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Zeng Z, Li W, Zhang J, Hu Z, Wu J, Ye G, Luo Y. Highly sensitive and specific graphene oxide-based FRET aptasensor for quantitative detection of human soluble growth stimulating gene protein 2. Talanta 2024; 271:125629. [PMID: 38245955 DOI: 10.1016/j.talanta.2024.125629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024]
Abstract
Soluble growth stimulation expressed gene 2 (sST2) is a new generation biomarker in the diagnosis and prognosis of heart failure (HF). Here, the sST2-specific aptamers were selected from a random ssDNA library with the full length of 88 nucleotides (nt) via target-immobilized magnetic beads (MB)-based systematic evolution of ligands by exponential enrichment (SELEX) technology. After eight rounds of selection, six aptamers with the most enrichment were selected. Among, the aptamer L1 showed the high-affinity binding to sST2 with the lowest Kd value (77.3 ± 0.05 nM), which was chosen as the optimal aptamer for further molecular docking. Then, the aptamer L1 was used to construct a graphene oxide (GO) - based fluorescence resonance energy transfer (FRET) biosensor for sST2, which exhibits a linear detection range of 0.1-100 μg/ml and a detection limit of 3.7 ng/ml. The aptasensor was applied to detect sST2 in real samples, with a good correlation and agreement with the traditional enzyme-linked immunosorbent assay (ELISA) when quantitative analyzing the sST2 concentration in serum samples from HF patients. The results show that not only an efficient strategy for screening the practicable aptamer, but also a rapid and sensitive detection platform for sST2 were established.
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Affiliation(s)
- Zhikun Zeng
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Wenfeng Li
- The Second Clinical College of Wuhan University, Wuhan, 430071, Hubei, China
| | - Jixuan Zhang
- The Second Clinical College of Wuhan University, Wuhan, 430071, Hubei, China
| | - Zijian Hu
- The First Clinical College of Wuhan University, Wuhan, 430060, Hubei, China
| | - Junyi Wu
- The Second Clinical College of Wuhan University, Wuhan, 430071, Hubei, China
| | - Guangming Ye
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China.
| | - Yi Luo
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China.
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2
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Lee JM, Lee JH, Kim SH, Sim TH, Kim YJ. NXP032 ameliorates cognitive impairment by alleviating the neurovascular aging process in aged mouse brain. Sci Rep 2023; 13:8594. [PMID: 37237085 DOI: 10.1038/s41598-023-35833-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/24/2023] [Indexed: 05/28/2023] Open
Abstract
Vascular aging is well known to be associated with the breakdown of the neurovascular unit (NVU), which is essential for maintaining brain homeostasis and linked to higher cognitive dysfunction. Oxidative stress is believed to be a significant cause of the vascular aging process. Vitamin C is easily oxidized under physiological conditions, so it loses its potent antioxidant activity. We developed a DNA aptamer that enhances the function of vitamin C. NXP032 is the binding form of the aptamer and vitamin C. In this study, we investigated the effect of NXP032 on neurovascular stabilization through the changes of PECAM-1, PDGFR-β, ZO-1, laminin, and glial cells involved in maintaining the integrity of the blood-brain barrier (BBB) in aged mice. NXP032 was orally administered daily for 8 weeks. Compared to young mice and NXP032-treated mice, 20-month-old mice displayed cognitive impairments in Y-maze and passive avoidance tests. NXP032 treatment contributed to reducing the BBB damage by attenuating the fragmentation of microvessels and reducing PDGFR-β, ZO-1, and laminin expression, thereby mitigating astrocytes and microglia activation during normal aging. Based on the results, we suggest that NXP032 reduces vascular aging and may be a novel intervention for aging-induced cognitive impairment.
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Affiliation(s)
- Jae-Min Lee
- College of Nursing Science, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Joo Hee Lee
- Korea Armed Forces Nursing Academy, Daejeon, 34059, Republic of Korea
| | - So Hee Kim
- Department of Nursing, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Tae Hyeok Sim
- Department of Nursing, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Youn-Jung Kim
- College of Nursing Science, Kyung Hee University, Seoul, 02447, Republic of Korea.
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3
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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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4
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Wu G, Liu C, Cao B, Cao Z, Zhai H, Liu B, Jin S, Yang X, Lv C, Wang J. Connective tissue growth factor-targeting DNA aptamer suppresses pannus formation as diagnostics and therapeutics for rheumatoid arthritis. Front Immunol 2022; 13:934061. [PMID: 35990694 PMCID: PMC9389230 DOI: 10.3389/fimmu.2022.934061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
Connective tissue growth factor (CTGF) has been recently acknowledged as an ideal biomarker in the early disease course, participating in the pathogenesis of pannus formation in rheumatoid arthritis (RA). However, existing approaches for the detection of or antagonist targeting CTGF are either lacking or unsatisfactory in the diagnosis and treatment of RA. To address this, we synthesized and screened high-affinity single-stranded DNA aptamers targeting CTGF through a protein-based SELEX procedure. The structurally optimized variant AptW2-1-39-PEG was characterized thoroughly for its high-affinity (KD 7.86 nM), sensitivity (minimum protein binding concentration, 2 ng), specificity (negative binding to other biomarkers of RA), and stability (viability-maintaining duration in human serum, 48 h) properties using various biochemical and biophysical assays. Importantly, we showed the antiproliferative and antiangiogenic activities of the aptamers obtained using functional experiments and further verified the therapeutic effect of the aptamers on joint injury and inflammatory response in collagen-induced arthritis (CIA) mice, thus advancing this study into actual therapeutic application. Furthermore, we revealed that the binding within AptW2-1-39-PEG/CTGF was mediated by the thrombospondin 1 (TSP1) domain of CTGF using robust bioinformatics tools together with immunofluorescence. In conclusion, our results revealed a novel aptamer that holds promise as an additive or alternative approach for CTGF-targeting diagnostics and therapeutics for RA.
