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Presela R, Prabu SS, Ch'ng ES, Tang TH, Citartan M. The diagnostic potentiality of the RNA aptamer against progesterone receptor isolated by crush and soak (CRUSOAK)-SELEX. Mikrochim Acta 2024; 191:346. [PMID: 38802696 DOI: 10.1007/s00604-024-06423-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024]
Abstract
Aptamers are a class of molecular recognition elements that exhibit high binding affinity and specificity against their respective targets. In view of the many advantages aptamers harbor over their counterpart antibodies, we were impelled to isolate an RNA aptamer against progesterone receptor, particularly its DNA binding domain. A total of eight SELEX cycles were executed against the recombinant Progesterone Receptor DNA-binding domain (PR DBD). The RNA-protein complex in the gel shift assay was subjected to crush and soak method to elute the binders prior to conventional sequencing, the step of which was based upon to coin the term CRUSOAK-SELEX. The sequencing revealed three different classes of sequences, with one class termed, PRapt-3, showing the strongest binding against PR DBD. The dissociation constant of PRapt-3 RNA aptamer was estimated at 380 nM ± 35 nM. PRapt-3 was successfully used to develop aptamer-based diagnostic assays such as ELASA, aptamer-based dot blot, and aptamer-based western blot. The prominent highlight is the performance of the aptamer in aptacytostaining, which was unachievable with antibodies. Compared to its counterpart antibodies, PRapt-3 has a better penetration capacity in aptahistostaining using the formalin-fixed paraffin-embedded (FFPE) breast cancer cells and tissue blocks. This study represents the first ever demonstration of an aptamer against progesterone receptor and its diagnostic capacity.
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Affiliation(s)
- Ravinderan Presela
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Siva Sankar Prabu
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Ewe Seng Ch'ng
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Thean-Hock Tang
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Marimuthu Citartan
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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2
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Ropii B, Bethasari M, Anshori I, Koesoema AP, Shalannanda W, Satriawan A, Setianingsih C, Akbar MR, Aditama R, Fahmi F, Sutanto E, Yazid M, Aziz M. The molecular interaction of six single-stranded DNA aptamers to cardiac troponin I revealed by docking and molecular dynamics simulation. PLoS One 2024; 19:e0302475. [PMID: 38748685 PMCID: PMC11095691 DOI: 10.1371/journal.pone.0302475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 04/04/2024] [Indexed: 05/19/2024] Open
Abstract
Cardiac troponin I (cTnI) is a cardiac biomarker for diagnosing ischemic heart disease and acute myocardial infarction. Current biochemical assays use antibodies (Abs) due to their high specificity and sensitivity. However, there are some limitations, such as the high-cost production of Abs due to complex instruments, reagents, and steps; the variability of Abs quality from batch to batch; the low stability at high temperatures; and the difficulty of chemical modification. Aptamer overcomes the limitations of antibodies, such as relatively lower cost, high reproducibility, high stability, and ease of being chemically modified. Aptamers are three-dimensional architectures of single-stranded RNA or DNA that bind to targets such as proteins. Six aptamers (Tro1-Tro6) with higher binding affinity than an antibody have been identified, but the molecular interaction has not been studied. In this study, six DNA aptamers were modeled and docked to cTnI protein. Molecular docking revealed that the interaction between all aptamer and cTnI happened in the similar cTnI region. The interaction between aptamer and cTnI involved hydrophobic interaction, hydrogen bonds, π-cation interactions, π-stack interactions, and salt-bridge formation. The calculated binding energy of all complexes was negative, which means that the complex formation was thermodynamically favorable. The electrostatic energy term was the main driving force of the interaction between all aptamer and cTnI. This study could be used to predict the behavior of further modified aptamer to improve aptamer performance.
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Affiliation(s)
- Bejo Ropii
- School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Maulidwina Bethasari
- Department of Pharmacy, Universitas Muhammadiyah Bandung, Bandung, West Java, Indonesia
| | - Isa Anshori
- School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, West Java, Indonesia
- Center for Health and Sports Technology, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Allya Paramita Koesoema
- School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Wervyan Shalannanda
- School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Ardianto Satriawan
- School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Casi Setianingsih
- Department of Computer Engineering, School of Electrical Engineering, Telkom University, Bandung Regency, West Java, Indonesia
| | - Mohammad Rizki Akbar
- Department of Cardiology and Vascular Medicine, Faculty of Medicine, Universitas Padjadjaran and Dr. Hasan Sadikin General Hospital, Bandung, Indonesia
| | - Reza Aditama
- Biochemistry and Biomolecular Engineering Research Division, Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Fahmi Fahmi
- Department of Electrical Engineering, Faculty of Engineering, Universitas Sumatera Utara, Medan, North Sumatera, Indonesia
| | - Erwin Sutanto
- Department of Physics, Faculty of Science and Technology, Universitas Airlangga, Kampus C Unair Mulyorejo, Surabaya, East Java, Indonesia
| | - Muhammad Yazid
- Biomedical Engineering Department, Institut Teknologi Sepuluh Nopember, Surabaya, East Java, Indonesia
| | - Muhammad Aziz
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
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3
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Ding X, Xu C, Zheng B, Yu H, Zheng P. Molecular Mechanism of Interaction between DNA Aptamer and Receptor-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus 2 Variants Revealed by Steered Molecular Dynamics Simulations. Molecules 2024; 29:2215. [PMID: 38792076 PMCID: PMC11124494 DOI: 10.3390/molecules29102215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
The ongoing SARS-CoV-2 pandemic has underscored the urgent need for versatile and rapidly deployable antiviral strategies. While vaccines have been pivotal in controlling the spread of the virus, the emergence of new variants continues to pose significant challenges to global health. Here, our study focuses on a novel approach to antiviral therapy using DNA aptamers, short oligonucleotides with high specificity and affinity for their targets, as potential inhibitors against the spike protein of SARS-CoV-2 variants Omicron and JN.1. Our research utilizes steered molecular dynamics (SMD) simulations to elucidate the binding mechanisms of a specifically designed DNA aptamer, AM032-4, to the receptor-binding domain (RBD) of the aforementioned variants. The simulations reveal detailed molecular insights into the aptamer-RBD interaction, demonstrating the aptamer's potential to maintain effective binding in the face of rapid viral evolution. Our work not only demonstrates the dynamic interaction between aptamer-RBD for possible antiviral therapy but also introduces a computational method to study aptamer-protein interactions.
