.)
| | - Yi Ju
- Laboratory of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.-Q.F.); (Y.J.)
- Shanghai Center for Clinical Laboratory, Shanghai 200237, China; (Q.L.); (Z.-G.J.)
| | - Wei-Tao Dou
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd., Shanghai 200237, China;
| | - Qing Li
- Shanghai Center for Clinical Laboratory, Shanghai 200237, China; (Q.L.); (Z.-G.J.)
| | - Zhong-Gan Jin
- Shanghai Center for Clinical Laboratory, Shanghai 200237, China; (Q.L.); (Z.-G.J.)
| | - Xiao-Peng He
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd., Shanghai 200237, China;
| | - Tony D. James
- Department of Chemistry, University of Bath, Bath BA2 7AY, UK
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Bang-Ce Ye
- Laboratory of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.-Q.F.); (Y.J.)
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