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Affiliation(s)
- Gan Wu
- Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Biochemistry, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Can Liu
- Department of Biochemistry, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ben Cao
- Department of Biochemistry, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zelin Cao
- Department of Biochemistry, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Haige Zhai
- Department of Biochemistry, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Bin Liu
- Department of Biochemistry, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shengwei Jin
- Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xinyu Yang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Jianguang Wang, ; Chen Lv, ; Xinyu Yang,
| | - Chen Lv
- Department of Orthopedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Jianguang Wang, ; Chen Lv, ; Xinyu Yang,
| | - Jianguang Wang
- Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Biochemistry, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Jianguang Wang, ; Chen Lv, ; Xinyu Yang,
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5
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Cruz-Hernández CD, Rodríguez-Martínez G, Cortés-Ramírez SA, Morales-Pacheco M, Cruz-Burgos M, Losada-García A, Reyes-Grajeda JP, González-Ramírez I, González-Covarrubias V, Camacho-Arroyo I, Cerbón M, Rodríguez-Dorantes M. Aptamers as Theragnostic Tools in Prostate Cancer. Biomolecules 2022; 12:biom12081056. [PMID: 36008950 PMCID: PMC9406110 DOI: 10.3390/biom12081056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 02/07/2023] Open
Abstract
Despite of the capacity that several drugs have for specific inhibition of the androgen receptor (AR), in most cases, PCa progresses to an androgen-independent stage. In this context, the development of new targeted therapies for prostate cancer (PCa) has remained as a challenge. To overcome this issue, new tools, based on nucleic acids technology, have been developed. Aptamers are small oligonucleotides with a three-dimensional structure capable of interacting with practically any desired target, even large targets such as mammalian cells or viruses. Recently, aptamers have been studied for treatment and detection of many diseases including cancer. In PCa, numerous works have reported their use in the development of new approaches in diagnostics and treatment strategies. Aptamers have been joined with drugs or other specific molecules such as silencing RNAs (aptamer–siRNA chimeras) to specifically reduce the expression of oncogenes in PCa cells. Even though these studies have shown good results in the early stages, more research is still needed to demonstrate the clinical value of aptamers in PCa. The aim of this review was to compile the existing scientific literature regarding the use of aptamers in PCa in both diagnosis and treatment studies. Since Prostate-Specific Membrane Antigen (PSMA) aptamers are the most studied type of aptamers in this field, special emphasis was given to these aptamers.
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Affiliation(s)
- Carlos David Cruz-Hernández
- Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (C.D.C.-H.); (G.R.-M.); (S.A.C.-R.); (M.M.-P.); (M.C.-B.); (A.L.-G.)
| | - Griselda Rodríguez-Martínez
- Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (C.D.C.-H.); (G.R.-M.); (S.A.C.-R.); (M.M.-P.); (M.C.-B.); (A.L.-G.)
| | - Sergio A. Cortés-Ramírez
- Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (C.D.C.-H.); (G.R.-M.); (S.A.C.-R.); (M.M.-P.); (M.C.-B.); (A.L.-G.)
| | - Miguel Morales-Pacheco
- Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (C.D.C.-H.); (G.R.-M.); (S.A.C.-R.); (M.M.-P.); (M.C.-B.); (A.L.-G.)
| | - Marian Cruz-Burgos
- Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (C.D.C.-H.); (G.R.-M.); (S.A.C.-R.); (M.M.-P.); (M.C.-B.); (A.L.-G.)
| | - Alberto Losada-García
- Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (C.D.C.-H.); (G.R.-M.); (S.A.C.-R.); (M.M.-P.); (M.C.-B.); (A.L.-G.)
| | - Juan Pablo Reyes-Grajeda
- Laboratorio de Estructura de Proteínas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico;
| | - Imelda González-Ramírez
- Departamento de Atención a la Salud, Universidad Autónoma Metropolitana–Xochimilco, Mexico City 04960, Mexico;
| | | | - Ignacio Camacho-Arroyo
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico; (I.C.-A.); (M.C.)
| | - Marco Cerbón
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico; (I.C.-A.); (M.C.)
| | - Mauricio Rodríguez-Dorantes
- Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (C.D.C.-H.); (G.R.-M.); (S.A.C.-R.); (M.M.-P.); (M.C.-B.); (A.L.-G.)
- Correspondence:
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6
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The use of high-affinity polyhistidine binders as masking probes for the selection of an NDM-1 specific aptamer. Sci Rep 2022; 12:7936. [PMID: 35562409 PMCID: PMC9106695 DOI: 10.1038/s41598-022-12062-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/04/2022] [Indexed: 12/02/2022] Open
Abstract
The emergence of carbapenemase-producing multi-drug resistant Enterobacteriaceae poses a dramatic, world-wide health risk. Limited treatment options and a lack of easy-to-use methods for the detection of infections with multi-drug resistant bacteria leave the health-care system with a fast-growing challenge. Aptamers are single stranded DNA or RNA molecules that bind to their targets with high affinity and specificity and can therefore serve as outstanding detection probes. However, an effective aptamer selection process is often hampered by non-specific binding. When selections are carried out against recombinant proteins, purification tags (e.g. polyhistidine) serve as attractive side targets, which may impede protein target binding. In this study, aptamer selection was carried out against N-terminally hexa-histidine tagged New Delhi metallo-ß-lactamase 1. After 14 selection rounds binding to polyhistidine was detected rather than to New Delhi metallo-ß-lactamase 1. Hence, the selection strategy was changed. As one aptamer candidate showed remarkable binding affinity to polyhistidine, it was used as a masking probe and selection was restarted from selection round 10. Finally, after three consecutive selection rounds, an aptamer with specific binding properties to New Delhi metallo-ß-lactamase 1 was identified. This aptamer may serve as a much-needed detection probe for New Delhi metallo-ß-lactamase 1 expressing Enterobacteriaceae.