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Affiliation(s)
- Xuan Ding
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210093, China
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Chao Xu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Bin Zheng
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Hanyang Yu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
| | - Peng Zheng
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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Li Y, Qian M, Liu Y, Qiu X. APPROACH: Sensitive Detection of Exosomal Biomarkers by Aptamer-Mediated Proximity Ligation Assay and Time-Resolved Förster Resonance Energy Transfer. BIOSENSORS 2024; 14:233. [PMID: 38785707 PMCID: PMC11117858 DOI: 10.3390/bios14050233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/29/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024]
Abstract
Exosomal biomarker detection holds great importance in the field of in vitro diagnostics, offering a non-invasive and highly sensitive approach for early disease detection and personalized treatment. Here, we proposed an "APPROACH" strategy, combining aptamer-mediated proximity ligation assay (PLA) with rolling circle amplification (RCA) and time-resolved Förster resonance energy transfer (TR-FRET) for the sensitive and semi-homogenous detection of exosomal biomarkers. PLA probes consisted of a cholesterol-conjugated oligonucleotide, which anchored to the membrane of an exosome, and a specific aptamer oligonucleotide that recognized a target protein of the exosome; the proximal binding of pairs of PLA probes to the same exosome positioned the oligonucleotides in the vicinity of each other, guiding the hybridization and ligation of two subsequently added backbone and connector oligonucleotides to form a circular DNA molecule. Circular DNA formed from PLA underwent rolling circle amplification (RCA) for signal amplification, and the resulting RCA products were subsequently quantified by TR-FRET. The limits of detection provided by APPROACH for the exosomal biomarkers CD63, PD-L1, and HER2 were 0.46 ng∙μL-1, 0.77 ng∙μL-1, and 1.1 ng∙μL-1, respectively, demonstrating excellent analytical performance with high sensitivity and quantification accuracy. Furthermore, the strategy afforded sensitive detection of exosomal CD63 with a LOD of 1.56 ng∙μL-1 in complex biological matrices, which underscored its anti-interference capability and potential for in vitro detection. The proposed strategy demonstrates wide-ranging applicability in quantifying diverse exosomal biomarkers while exhibiting robust analytical characteristics, including high sensitivity and accuracy.
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Affiliation(s)
- Ying Li
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drug, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (Y.L.); (M.Q.)
| | - Meiqi Qian
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drug, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (Y.L.); (M.Q.)
| | | | - Xue Qiu
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drug, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (Y.L.); (M.Q.)
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5
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Bruce-Tagoe TA, Harnish MT, Soleimani S, Ullah N, Shen T, Danquah MK. Surface plasmon resonance aptasensing and computational analysis of Staphylococcus aureus IsdA surface protein. Biotechnol Prog 2024:e3475. [PMID: 38682836 DOI: 10.1002/btpr.3475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/01/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024]
Abstract
Staphylococcus aureus (S. aureus), a common foodborne pathogen, poses significant public health challenges due to its association with various infectious diseases. A key player in its pathogenicity, which is the IsdA protein, is an essential virulence factor in S. aureus infections. In this work, we present an integrated in-silico and experimental approach using MD simulations and surface plasmon resonance (SPR)-based aptasensing measurements to investigate S. aureus biorecognition via IsdA surface protein binding. SPR, a powerful real-time and label-free technique, was utilized to characterize interaction dynamics between the aptamer and IsdA protein, and MD simulations was used to characterize the stable and dynamic binding regions. By characterizing and optimizing pivotal parameters such as aptamer concentration and buffer conditions, we determined the aptamer's binding performance. Under optimal conditions of pH 7.4 and 150 mM NaCl concentration, the kinetic parameters were determined; ka = 3.789 × 104/Ms, kd = 1.798 × 103/s, and KD = 4.745 × 10-8 M. The simulations revealed regions of interest in the IsdA-aptamer complex. Region I, which includes interactions between amino acid residues H106 and R107 and nucleotide residues 9G, 10U, 11G and 12U of the aptamer, had the strongest interaction, based on ΔG and B-factor values, and hence contributed the most to the stability of the interaction. Region II, which covers residue 37A reflects the dynamic nature of the interaction due to frequent contacts. The approach presents a rigorous characterization of aptamer-IsdA binding behavior, supporting the potential application of the IsdA-binding aptamer system for S. aureus biosensing.
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Affiliation(s)
- Tracy Ann Bruce-Tagoe
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Michael T Harnish
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Shokoufeh Soleimani
- Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Najeeb Ullah
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Michael K Danquah
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
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Léguillier V, Heddi B, Vidic J. Recent Advances in Aptamer-Based Biosensors for Bacterial Detection. BIOSENSORS 2024; 14:210. [PMID: 38785684 PMCID: PMC11117931 DOI: 10.3390/bios14050210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/09/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
The rapid and sensitive detection of pathogenic bacteria is becoming increasingly important for the timely prevention of contamination and the treatment of infections. Biosensors based on nucleic acid aptamers, integrated with optical, electrochemical, and mass-sensitive analytical techniques, have garnered intense interest because of their versatility, cost-efficiency, and ability to exhibit high affinity and specificity in binding bacterial biomarkers, toxins, and whole cells. This review highlights the development of aptamers, their structural characterization, and the chemical modifications enabling optimized recognition properties and enhanced stability in complex biological matrices. Furthermore, recent examples of aptasensors for the detection of bacterial cells, biomarkers, and toxins are discussed. Finally, we explore the barriers to and discuss perspectives on the application of aptamer-based bacterial detection.
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Affiliation(s)
- Vincent Léguillier
- INRAE, AgroParisTech, Micalis Institut, Université Paris-Saclay, UMR 1319, 78350 Jouy-en-Josas, France;
- ENS Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), UMR8113 CNRS, 91190 Gif-sur-Yvette, France
| | - Brahim Heddi
- ENS Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), UMR8113 CNRS, 91190 Gif-sur-Yvette, France
| | - Jasmina Vidic
- INRAE, AgroParisTech, Micalis Institut, Université Paris-Saclay, UMR 1319, 78350 Jouy-en-Josas, France;
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7
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Mahmoudian F, Ahmari A, Shabani S, Sadeghi B, Fahimirad S, Fattahi F. Aptamers as an approach to targeted cancer therapy. Cancer Cell Int 2024; 24:108. [PMID: 38493153 PMCID: PMC10943855 DOI: 10.1186/s12935-024-03295-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Conventional cancer treatments can cause serious side effects because they are not specific to cancer cells and can damage healthy cells. Aptamers often are single-stranded oligonucleotides arranged in a unique architecture, allowing them to bind specifically to target sites. This feature makes them an ideal choice for targeted therapeutics. They are typically produced through the systematic evolution of ligands by exponential enrichment (SELEX) and undergo extensive pharmacological revision to modify their affinity, specificity, and therapeutic half-life. Aptamers can act as drugs themselves, directly inhibiting tumor cells. Alternatively, they can be used in targeted drug delivery systems to transport drugs directly to tumor cells, minimizing toxicity to healthy cells. In this review, we will discuss the latest and most advanced approaches to using aptamers for cancer treatment, particularly targeted therapy overcoming resistance to conventional therapies.