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7
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Ivanov YD, Romanova TS, Malsagova KA, Pleshakova TO, Archakov AI. Use of Silicon Nanowire Sensors for Early Cancer Diagnosis. Molecules 2021; 26:3734. [PMID: 34207397 PMCID: PMC8234636 DOI: 10.3390/molecules26123734] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 11/17/2022] Open
Abstract
The review covers some research conducted in the field of medical and biomedical application of devices based on silicon sensor elements (Si-NW-sensors). The use of Si-NW-sensors is one of the key methods used in a whole range of healthcare fields. Their biomedical use is among the most important ones as they offer opportunities for early diagnosis of oncological pathologies, for monitoring the prescribed therapy and for improving the people's quality of life.
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Affiliation(s)
| | | | - Kristina A. Malsagova
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (Y.D.I.); (T.S.R.); (T.O.P.); (A.I.A.)
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8
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Structural Biology for the Molecular Insight between Aptamers and Target Proteins. Int J Mol Sci 2021; 22:ijms22084093. [PMID: 33920991 PMCID: PMC8071422 DOI: 10.3390/ijms22084093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are promising therapeutic and diagnostic agents for various diseases due to their high affinity and specificity against target proteins. Structural determination in combination with multiple biochemical and biophysical methods could help to explore the interacting mechanism between aptamers and their targets. Regrettably, structural studies for aptamer–target interactions are still the bottleneck in this field, which are facing various difficulties. In this review, we first reviewed the methods for resolving structures of aptamer–protein complexes and for analyzing the interactions between aptamers and target proteins. We summarized the general features of the interacting nucleotides and residues involved in the interactions between aptamers and proteins. Challenges and perspectives in current methodologies were discussed. Approaches for determining the binding affinity between aptamers and target proteins as well as modification strategies for stabilizing the binding affinity of aptamers to target proteins were also reviewed. The review could help to understand how aptamers interact with their targets and how alterations such as chemical modifications in the structures affect the affinity and function of aptamers, which could facilitate the optimization and translation of aptamers-based theranostics.
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9
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Sullivan MV, Clay O, Moazami MP, Watts JK, Turner NW. Hybrid Aptamer-Molecularly Imprinted Polymer (aptaMIP) Nanoparticles from Protein Recognition-A Trypsin Model. Macromol Biosci 2021; 21:e2100002. [PMID: 33760365 DOI: 10.1002/mabi.202100002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/24/2021] [Indexed: 12/18/2022]
Abstract
Aptamers offer excellent potential for replacing antibodies for molecular recognition purposes however their performance can compromise with biological/environmental degradation being a particular problem. Molecularly imprinted Polymers (MIPs) offer an alternative to biological materials and while these offer the robustness and ability to work in extreme environmental conditions, they often lack the same recognition performance. By slightly adapting the chemical structure of a DNA aptamer it is incorporated for use as the recognition part of a MIP, thus creating an aptamer-MIP hybrid or aptaMIP. Here these are developed for the detection of the target protein trypsin. The aptaMIP nanoparticles offer superior binding affinity over conventional MIP nanoparticles (nanoMIPs), with KD values of 6.8 × 10-9 (±0.2 × 10-9 ) m and 12.3 × 10-9 (±0.4 × 10-9 ) m for the aptaMIP and nanoMIP, respectively. The aptaMIP also outperforms the aptamer only (10.3 × 10-9 m). Good selectivity against other protein targets is observed. Using surface plasmon resonance, the limit of detection for aptaMIP nanoparticles is twofold lower (2 nm) compared to the nanoMIP (4 nm). Introduction of the aptamer as a "macro-monomer" into the MIP scaffold has beneficial effects and offers potential to improve this class of polymers significantly.
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Affiliation(s)
- Mark V Sullivan
- Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester, LE1 9BH, UK
| | - Oliver Clay
- Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester, LE1 9BH, UK
| | - Michael P Moazami
- RNA Therapeutics Institute, UMass Medical School, Worcester, MA, 01605, USA.,Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, 01605, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, UMass Medical School, Worcester, MA, 01605, USA.,Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, 01605, USA
| | - Nicholas W Turner
- Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester, LE1 9BH, UK
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10
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Selection and applications of functional nucleic acids for infectious disease detection and prevention. Anal Bioanal Chem 2021; 413:4563-4579. [PMID: 33506341 PMCID: PMC7840224 DOI: 10.1007/s00216-020-03124-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 11/30/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
Infectious diseases caused by pathogenic microorganisms such as viruses and bacteria pose a great threat to human health. Although a significant progress has been obtained in the diagnosis and prevention of infectious diseases, it still remains challenging to develop rapid and cost-effective detection approaches and overcome the side effects of therapeutic agents and pathogen resistance. Functional nucleic acids (FNAs), especially the most widely used aptamers and DNAzymes, hold the advantages of high stability and flexible design, which make them ideal molecular recognition tools for bacteria and viruses, as well as potential therapeutic drugs for infectious diseases. This review summarizes important advances in the selection and detection of bacterial- and virus-associated FNAs, along with their potential prevention ability of infectious disease in recent years. Finally, the challenges and future development directions are concluded.