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Affiliation(s)
- Fatemeh Mahmoudian
- Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran
| | - Azin Ahmari
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran
- Department of Radiation Oncology, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Shiva Shabani
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran
- Department of Infectious Diseases, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Bahman Sadeghi
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran
- Department of Community Medicine, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Shohreh Fahimirad
- Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran.
| | - Fahimeh Fattahi
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran.
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.
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8
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Autiero I, Vitagliano L. Enhanced molecular dynamic simulation studies unravel long-range effects caused by sequence variations and partner binding in RNA aptamers. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102039. [PMID: 37869259 PMCID: PMC10585333 DOI: 10.1016/j.omtn.2023.102039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 09/23/2023] [Indexed: 10/24/2023]
Abstract
Intrinsic flexibility and structural modularity are two common features of RNA molecules. Although functionally crucial, RNA plasticity often represents a major complication in high-resolution structural studies. To overcome this problem, RNAs may be rigidified through the complexation with high-affinity partners such as Fab molecules. This approach has been previously used to characterize the DIR2-aptamer. However, possible perturbations induced by the insertion of the Fab binding site on the DIR2-aptamer conformational properties were not investigated. Here, using enhanced molecular dynamics simulations, we compared the dynamics of the DIR2 aptamer holding the Fab binding site with that of the parental sequence. Our results suggest that the L2-loop modification for the Fab recognition leads to a significant increase in local flexibility that also affects the mobility of distant regions. The trajectories provide clear indications of the groups and the interactions mediating the dynamics transfer in DIR2. The effectiveness of our approach in addressing RNA flexibility was further corroborated by showing its ability to reproduce the most important events affecting the NF-κB RNA aptamer upon dissociation from the partner. Therefore, REMD analyses, a rarely adopted technique to unravel the structural/dynamical properties of aptamers, could efficiently complement experimental data guiding the rational design of nucleic acid therapeutics.
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Affiliation(s)
- Ida Autiero
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
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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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10
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Troisi R, Balasco N, Autiero I, Vitagliano L, Sica F. Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies. Int J Mol Sci 2023; 24:16318. [PMID: 38003510 PMCID: PMC10671752 DOI: 10.3390/ijms242216318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Aptamers are synthetic nucleic acids that are developed to target with high affinity and specificity chemical entities ranging from single ions to macromolecules and present a wide range of chemical and physical properties. Their ability to selectively bind proteins has made these compounds very attractive and versatile tools, in both basic and applied sciences, to such an extent that they are considered an appealing alternative to antibodies. Here, by exhaustively surveying the content of the Protein Data Bank (PDB), we review the structural aspects of the protein-aptamer recognition process. As a result of three decades of structural studies, we identified 144 PDB entries containing atomic-level information on protein-aptamer complexes. Interestingly, we found a remarkable increase in the number of determined structures in the last two years as a consequence of the effective application of the cryo-electron microscopy technique to these systems. In the present paper, particular attention is devoted to the articulated architectures that protein-aptamer complexes may exhibit. Moreover, the molecular mechanism of the binding process was analyzed by collecting all available information on the structural transitions that aptamers undergo, from their protein-unbound to the protein-bound state. The contribution of computational approaches in this area is also highlighted.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Department of Chemistry, University of Rome Sapienza, 00185 Rome, Italy;
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
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11
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Venkatesan S, Chanda K, Balamurali MM. Recent Advancements of Aptamers in Cancer Therapy. ACS OMEGA 2023; 8:32231-32243. [PMID: 37720779 PMCID: PMC10500573 DOI: 10.1021/acsomega.3c04345] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/02/2023] [Indexed: 09/19/2023]
Abstract
Aptamers are chemical antibodies possessing the capability of overcoming the limitations posed by conventional antibodies, particularly for diagnostic, therapeutic, and theranostic applications in cancer. The ease of chemical modifications or functionalization, including conjugations with nucleic acids, drug molecules, and nanoparticles, has made these aptamers to gain priorities in research. In this Mini-review, various reports on therapeutics with aptamer-functionalized nanomaterials for controlled or multistep drug release, targeted delivery, stimuli-responsive drug release, etc. are discussed. In the case of nucleic-acid-conjugated aptamers, DNA nanotrains and DNA beacons are discussed in terms of the possibility of multidrug loading for chemotherapy and gene therapy. Developments with electrochemical aptasensors and signal-enhanced immune aptasensors are also discussed. Further, the future scope of aptamer technology in cancer theranostics and the prevailing limitations are discussed.
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Affiliation(s)
- Swathi Venkatesan
- Chemistry
Division, School of Advanced Sciences, Vellore
Institute of Technology, Chennai, Tamil Nadu 600027, India
| | - Kaushik Chanda
- Department
of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Musuvathi Motilal Balamurali
- Chemistry
Division, School of Advanced Sciences, Vellore
Institute of Technology, Chennai, Tamil Nadu 600027, India
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12
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Teng X, Wang Y, You L, Wei L, Zhang C, Du Y. Screening a DNA Aptamer Specifically Targeting Integrin β3 and Partially Inhibiting Tumor Cell Migration. Anal Chem 2023; 95:12406-12418. [PMID: 37555842 PMCID: PMC10448441 DOI: 10.1021/acs.analchem.3c01995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023]
Abstract
Due to its key roles in malignant tumor progression and reprograming of the tumor microenvironment, integrin β3 has attracted great attention as a new target for tumor therapy. However, the structure-function relationship of integrins β3 remains incompletely understood, leading to the shortage of specific and effective targeting probes. This work uses a purified extracellular domain of integrin β3 and integrin β3-positive cells to screen aptamers, specifically targeting integrin β3 in the native conformation on live cells through the SELEX approach. Following meticulous truncation and characterization of the initial aptamer candidates, the optimized aptamer S10yh2 was produced, exhibiting a low equilibrium dissociation constant (Kd) in the nanomolar range. S10yh2 displays specific recognition of cancer cells with varying levels of integrin β3 expression and demonstrates favorable stability in serum. Subsequent analysis of docking sites revealed that S10yh2 binds to the seven amino acid residues located in the core region of integrin β3. The S10yh2 aptamer can downregulate the level of integrin heterodimer αvβ3 on integrin β3 overexpressed cancer cells and partially inhibit cell migration behavior. In summary, S10yh2 is a promising probe with a small size, simple synthesis, good stability, high binding affinity, and selectivity. It therefore holds great potential for investigating the structure-function relationship of integrins.
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Affiliation(s)
- Xiaoyan Teng
- Department
of Laboratory Medicine, Shanghai Jiao Tong
University Affiliated Sixth People’s Hospital, Shanghai 200233, China
| | - Yu Wang
- State
Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute,
Department of Oncology, Institute of Molecular Medicine, Renji Hospital,
School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liuxia You
- Department
of Clinical Laboratory, The Second Affiliated
Hospital of Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Lirong Wei
- Department
of Laboratory Medicine, Shanghai Jiao Tong
University Affiliated Sixth People’s Hospital, Shanghai 200233, China
| | - Chao Zhang
- State
Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute,
Department of Oncology, Institute of Molecular Medicine, Renji Hospital,
School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yuzhen Du
- Department
of Laboratory Medicine, Shanghai Jiao Tong
University Affiliated Sixth People’s Hospital, Shanghai 200233, China
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13
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DeRosa M, Lin A, Mallikaratchy P, McConnell E, McKeague M, Patel R, Shigdar S. In vitro selection of aptamers and their applications. NATURE REVIEWS. METHODS PRIMERS 2023; 3:55. [PMID: 37969927 PMCID: PMC10647184 DOI: 10.1038/s43586-023-00247-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The introduction of the in-vitro evolution method known as SELEX (Systematic Evolution of Ligands by Exponential enrichment) more than 30 years ago led to the conception of versatile synthetic receptors known as aptamers. Offering many benefits such as low cost, high stability and flexibility, aptamers have sparked innovation in molecular diagnostics, enabled advances in synthetic biology and have facilitated new therapeutic approaches. The SELEX method itself is inherently adaptable and offers near limitless possibilities in yielding functional nucleic acid ligands. This Primer serves to provide guidance on experimental design and highlight new growth areas for this impactful technology.
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Affiliation(s)
- M.C. DeRosa
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - A. Lin
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
| | - P. Mallikaratchy
- Department of Molecular, Cellular, and Biomedical Sciences, City University of New York School of Medicine, New York, NY 10031, USA
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - E.M. McConnell
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - M. McKeague
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada, H3G 1Y6
| | - R. Patel
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - S. Shigdar
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC 3220, Australia
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14
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Rahman MS, Han MJ, Kim SW, Kang SM, Kim BR, Kim H, Lee CJ, Noh JE, Kim H, Lee JO, Jang SK. Structure-Guided Development of Bivalent Aptamers Blocking SARS-CoV-2 Infection. Molecules 2023; 28:4645. [PMID: 37375202 DOI: 10.3390/molecules28124645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused devastation to human society through its high virulence, infectivity, and genomic mutations, which reduced the efficacy of vaccines. Here, we report the development of aptamers that effectively interfere with SARS-CoV-2 infection by targeting its spike protein, which plays a pivotal role in host cell entry of the virus through interaction with the viral receptor angiotensin-converting enzyme 2 (ACE2). To develop highly effective aptamers and to understand their mechanism in inhibiting viral infection, we determined the three-dimensional (3D) structures of aptamer/receptor-binding domain (RBD) complexes using cryogenic electron microscopy (cryo-EM). Moreover, we developed bivalent aptamers targeting two distinct regions of the RBD in the spike protein that directly interact with ACE2. One aptamer interferes with the binding of ACE2 by blocking the ACE2-binding site in RBD, and the other aptamer allosterically inhibits ACE2 by binding to a distinct face of RBD. Using the 3D structures of aptamer-RBD complexes, we minimized and optimized these aptamers. By combining the optimized aptamers, we developed a bivalent aptamer that showed a stronger inhibitory effect on virus infection than the component aptamers. This study confirms that the structure-based aptamer-design approach has a high potential in developing antiviral drugs against SARS-CoV-2 and other viruses.
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Affiliation(s)
- Md Shafiqur Rahman
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Min Jung Han
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Sang Won Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Seong Mu Kang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Bo Ri Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Heesun Kim
- Division of Integrative Bioscience & Biotechnology, POSTECH Biotech Center, Pohang University of Science and Technology, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Chang Jun Lee
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Jung Eun Noh
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Hanseong Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Jie-Oh Lee
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Sung Key Jang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
- Division of Integrative Bioscience & Biotechnology, POSTECH Biotech Center, Pohang University of Science and Technology, Nam-gu, Pohang-si 37673, Republic of Korea
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15
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Sullivan MV, Allabush F, Flynn H, Balansethupathy B, Reed JA, Barnes ET, Robson C, O'Hara P, Milburn LJ, Bunka D, Tolley A, Mendes PM, Tucker JHR, Turner NW. Highly Selective Aptamer-Molecularly Imprinted Polymer Hybrids for Recognition of SARS-CoV-2 Spike Protein Variants. GLOBAL CHALLENGES (HOBOKEN, NJ) 2023; 7:2200215. [PMID: 37287590 PMCID: PMC10242533 DOI: 10.1002/gch2.202200215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/17/2023] [Indexed: 06/09/2023]
Abstract
Virus recognition has been driven to the forefront of molecular recognition research due to the COVID-19 pandemic. Development of highly sensitive recognition elements, both natural and synthetic is critical to facing such a global issue. However, as viruses mutate, it is possible for their recognition to wane through changes in the target substrate, which can lead to detection avoidance and increased false negatives. Likewise, the ability to detect specific variants is of great interest for clinical analysis of all viruses. Here, a hybrid aptamer-molecularly imprinted polymer (aptaMIP), that maintains selective recognition for the spike protein template across various mutations, while improving performance over individual aptamer or MIP components (which themselves demonstrate excellent performance). The aptaMIP exhibits an equilibrium dissociation constant of 1.61 nM toward its template which matches or exceeds published examples of imprinting of the spike protein. The work here demonstrates that "fixing" the aptamer within a polymeric scaffold increases its capability to selectivity recognize its original target and points toward a methodology that will allow variant selective molecular recognition with exceptional affinity.