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11
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Sullivan M, Hand R, Turner N. Generation of High-Affinity Aptamer-MIP Hybrid Nanoparticles. Methods Mol Biol 2021; 2359:109-121. [PMID: 34410663 DOI: 10.1007/978-1-0716-1629-1_9] [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: 06/13/2023]
Abstract
Aptamers and molecularly imprinted polymers (MIPs) are two leading technologies used for the development of protein biomimetics. By combining the two technologies, a new hybrid class of materials can be created, which utilizes the interesting characteristics of both recognition materials, while negating several of their drawbacks. This chapter describes the protocol for the synthesis of aptamer-MIP hybrid nanoparticles. These materials exhibit exceptional affinity (into the nM range) and selectivity for their target template. They can be developed for a wide range of targets, while exhibiting excellent robustness, solubility, and flexibility in use. These are a new class of recognition materials with the potential for use as drug delivery vectors, as well as use within sensing and recognition assays.
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Affiliation(s)
- Mark Sullivan
- School of Pharmacy, De Montfort University, Leicester, UK
| | - Rachel Hand
- School of Pharmacy, De Montfort University, Leicester, UK
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12
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Yasmeen F, Seo H, Javaid N, Kim MS, Choi S. Therapeutic Interventions into Innate Immune Diseases by Means of Aptamers. Pharmaceutics 2020; 12:pharmaceutics12100955. [PMID: 33050544 PMCID: PMC7600108 DOI: 10.3390/pharmaceutics12100955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/03/2020] [Accepted: 10/04/2020] [Indexed: 12/25/2022] Open
Abstract
The immune system plays a crucial role in the body's defense system against various pathogens, such as bacteria, viruses, and parasites, as well as recognizes non-self- and self-molecules. The innate immune system is composed of special receptors known as pattern recognition receptors, which play a crucial role in the identification of pathogen-associated molecular patterns from diverse microorganisms. Any disequilibrium in the activation of a particular pattern recognition receptor leads to various inflammatory, autoimmune, or immunodeficiency diseases. Aptamers are short single-stranded deoxyribonucleic acid or ribonucleic acid molecules, also termed "chemical antibodies," which have tremendous specificity and affinity for their target molecules. Their features, such as stability, low immunogenicity, ease of manufacturing, and facile screening against a target, make them preferable as therapeutics. Immune-system-targeting aptamers have a great potential as a targeted therapeutic strategy against immune diseases. This review summarizes components of the innate immune system, aptamer production, pharmacokinetic characteristics of aptamers, and aptamers related to innate-immune-system diseases.
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13
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High bio-recognizing aptamer designing and optimization against human herpes virus-5. Eur J Pharm Sci 2020; 156:105572. [PMID: 32980430 DOI: 10.1016/j.ejps.2020.105572] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/20/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023]
Abstract
While the world is tackling one of the direst health emergencies, it has come to light that in the fight against viruses, preparedness is everything. A disease with the initial symptoms of the common flu has the capacity to disrupt the life of 7.8 billion people and thus no infection and especially no virus can be ignored. Hence, we have designed the high bio-recognizing DNA aptamer for diagnosis and therapeutics role against glycoprotein-B (gB) of Human Herpes Virus-5 (HHV-5). HHV-5 is linked with epidemiological and asymptomatic diseases leading to high mortality. Herein, we report potent aptamer (5'CTCGCTTACCCCTGGGTGTGCGGG3') which has high specificity to gB with energy score -523.28 kJ/mol, more than reference aptamer L19 (-363.50 kJ/mol). The stable binding of aptamer with gB was confirmed with atomic fluctuations 0.1 to 1.8 Å through anisotropic network analysis. Aptamer formed stem-loop conformation (-1.0 kcal/mol) by stochastic simulation and found stable with physicochemical properties. Importantly, aptamer was found biologically significant with consisting of putative transcription factors in its vicinity (SP1, GATA1, AP2, NF1) and also possesses homology with exonic sequence of SGSH gene which indicated regulatory role in blockade of viruses. Inaddition, we also proposed plausible mechanism of action of aptamer as antiviral therapeutics.
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14
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Zhang N, Zhang ZK, Yu Y, Zhuo Z, Zhang G, Zhang BT. Pros and Cons of Denosumab Treatment for Osteoporosis and Implication for RANKL Aptamer Therapy. Front Cell Dev Biol 2020; 8:325. [PMID: 32478071 PMCID: PMC7240042 DOI: 10.3389/fcell.2020.00325] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 04/16/2020] [Indexed: 12/26/2022] Open
Abstract
Osteoporosis is age-related deterioration in bone mass and micro-architecture. Denosumab is a novel human monoclonal antibody for osteoporosis. It is a receptor activator of nuclear factor-κB ligand (RANKL) inhibitor, which binds to and inhibits osteoblast-produced RANKL, in turn reduces the binding between RANKL and osteoclast receptor RANK, therefore decreases osteoclast-mediated bone resorption and turnover. However, adverse events have also been reported after denosumab treatment, including skin eczema, flatulence, cellulitis and osteonecrosis of the jaw (ONJ). Extensive researches on the mechanism of adverse reactions caused by denosumab have been conducted and may provide new insights into developing new RANKL inhibitors that achieve better specificity and safety. Aptamers are single-stranded oligonucleotides that can bind to target molecules with high specificity and affinity. They are screened from large single-stranded synthetic oligonucleotides and enriched by a technology named SELEX (systematic evolution of ligands by exponential enrichment). With extra advantages such as high stability, low immunogenicity and easy production over antibodies, aptamers are hypothesized to be promising candidates for therapeutic drugs targeting RANKL to counteract osteoporosis. In this review, we focus on the pros and cons of denosumab treatment in osteoporosis and the implication for novel aptamer treatment.