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Affiliation(s)
- Mark V. Sullivan
- Leicester School of PharmacyDe Montfort UniversityThe GatewayLeicesterLE1 9BHUK
| | - Francia Allabush
- School of Chemical EngineeringUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Harriet Flynn
- The Aptamer GroupWindmill HouseInnovation WayHeslingtonYork, YO10 5BRUK
| | | | - Joseph A. Reed
- The Aptamer GroupWindmill HouseInnovation WayHeslingtonYork, YO10 5BRUK
| | - Edward T. Barnes
- The Aptamer GroupWindmill HouseInnovation WayHeslingtonYork, YO10 5BRUK
| | - Callum Robson
- The Aptamer GroupWindmill HouseInnovation WayHeslingtonYork, YO10 5BRUK
| | - Phoebe O'Hara
- The Aptamer GroupWindmill HouseInnovation WayHeslingtonYork, YO10 5BRUK
| | - Laura J. Milburn
- The Aptamer GroupWindmill HouseInnovation WayHeslingtonYork, YO10 5BRUK
| | - David Bunka
- The Aptamer GroupWindmill HouseInnovation WayHeslingtonYork, YO10 5BRUK
| | - Arron Tolley
- The Aptamer GroupWindmill HouseInnovation WayHeslingtonYork, YO10 5BRUK
| | - Paula M. Mendes
- School of Chemical EngineeringUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | | | - Nicholas W. Turner
- Leicester School of PharmacyDe Montfort UniversityThe GatewayLeicesterLE1 9BHUK
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16
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Aslan Y, Atabay M, Chowdhury HK, Göktürk I, Saylan Y, Inci F. Aptamer-Based Point-of-Care Devices: Emerging Technologies and Integration of Computational Methods. BIOSENSORS 2023; 13:bios13050569. [PMID: 37232930 DOI: 10.3390/bios13050569] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
Recent innovations in point-of-care (POC) diagnostic technologies have paved a critical road for the improved application of biomedicine through the deployment of accurate and affordable programs into resource-scarce settings. The utilization of antibodies as a bio-recognition element in POC devices is currently limited due to obstacles associated with cost and production, impeding its widespread adoption. One promising alternative, on the other hand, is aptamer integration, i.e., short sequences of single-stranded DNA and RNA structures. The advantageous properties of these molecules are as follows: small molecular size, amenability to chemical modification, low- or nonimmunogenic characteristics, and their reproducibility within a short generation time. The utilization of these aforementioned features is critical in developing sensitive and portable POC systems. Furthermore, the deficiencies related to past experimental efforts to improve biosensor schematics, including the design of biorecognition elements, can be tackled with the integration of computational tools. These complementary tools enable the prediction of the reliability and functionality of the molecular structure of aptamers. In this review, we have overviewed the usage of aptamers in the development of novel and portable POC devices, in addition to highlighting the insights that simulations and other computational methods can provide into the use of aptamer modeling for POC integration.
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Affiliation(s)
- Yusuf Aslan
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Maryam Atabay
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Hussain Kawsar Chowdhury
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Ilgım Göktürk
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Yeşeren Saylan
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Fatih Inci
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
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17
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Carrión-Marchante R, Pinto-Díez C, Klett-Mingo JI, Palacios E, Barragán-Usero M, Pérez-Morgado MI, Pascual-Mellado M, Alcalá S, Ruiz-Cañas L, Sainz B, González VM, Martín ME. An Aptamer against MNK1 for Non-Small Cell Lung Cancer Treatment. Pharmaceutics 2023; 15:pharmaceutics15041273. [PMID: 37111758 PMCID: PMC10146192 DOI: 10.3390/pharmaceutics15041273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related death worldwide. Its late diagnosis and consequently poor survival make necessary the search for new therapeutic targets. The mitogen-activated protein kinase (MAPK)-interacting kinase 1 (MNK1) is overexpressed in lung cancer and correlates with poor overall survival in non-small cell lung cancer (NSCLC) patients. The previously identified and optimized aptamer from our laboratory against MNK1, apMNKQ2, showed promising results as an antitumor drug in breast cancer in vitro and in vivo. Thus, the present study shows the antitumor potential of apMNKQ2 in another type of cancer where MNK1 plays a significant role, such as NSCLC. The effect of apMNKQ2 in lung cancer was studied with viability, toxicity, clonogenic, migration, invasion, and in vivo efficacy assays. Our results show that apMNKQ2 arrests the cell cycle and reduces viability, colony formation, migration, invasion, and epithelial-mesenchymal transition (EMT) processes in NSCLC cells. In addition, apMNKQ2 reduces tumor growth in an A549-cell line NSCLC xenograft model. In summary, targeting MNK1 with a specific aptamer may provide an innovative strategy for lung cancer treatment.
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Affiliation(s)
- Rebeca Carrión-Marchante
- Aptamer Group, Deparment Biochemistry-Research, IRYCIS-Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | | | - José Ignacio Klett-Mingo
- Aptamer Group, Deparment Biochemistry-Research, IRYCIS-Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Esther Palacios
- Aptamer Group, Deparment Biochemistry-Research, IRYCIS-Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Miriam Barragán-Usero
- Aptamer Group, Deparment Biochemistry-Research, IRYCIS-Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - M Isabel Pérez-Morgado
- Aptamer Group, Deparment Biochemistry-Research, IRYCIS-Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Manuel Pascual-Mellado
- Aptamer Group, Deparment Biochemistry-Research, IRYCIS-Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Sonia Alcalá
- Department of Cancer, Instituto de Investigaciones-Biomédicas "Alberto Sols" (IIBM), CSIC-UAM, 28034 Madrid, Spain
- Chronic Diseases and Cancer Area 3-Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Laura Ruiz-Cañas
- Department of Cancer, Instituto de Investigaciones-Biomédicas "Alberto Sols" (IIBM), CSIC-UAM, 28034 Madrid, Spain
- Chronic Diseases and Cancer Area 3-Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Bruno Sainz
- Department of Cancer, Instituto de Investigaciones-Biomédicas "Alberto Sols" (IIBM), CSIC-UAM, 28034 Madrid, Spain
- Chronic Diseases and Cancer Area 3-Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- Centro de Investigación Biomédica en Red, Área Cáncer-CIBERONC, ISCIII, 28029 Madrid, Spain
| | - Víctor M González
- Aptamer Group, Deparment Biochemistry-Research, IRYCIS-Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - M Elena Martín
- Aptamer Group, Deparment Biochemistry-Research, IRYCIS-Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
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18
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Aptamer-functionalized capacitive biosensors. Biosens Bioelectron 2023; 224:115014. [PMID: 36628826 DOI: 10.1016/j.bios.2022.115014] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/17/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022]
Abstract
The growing use of aptamers as target recognition elements in label-free biosensing necessitates corresponding transducers that can be used in relevant environments. While popular in many fields, capacitive sensors have seen relatively little, but growing use in conjunction with aptamers for sensing diverse targets. Few reports have shown physiologically relevant sensitivity in laboratory conditions and a cohesive picture on how target capture modifies the measured capacitance has been lacking. In this review, we assess the current state of the field in three areas: small molecule, protein, and cell sensing. We critically analyze the proposed hypotheses on how aptamer-target capture modifies the capacitance, as many mechanistic postulations appear to conflict between published works. As the field matures, we encourage future works to investigate individual aptamer-target interactions and to interrogate the physical mechanisms leading to measured changes in capacitance. To this point, we provide recommendations on best practices for developing aptasensors with a particular focus on considerations for biosensing in clinical settings.
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19
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Shien Yeoh T, Yusof Hazrina H, Bukari BA, Tang TH, Citartan M. Generation of an RNA aptamer against LipL32 of Leptospira isolated by Tripartite-hybrid SELEX coupled with in-house Python-aided unbiased data sorting. Bioorg Med Chem 2023; 81:117186. [PMID: 36812779 DOI: 10.1016/j.bmc.2023.117186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023]
Abstract
Leptospirosis is a potentially life-threatening zoonosis caused by pathogenic Leptospira. The major hurdle of the diagnosis of Leptospirosis lies in the issues associated with current methods of detection, which are time-consuming, tedious and the need for sophisticated, special equipments. Restrategizing the diagnostics of Leptospirosis may involve considerations of the direct detection of the outer membrane protein, which can be faster, cost-saving and require fewer equipments. One such promising marker is LipL32, which is an antigen with high amino acid sequence conservation among all the pathogenic strains. In this study, we endeavored to isolate an aptamer against LipL32 protein via a modified SELEX strategy known as tripartite-hybrid SELEX, based on 3 different partitioning strategies. In this study, we also demonstrated the deconvolution of the candidate aptamers by using in-house Python-aided unbiased data sorting in examining multiple parameters to isolate potent aptamers. We have successfully generated an RNA aptamer against LipL32 of Leptospira, LepRapt-11, which is applicable in a simple direct ELASA for the detection of LipL32. LepRapt-11 can be a promising molecular recognition element for the diagnosis of leptospirosis by targeting LipL32.
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Affiliation(s)
- Tzi Shien Yeoh
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Hamdani Yusof Hazrina
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Bakhtiar A Bukari
- School of Medicine, Deakin University, 3216 Geelong, Victoria, Australia
| | - Thean-Hock Tang
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Marimuthu Citartan
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia.
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20
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Banerjee S, Hemmat MA, Shubham S, Gosai A, Devarakonda S, Jiang N, Geekiyanage C, Dillard JA, Maury W, Shrotriya P, Lamm MH, Nilsen-Hamilton M. Structurally Different Yet Functionally Similar: Aptamers Specific for the Ebola Virus Soluble Glycoprotein and GP1,2 and Their Application in Electrochemical Sensing. Int J Mol Sci 2023; 24:4627. [PMID: 36902059 PMCID: PMC10003157 DOI: 10.3390/ijms24054627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023] Open
Abstract
The Ebola virus glycoprotein (GP) gene templates several mRNAs that produce either the virion-associated transmembrane protein or one of two secreted glycoproteins. Soluble glycoprotein (sGP) is the predominant product. GP1 and sGP share an amino terminal sequence of 295 amino acids but differ in quaternary structure, with GP1 being a heterohexamer with GP2 and sGP a homodimer. Two structurally different DNA aptamers were selected against sGP that also bound GP1,2. These DNA aptamers were compared with a 2'FY-RNA aptamer for their interactions with the Ebola GP gene products. The three aptamers have almost identical binding isotherms for sGP and GP1,2 in solution and on the virion. They demonstrated high affinity and selectivity for sGP and GP1,2. Furthermore, one aptamer, used as a sensing element in an electrochemical format, detected GP1,2 on pseudotyped virions and sGP with high sensitivity in the presence of serum, including from an Ebola-virus-infected monkey. Our results suggest that the aptamers interact with sGP across the interface between the monomers, which is different from the sites on the protein bound by most antibodies. The remarkable similarity in functional features of three structurally distinct aptamers suggests that aptamers, like antibodies, have preferred binding sites on proteins.
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Affiliation(s)
- Soma Banerjee
- Ames Laboratory, U.S. Department of Energy, Ames, IA 50011, USA
| | - Mahsa Askary Hemmat
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Shambhavi Shubham
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Agnivo Gosai
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA
| | | | - Nianyu Jiang
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA
| | | | - Jacob A. Dillard
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 50011, USA
| | - Wendy Maury
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 50011, USA
| | - Pranav Shrotriya
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA
| | - Monica H. Lamm
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
| | - Marit Nilsen-Hamilton
- Ames Laboratory, U.S. Department of Energy, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
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21
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Hemin-catalyzed SI-RAFT polymerization for thrombin detection. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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22
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Selection of spore-specific aptamers for Geobacillus stearothermophilus, a food spoilage bacterium. Anal Biochem 2023; 662:114999. [PMID: 36519741 DOI: 10.1016/j.ab.2022.114999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Due to their ability to form extremely heat resistant spores, anaerobic bacteria are responsible for frequent food spoilage. The development of rapid and specific methods for the detection and quantification of spore contamination is therefore of major interest. In this paper, we describe for the first time the selection of aptamers specific to spores of Geobacillus stearothermophilus (Gbs), which induce flat sour spoilage in vegetable cans. Eighteen Spore-SELEX cycles were performed including 4 counter-selections with 12 bacteria commonly found in cannery. To optimise candidate amplification, PCR in emulsion was performed, and high-throughput sequencing analysis was applied to follow candidate evolution. Sequencing of aptamers from cycle 18 revealed 43 overrepresented sequences whose copy number exceeds 0.15% of the total obtained sequences. Within this group, the A01 aptamer presented a much higher enrichment with a relative abundance of 17.71%. Affinity and specificity for Gbs spores of the 10 most abundant candidates at cycle 18 were confirmed by PCR assay based on aptamer-spore complex formation and filtration step. Obtaining these aptamers is the starting point for the future development of biosensors dedicated to the detection of Gbs spores.