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Affiliation(s)
- Ning Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Zong-Kang Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuanyuan Yu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Zhenjian Zhuo
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Bao-Ting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
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15
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Lu C, Liu C, Shi G. Colorimetric enzyme-linked aptamer assay utilizing hybridization chain reaction for determination of bovine pregnancy-associated glycoproteins. Mikrochim Acta 2020; 187:316. [PMID: 32383031 DOI: 10.1007/s00604-020-04301-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/23/2020] [Indexed: 11/25/2022]
Abstract
DNA aptamers that bind to bovine pregnancy-associated glycoproteins (bPAGs) were selected by the systematic evolution of ligands by exponential enrichment (SELEX) procedure coupled to surface plasmon resonance (SPR) and high-throughput sequencing (HTS) technology. After seven rounds of selection using carboxylated magnetic beads (MB) coated with bovine pregnancy-associated glycoproteins 9 (bPAG9) and bovine serum albumin (BSA) as target and counter targets, respectively, two aptamers designated as A1 and A24 showed high affinities to bPAG9 (Kd = 1.04 and 2.5 nM). Moreover, the specificity was determined by testing the non-targets bPAG4, bPAG6, bPAG16, BSA, and ovalbumin (OVA). Results showed that two aptamers demonstrated broad group specificity to bPAG family. Subsequently, a colorimetric sandwich enzyme-linked aptamer assay was developed for ultrasensitive detection of bPAG9 based on hybridization chain reaction (HCR) amplification strategy. The method exhibited a broad determination from 0.134 to 134 ng/mL with a detection limit of 0.037 ng/mL. The method has been successfully applied to determine bPAGs in real samples. The results demonstrate that the developed aptamers could be used as promising molecular probes for the development of pregnancy diagnostic tools. Graphical abstract In this study, we first selected aptamers against bovine pregnancy-associated glycoproteins (bPAGs) as molecular recognition elements and then developed a colorimetric enzyme-linked aptamer assay utilizing hybridization chain reaction to detect bPAGs in the serum.The GA can't be deleted, the modified GA can not upload. So themodified GA and figures will be send to CorrAdmin3@spi-global.com.
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Affiliation(s)
- Chunxia Lu
- College of Life Science and Technology, Yangtze Normal University, Chongqing, 408100, People's Republic of China
| | - Changbin Liu
- Institute of Animal Husbandry and Veterinary Science, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi, 832000, People's Republic of China.
| | - Guoqing Shi
- Institute of Animal Husbandry and Veterinary Science, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi, 832000, People's Republic of China
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16
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Fu Z, Xiang J. Aptamers, the Nucleic Acid Antibodies, in Cancer Therapy. Int J Mol Sci 2020; 21:ijms21082793. [PMID: 32316469 PMCID: PMC7215806 DOI: 10.3390/ijms21082793] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023] Open
Abstract
The arrival of the monoclonal antibody (mAb) technology in the 1970s brought with it the hope of conquering cancers to the medical community. However, mAbs, on the whole, did not achieve the expected wonder in cancer therapy although they do have demonstrated successfulness in the treatment of a few types of cancers. In 1990, another technology of making biomolecules capable of specific binding appeared. This technique, systematic evolution of ligands by exponential enrichment (SELEX), can make aptamers, single-stranded DNAs or RNAs that bind targets with high specificity and affinity. Aptamers have some advantages over mAbs in therapeutic uses particularly because they have little or no immunogenicity, which means the feasibility of repeated use and fewer side effects. In this review, the general properties of the aptamer, the advantages and limitations of aptamers, the principle and procedure of aptamer production with SELEX, particularly the undergoing studies in aptamers for cancer therapy, and selected anticancer aptamers that have entered clinical trials or are under active investigations are summarized.
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Affiliation(s)
- Zhaoying Fu
- Department of Biochemistry and Molecular Biology, College of Medicine, Yanan University, Yanan 716000, China
- Correspondence: (Z.F.); (J.X.)
| | - Jim Xiang
- Division of Oncology, University of Saskatchewan, Saskatoon, SA S7N 4H4, Canada
- Correspondence: (Z.F.); (J.X.)
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17
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Triple-Negative Breast Cancer: A Review of Conventional and Advanced Therapeutic Strategies. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17062078. [PMID: 32245065 PMCID: PMC7143295 DOI: 10.3390/ijerph17062078] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/14/2022]
Abstract
Triple-negative breast cancer (TNBC) cells are deficient in estrogen, progesterone and ERBB2 receptor expression, presenting a particularly challenging therapeutic target due to their highly invasive nature and relatively low response to therapeutics. There is an absence of specific treatment strategies for this tumor subgroup, and hence TNBC is managed with conventional therapeutics, often leading to systemic relapse. In terms of histology and transcription profile these cancers have similarities to BRCA-1-linked breast cancers, and it is hypothesized that BRCA1 pathway is non-functional in this type of breast cancer. In this review article, we discuss the different receptors expressed by TNBC as well as the diversity of different signaling pathways targeted by TNBC therapeutics, for example, Notch, Hedgehog, Wnt/b-Catenin as well as TGF-beta signaling pathways. Additionally, many epidermal growth factor receptor (EGFR), poly (ADP-ribose) polymerase (PARP) and mammalian target of rapamycin (mTOR) inhibitors effectively inhibit the TNBCs, but they face challenges of either resistance to drugs or relapse. The resistance of TNBC to conventional therapeutic agents has helped in the advancement of advanced TNBC therapeutic approaches including hyperthermia, photodynamic therapy, as well as nanomedicine-based targeted therapeutics of drugs, miRNA, siRNA, and aptamers, which will also be discussed. Artificial intelligence is another tool that is presented to enhance the diagnosis of TNBC.