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23
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Ramasanoff RR, Sokolov PA. The binding model of adenosine-specific DNA aptamer: Umbrella sampling study. J Mol Graph Model 2023; 118:108338. [PMID: 36201878 DOI: 10.1016/j.jmgm.2022.108338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/25/2022]
Abstract
We report a novel model of the selective binding mechanism of adenosine-specific DNA aptamer. Our theoretical investigations of AMP (Adenosine monophosphate) dissociation from aptamer-AMP complexes reveals new details of aptamer molecular specificity and stabilisation factors. Umbrella sampling MD calculations using parmbsc1 force field shows that the disordered structure of the internal loop of the unbound aptamer hairpin has a characteristic packing of guanines, which prevents barrier-free penetration of ligands into the site cavity. Also, this disordered structure of the unbound aptamer has a network of hydrogen bonds stabilising the cavity near the target guanines within the binding sites during the whole binding process. We suggested that the first AMP molecule binds to the disordered structure of the site closest to the aptamer hairpin stem and spends some free energy on ordering of the internal loop. Then the second AMP molecule binds to the ordered site closest to the aptamer hairpin loop with a lower energy gain. As a result, the induced-fit binding model is the most applicable for this aptamer and does not contradict the modern experimental NMR and calorimetry data.
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Affiliation(s)
- Ruslan R Ramasanoff
- Sevastopol State University, Universitetskaya 33, 299053, Sevastopol, Russia.
| | - Petr A Sokolov
- Sevastopol State University, Universitetskaya 33, 299053, Sevastopol, Russia; Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034, Saint Petersburg, Russia
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24
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Thalhammer A, Bröker NK. Biophysical Approaches for the Characterization of Protein-Metabolite Interactions. Methods Mol Biol 2023; 2554:199-229. [PMID: 36178628 DOI: 10.1007/978-1-0716-2624-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
With an estimate of hundred thousands of protein molecules per cell and the number of metabolites several orders of magnitude higher, protein-metabolite interactions are omnipresent. In vitro analyses are one of the main pillars on the way to establish a solid understanding of how these interactions contribute to maintaining cellular homeostasis. A repertoire of biophysical techniques is available by which protein-metabolite interactions can be quantitatively characterized in terms of affinity, specificity, and kinetics in a broad variety of solution environments. Several of those provide information on local or global conformational changes of the protein partner in response to ligand binding. This review chapter gives an overview of the state-of-the-art biophysical toolbox for the study of protein-metabolite interactions. It briefly introduces basic principles, highlights recent examples from the literature, and pinpoints promising future directions.
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Affiliation(s)
- Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Potsdam, Germany.
| | - Nina K Bröker
- Physical Biochemistry, University of Potsdam, Potsdam, Germany
- Health and Medical University Potsdam, Potsdam, Germany
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25
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Shraim AS, Abdel Majeed BA, Al-Binni M, Hunaiti A. Therapeutic Potential of Aptamer-Protein Interactions. ACS Pharmacol Transl Sci 2022; 5:1211-1227. [PMID: 36524009 PMCID: PMC9745894 DOI: 10.1021/acsptsci.2c00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Indexed: 11/06/2022]
Abstract
Aptamers are single-stranded oligonucleotides (RNA or DNA) with a typical length between 25 and 100 nucleotides which fold into three-dimensional structures capable of binding to target molecules. Specific aptamers can be isolated against a large variety of targets through efficient and relatively cheap methods, and they demonstrate target-binding affinities that sometimes surpass those of antibodies. Consequently, interest in aptamers has surged over the past three decades, and their application has shown promise in advancing knowledge in target analysis, designing therapeutic interventions, and bioengineering. With emphasis on their therapeutic applications, aptamers are emerging as a new innovative class of therapeutic agents with promising biochemical and biological properties. Aptamers have the potential of providing a feasible alternative to antibody- and small-molecule-based therapeutics given their binding specificity, stability, low toxicity, and apparent non-immunogenicity. This Review examines the general properties of aptamers and aptamer-protein interactions that help to understand their binding characteristics and make them important therapeutic candidates.
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Affiliation(s)
- Ala’a S. Shraim
- Department
of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, 19328 Amman, Jordan
- Pharmacological
and Diagnostic Research Center (PDRC), Al-Ahliyya
Amman University, 19328 Amman, Jordan
| | - Bayan A. Abdel Majeed
- Department
of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, 19328 Amman, Jordan
- Pharmacological
and Diagnostic Research Center (PDRC), Al-Ahliyya
Amman University, 19328 Amman, Jordan
| | - Maysaa’
Adnan Al-Binni
- Department
of Clinical Laboratory Sciences, School of Science, The University of Jordan, 11942 Amman, Jordan
| | - Abdelrahim Hunaiti
- Department
of Clinical Laboratory Sciences, School of Science, The University of Jordan, 11942 Amman, Jordan
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26
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Aptamers Regulating the Hemostasis System. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238593. [PMID: 36500686 PMCID: PMC9739204 DOI: 10.3390/molecules27238593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
The hemostasis system is a complex structure that includes the fibrinolysis system, and Yes this is correct coagulation and anticoagulation parts. Due to the multicomponent nature, it becomes relevant to study the key changes in the functioning of signaling pathways, and develop new diagnostic methods and modern drugs with high selectivity. One of the ways to solve this problem is the development of molecular recognition elements capable of blocking one of the hemostasis systems and/or activating another. Aptamers can serve as ligands for targeting specific clinical needs, promising anticoagulants with minor side effects and significant biological activity. Aptamers with several clotting factors and platelet proteins are used for the treatment of thrombosis. This review is focused on the aptamers used for the correction of the hemostasis system, and their structural and functional features. G-rich nucleic acid aptamers, mostly versatile G-quadruplexes, recognize different components of the hemostasis system and are capable of correcting the functioning.