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18
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Zhao L, Qi X, Yan X, Huang Y, Liang X, Zhang L, Wang S, Tan W. Engineering Aptamer with Enhanced Affinity by Triple Helix-Based Terminal Fixation. J Am Chem Soc 2019; 141:17493-17497. [DOI: 10.1021/jacs.9b09292] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Lianhui Zhao
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Xiaoyan Qi
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Xiaochen Yan
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Yunfei Huang
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Liqin Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Inspiratio Biosciences, Inc., Fremont, California 94538, United States
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Sai Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611, United States
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19
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Shraim AS, Hunaiti A, Awidi A, Alshaer W, Ababneh NA, Abu-Irmaileh B, Odeh F, Ismail S. Developing and Characterization of Chemically Modified RNA Aptamers for Targeting Wild Type and Mutated c-KIT Receptor Tyrosine Kinases. J Med Chem 2019; 63:2209-2228. [PMID: 31369705 DOI: 10.1021/acs.jmedchem.9b00868] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The c-KIT receptor represents an attractive target for cancer therapy. Aptamers are emerging as a new promising class of nucleic acid therapeutics. In this study, a conventional SELEX approach was applied against the kinase domain of a group of c-KIT proteins (c-KITWT, c-KITD816V, and c-KITD816H) to select aptamers from a random RNA pool that can bind to the kinase domain of each target with high affinity and can selectively interfere with their kinase activities. Interestingly, our data indicated that one candidate aptamer, called V15, can specifically inhibit the in vitro kinase activity of mutant c-KITD816V with an IC50 value that is 9-fold more potent than the sunitinib drug tested under the same conditions. Another aptamer, named as H5/V36, showed the potential to distinguish between the c-KIT kinases by modulating the phosphorylation activity of each in a distinct mechanism of action and in a different potency.
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Affiliation(s)
- Ala'a S Shraim
- Department of Biological Sciences, School of Science, The University of Jordan, Amman JO 11942, Jordan.,Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman JO 19328, Jordan
| | - Abdelrahim Hunaiti
- Department of Clinical Laboratory Sciences, School of Science, The University of Jordan, Amman JO 11942, Jordan
| | - Abdalla Awidi
- Cell Therapy Center, The University of Jordan, Amman JO 11942, Jordan
| | - Walhan Alshaer
- Cell Therapy Center, The University of Jordan, Amman JO 11942, Jordan
| | - Nidaa A Ababneh
- Cell Therapy Center, The University of Jordan, Amman JO 11942, Jordan
| | - Bashaer Abu-Irmaileh
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman JO 11942, Jordan
| | - Fadwa Odeh
- Department of Chemistry, School of Science, The University of Jordan, Amman JO 11942, Jordan
| | - Said Ismail
- Department of Biochemistry and Physiology, School of Medicine, The University of Jordan, Amman JO 11942, Jordan.,Qatar Genome Project, Qatar Foundation, Doha, Qatar
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20
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Ali MH, Elsherbiny ME, Emara M. Updates on Aptamer Research. Int J Mol Sci 2019; 20:E2511. [PMID: 31117311 PMCID: PMC6566374 DOI: 10.3390/ijms20102511] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023] Open
Abstract
For many years, different probing techniques have mainly relied on antibodies for molecular recognition. However, with the discovery of aptamers, this has changed. The science community is currently considering using aptamers in molecular targeting studies because of the many potential advantages they have over traditional antibodies. Some of these possible advantages are their specificity, higher binding affinity, better target discrimination, minimized batch-to-batch variation, and reduced side effects. Overall, these characteristics of aptamers have attracted scholars to use them as molecular probes in place of antibodies, with some aptamer-based targeting products being now available in the market. The present review is aimed at discussing the potential of aptamers as probes in molecular biology and in super-resolution microscopy.
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Affiliation(s)
- Mohamed H Ali
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
- current address: Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
| | - Marwa E Elsherbiny
- Department of Pharmacology and Toxicology, Ahram Canadian University, 6th of October City, Giza 12566, Egypt.
| | - Marwan Emara
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
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21
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Belinskaia DA, Avdonin PV, Avdonin PP, Jenkins RO, Goncharov NV. Rational in silico design of aptamers for organophosphates based on the example of paraoxon. Comput Biol Chem 2019; 80:452-462. [PMID: 31170561 DOI: 10.1016/j.compbiolchem.2019.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 01/20/2019] [Accepted: 05/08/2019] [Indexed: 01/14/2023]
Abstract
Poisoning by organophosphates (OPs) takes one of the leading places in the total number of exotoxicoses. Detoxication of OPs at the first stage of the poison entering the body could be achieved with the help of DNA- or RNA-aptamers, which are able to bind poisons in the bloodstream. The aim of the research was to develop an approach to rational in silico design of aptamers for OPs based on the example of paraoxon. From the published sequence of an aptamer binding organophosphorus pesticides, its three-dimensional model has been constructed. The most probable binding site for paraoxon was determined by molecular docking and molecular dynamics (MD) methods. Then the nucleotides of the binding site were mutated consequently and the values of free binding energy have been calculated using MD trajectories and MM-PBSA approach. On the basis of the energy values, two sequences that bind paraoxon most efficiently have been selected. The value of free binding energy of paraoxon with peripheral anionic site of acetylcholinesterase (AChE) has been calculated as well. It has been revealed that the aptamers found bind paraoxon more effectively than AChE. The peculiarities of paraoxon interaction with the aptamers nucleotides have been analyzed. The possibility of improving in silico approach for aptamer selection is discussed.
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Affiliation(s)
- Daria A Belinskaia
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, St. Petersburg 194223, Russia.
| | - Pavel V Avdonin
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilova str., Moscow 119334, Russia
| | - Piotr P Avdonin
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilova str., Moscow 119334, Russia
| | - Richard O Jenkins
- Leicester School of Allied Health Sciences, De Montfort University, The Gateway, Leicester LE1 9BH, UK
| | - Nikolay V Goncharov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, St. Petersburg 194223, Russia; Research Institute of Hygiene, Occupational Pathology and Human Ecology, bld.93 p.o.Kuz'molovsky, Leningrad Region 188663, Russia
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22
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Molefe PF, Masamba P, Oyinloye BE, Mbatha LS, Meyer M, Kappo AP. Molecular Application of Aptamers in the Diagnosis and Treatment of Cancer and Communicable Diseases. Pharmaceuticals (Basel) 2018; 11:ph11040093. [PMID: 30274155 PMCID: PMC6315466 DOI: 10.3390/ph11040093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/18/2022] Open
Abstract
Cancer and infectious diseases such as Ebola, HIV, tuberculosis, Zika, hepatitis, measles and human schistosomiasis are serious global health hazards. The increasing annual morbidities and mortalities of these diseases have been blamed on drug resistance and the inefficacy of available diagnostic tools, particularly those which are immunologically-based. Antibody-based tools rely solely on antibody production for diagnosis and for this reason they are the major cause of diagnostic delays. Unfortunately, the control of these diseases depends on early detection and administration of effective treatment therefore any diagnostic delay is a huge challenge to curbing these diseases. Hence, there is a need for alternative diagnostic tools, discovery and development of novel therapeutic agents. Studies have demonstrated that aptamers could potentially offer one of the best solutions to these problems. Aptamers are short sequences of either DNA or RNA molecules, which are identified in vitro through a SELEX process. They are sensitive and bind specifically to target molecules. Their promising features suggest they may serve as better diagnostic agents and can be used as drug carriers for therapeutic purposes. In this article, we review the applications of aptamers in the theranostics of cancer and some infectious diseases.
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Affiliation(s)
- Philisiwe Fortunate Molefe
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Priscilla Masamba
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Babatunji Emmanuel Oyinloye
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
- Department of Biochemistry, College of Sciences, Afe Babalola University, PMB 5454, Ado-Ekiti 360001, Nigeria.
| | - Londiwe Simphiwe Mbatha
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Mervin Meyer
- DST/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa.
| | - Abidemi Paul Kappo
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
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23
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Pereira RL, Nascimento IC, Santos AP, Ogusuku IEY, Lameu C, Mayer G, Ulrich H. Aptamers: novelty tools for cancer biology. Oncotarget 2018; 9:26934-26953. [PMID: 29928493 PMCID: PMC6003562 DOI: 10.18632/oncotarget.25260] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/22/2018] [Indexed: 02/07/2023] Open
Abstract
Although the term ‘cancer’ was still over two thousand years away of being coined, the first known cases of the disease date back to about 3000BC, in ancient Egypt. Five thousand years later, still lacking a cure, it has become one of the leading causes of death, killing over half a dozen million people yearly. So far, monoclonal antibodies are the most successful immune-therapy tools when it comes to fighting cancer. The number of clinical trials that use them has been increasing steadily during the past few years, especially since the Food and Drug Administration greenlit the use of the first immune-checkpoint blockade antibodies. However, albeit successful, this approach does come with the cost of auto-inflammatory toxicity. Taking this into account, the development of new therapeutic reagents with low toxicity becomes evident, particularly ones acting in tandem with the tools currently at our disposal. Ever since its discovery in the early nineties, aptamer technology has been used for a wide range of diagnostic and therapeutic applications. With similar properties to those of monoclonal antibodies, such as high-specificity of recognition and high-affinity binding, and the advantages of being developed using in vitro selection procedures, aptamers quickly became convenient building blocks for the generation of multifunctional constructs. In this review, we discuss the steps involved in the in vitro selection process that leads to functional aptamers - known as Systematic Evolution of Ligands by Exponential Enrichment - as well as the most recent applications of this technology in diagnostic and treatment of oncological illnesses. Moreover, we also suggest ways to improve such use.