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27
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Cai R, Chen X, Zhang Y, Wang X, Zhou N. Systematic bio-fabrication of aptamers and their applications in engineering biology. SYSTEMS MICROBIOLOGY AND BIOMANUFACTURING 2022; 3:223-245. [PMID: 38013802 PMCID: PMC9550155 DOI: 10.1007/s43393-022-00140-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 10/27/2022]
Abstract
Aptamers are single-stranded DNA or RNA molecules that have high affinity and selectivity to bind to specific targets. Compared to antibodies, aptamers are easy to in vitro synthesize with low cost, and exhibit excellent thermal stability and programmability. With these features, aptamers have been widely used in biology and medicine-related fields. In the meantime, a variety of systematic evolution of ligands by exponential enrichment (SELEX) technologies have been developed to screen aptamers for various targets. According to the characteristics of targets, customizing appropriate SELEX technology and post-SELEX optimization helps to obtain ideal aptamers with high affinity and specificity. In this review, we first summarize the latest research on the systematic bio-fabrication of aptamers, including various SELEX technologies, post-SELEX optimization, and aptamer modification technology. These procedures not only help to gain the aptamer sequences but also provide insights into the relationship between structure and function of the aptamers. The latter provides a new perspective for the systems bio-fabrication of aptamers. Furthermore, on this basis, we review the applications of aptamers, particularly in the fields of engineering biology, including industrial biotechnology, medical and health engineering, and environmental and food safety monitoring. And the encountered challenges and prospects are discussed, providing an outlook for the future development of aptamers.
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Affiliation(s)
- Rongfeng Cai
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Xin Chen
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Yuting Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Xiaoli Wang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Nandi Zhou
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
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28
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Evtugyn G, Porfireva A, Tsekenis G, Oravczova V, Hianik T. Electrochemical Aptasensors for Antibiotics Detection: Recent Achievements and Applications for Monitoring Food Safety. SENSORS (BASEL, SWITZERLAND) 2022; 22:3684. [PMID: 35632093 PMCID: PMC9143886 DOI: 10.3390/s22103684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Antibiotics are often used in human and veterinary medicine for the treatment of bacterial diseases. However, extensive use of antibiotics in agriculture can result in the contamination of common food staples such as milk. Consumption of contaminated products can cause serious illness and a rise in antibiotic resistance. Conventional methods of antibiotics detection such are microbiological assays chromatographic and mass spectroscopy methods are sensitive; however, they require qualified personnel, expensive instruments, and sample pretreatment. Biosensor technology can overcome these drawbacks. This review is focused on the recent achievements in the electrochemical biosensors based on nucleic acid aptamers for antibiotic detection. A brief explanation of conventional methods of antibiotic detection is also provided. The methods of the aptamer selection are explained, together with the approach used for the improvement of aptamer affinity by post-SELEX modification and computer modeling. The substantial focus of this review is on the explanation of the principles of the electrochemical detection of antibiotics by aptasensors and on recent achievements in the development of electrochemical aptasensors. The current trends and problems in practical applications of aptasensors are also discussed.
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Affiliation(s)
- Gennady Evtugyn
- A.M. Butlerov’ Chemistry Institute, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (G.E.); (A.P.)
- Analytical Chemistry Department, Chemical Technology Institute, Ural Federal University, 19 Mira Street, 620002 Ekaterinburg, Russia
| | - Anna Porfireva
- A.M. Butlerov’ Chemistry Institute, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (G.E.); (A.P.)
| | - George Tsekenis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27 Athens, Greece;
| | - Veronika Oravczova
- Department of Nuclear Physics and Biophysics, Comenius University, Mlynska Dolina F1, 842 48 Bratislava, Slovakia;
| | - Tibor Hianik
- Department of Nuclear Physics and Biophysics, Comenius University, Mlynska Dolina F1, 842 48 Bratislava, Slovakia;
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29
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Aptamers: Functional-Structural Studies and Biomedical Applications. Int J Mol Sci 2022; 23:ijms23094796. [PMID: 35563186 PMCID: PMC9101710 DOI: 10.3390/ijms23094796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 04/24/2022] [Indexed: 11/26/2022] Open
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30
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Chakraborty B, Das S, Gupta A, Xiong Y, Vyshnavi TV, Kizer ME, Duan J, Chandrasekaran AR, Wang X. Aptamers for Viral Detection and Inhibition. ACS Infect Dis 2022; 8:667-692. [PMID: 35220716 PMCID: PMC8905934 DOI: 10.1021/acsinfecdis.1c00546] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Indexed: 02/07/2023]
Abstract
Recent times have experienced more than ever the impact of viral infections in humans. Viral infections are known to cause diseases not only in humans but also in plants and animals. Here, we have compiled the literature review of aptamers selected and used for detection and inhibition of viral infections in all three categories: humans, animals, and plants. This review gives an in-depth introduction to aptamers, different types of aptamer selection (SELEX) methodologies, the benefits of using aptamers over commonly used antibody-based strategies, and the structural and functional mechanism of aptasensors for viral detection and therapy. The review is organized based on the different characterization and read-out tools used to detect virus-aptasensor interactions with a detailed index of existing virus-targeting aptamers. Along with addressing recent developments, we also discuss a way forward with aptamers for DNA nanotechnology-based detection and treatment of viral diseases. Overall, this review will serve as a comprehensive resource for aptamer-based strategies in viral diagnostics and treatment.
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Affiliation(s)
- Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sreyashi Das
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, Uttar Pradesh 208016, India
| | - Arushi Gupta
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - T-V Vyshnavi
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Megan E. Kizer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jinwei Duan
- Department of Chemistry and Materials Science, Chang’an University, Xi’an, Shaanxi 710064, China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Xing Wang
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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31
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A Comprehensive Analysis of the Thrombin Binding Aptamer Containing Functionalized Pyrrolo-2'-deoxycytidines. Pharmaceuticals (Basel) 2021; 14:ph14121326. [PMID: 34959726 PMCID: PMC8709445 DOI: 10.3390/ph14121326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 01/07/2023] Open
Abstract
Aptamers constitute an answer for the growing need for targeted therapy development. One of the most well-known representatives of this group of compounds is thrombin binding aptamers (TBA) targeted towards thrombin. The TBA inhibitory activity is determined by its spatial arrangement, which consists of two G-tetrads linked by two shorter TT loops and one longer TGT loop and folds into a unimolecular, antiparallel G-quadruplex structure. Interesting properties of the aptamer can be further improved via the introduction of a number of chemical modifications. Herein, a comprehensive analysis of the influence of pyrrolo-2’-deoxycytidine (Py-dC) and its derivatives on TBA physicochemical and biological properties has been presented. The studies have shown that the presence of modified residues at the T7 position of the TGT loop has only minor effects on TBA thermodynamic stability without affecting its folding topology. All analyzed oligomers exhibit anticoagulant properties, but only aptamer modified with a decyl derivative of Py-dC was able to inhibit thrombin activity more efficiently than unmodified, parental compounds. Importantly, the same compound also possessed the potential to effectively restrain HeLa cell line growth.
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