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Affiliation(s)
- Ricardo L Pereira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Isis C Nascimento
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Ana P Santos
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Isabella E Y Ogusuku
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Claudiana Lameu
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Günter Mayer
- Chemical Biology and Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53121, Bonn, Germany.,Center of Aptamer Research and Development (CARD), University of Bonn, 53121, Bonn, Germany
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
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24
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Sypabekova M, Bekmurzayeva A, Wang R, Li Y, Nogues C, Kanayeva D. Selection, characterization, and application of DNA aptamers for detection of Mycobacterium tuberculosis secreted protein MPT64. Tuberculosis (Edinb) 2017; 104:70-78. [PMID: 28454652 DOI: 10.1016/j.tube.2017.03.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/05/2017] [Accepted: 03/14/2017] [Indexed: 12/30/2022]
Abstract
Rapid detection of Mycobacterium tuberculosis (Mtb), an etiological agent of tuberculosis (TB), is important for global control of this disease. Aptamers have emerged as a potential rival for antibodies in therapeutics, diagnostics and biosensing due to their inherent characteristics. The aim of the current study was to select and characterize single-stranded DNA aptamers against MPT64 protein, one of the predominant secreted proteins of Mtb pathogen. Aptamers specific to MPT64 protein were selected in vitro using systematic evolution of ligands through exponential enrichment (SELEX) method. The selection was started with a pool of ssDNA library with randomized 40-nucleotide region. A total of 10 cycles were performed and seventeen aptamers with unique sequences were identified by sequencing. Dot Blot analysis was performed to monitor the SELEX process and to conduct the preliminary tests on the affinity and specificity of aptamers. Enzyme linked oligonucleotide assay (ELONA) showed that most of the aptamers were specific to the MPT64 protein with a linear correlation of R2 = 0.94 for the most selective. Using Surface Plasmon Resonance (SPR), dissociation equilibrium constant KD of 8.92 nM was obtained. Bioinformatics analysis of the most specific aptamers revealed the existence of a conserved as well as distinct sequences and possible binding site on MPT64. The specificity was determined by testing non-target ESAT-6 and CFP-10. Negligible cross-reactivity confirmed the high specificity of the selected aptamer. The selected aptamer was further tested on clinical sputum samples using ELONA and had sensitivity and specificity of 91.3% and 90%, respectively. Microscopy, culture positivity and nucleotide amplification methods were used as reference standards. The aptamers studied could be further used for the development of medical diagnostic tools and detection assays for Mtb.
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Affiliation(s)
- Marzhan Sypabekova
- Laboratory of Biosensors and Bioinstruments, National Laboratory Astana, Nazarbayev University, 53 Kabanbay batyr Avenue, Astana, 010000, Kazakhstan; School of Engineering, Nazarbayev University, 53 Kabanbay batyr Avenue, Astana, 010000, Kazakhstan
| | - Aliya Bekmurzayeva
- Laboratory of Biosensors and Bioinstruments, National Laboratory Astana, Nazarbayev University, 53 Kabanbay batyr Avenue, Astana, 010000, Kazakhstan; School of Engineering, Nazarbayev University, 53 Kabanbay batyr Avenue, Astana, 010000, Kazakhstan
| | - Ronghui Wang
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Yanbin Li
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Claude Nogues
- LBPA, IDA, ENS Cachan, CNRS, Université Paris-Saclay, F-94235, Cachan, France
| | - Damira Kanayeva
- Department of Biology, School of Science and Technology, Nazarbayev University, 53 Kabanbay batyr Avenue, Astana, 010000, Kazakhstan.
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25
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Abstract
Nucleic acid aptamers, often termed 'chemical antibodies', are functionally comparable to traditional antibodies, but offer several advantages, including their relatively small physical size, flexible structure, quick chemical production, versatile chemical modification, high stability and lack of immunogenicity. In addition, many aptamers are internalized upon binding to cellular receptors, making them useful targeted delivery agents for small interfering RNAs (siRNAs), microRNAs and conventional drugs. However, several crucial factors have delayed the clinical translation of therapeutic aptamers, such as their inherent physicochemical characteristics and lack of safety data. This Review discusses these challenges, highlighting recent clinical developments and technological advances that have revived the impetus for this promising class of therapeutics.
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Affiliation(s)
- Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - John Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
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26
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An Update on Aptamer-Based Multiplex System Approaches for the Detection of Common Foodborne Pathogens. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-0814-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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27
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Ouellet E, Foley JH, Conway EM, Haynes C. Hi-Fi SELEX: A High-Fidelity Digital-PCR Based Therapeutic Aptamer Discovery Platform. Biotechnol Bioeng 2016; 112:1506-22. [PMID: 25727321 DOI: 10.1002/bit.25581] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 02/14/2015] [Indexed: 12/30/2022]
Abstract
Current technologies for aptamer discovery typically leverage the systematic evolution of ligands by exponential enrichment (SELEX) concept by recursively panning semi-combinatorial ssDNA or RNA libraries against a molecular target. The expectation is that this iterative selection process will be sufficiently stringent to identify a candidate pool of specific high-affinity aptamers. However, failure of this process to yield promising aptamers is common, due in part to (i) limitations in library designs, (ii) retention of non-specific aptamers during screening rounds, (iii) excessive accumulation of amplification artifacts, and (iv) the use of screening criteria (binding affinity) that does not reflect therapeutic activity. We report a new selection platform, High-Fidelity (Hi-Fi) SELEX, that introduces fixed-region blocking elements to safeguard the functional diversity of the library. The chemistry of the target-display surface and the composition of the equilibration solvent are engineered to strongly inhibit non-specific retention of aptamers. Partition efficiencies approaching 10(6) are thereby realized. Retained members are amplified in Hi-Fi SELEX by digital PCR in a manner that ensures both elimination of amplification artifacts and stoichiometric conversion of amplicons into the single-stranded library required for the next selection round. Improvements to aptamer selections are first demonstrated using human α-thrombin as the target. Three clinical targets (human factors IXa, X, and D) are then subjected to Hi-Fi SELEX. For each, rapid enrichment of ssDNA aptamers offering an order-nM mean equilibrium dissociation constant (Kd) is achieved within three selection rounds, as quantified by a new label-free qPCR assay reported here. Therapeutic candidates against factor D are identified.
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Cao F, Lu X, Hu X, Zhang Y, Zeng L, Chen L, Sun M. In vitro selection of DNA aptamers binding pesticide fluoroacetamide. Biosci Biotechnol Biochem 2016; 80:823-32. [PMID: 26873572 DOI: 10.1080/09168451.2015.1136876] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Fluoroacetamide (Mw = 77.06) is a lethal rodenticide to humans and animals which is still frequently abused in food storage somewhere in China. The production of antibodies for fluoroacetamide is difficult due to its high toxicity to animals, which limits the application of immunoassay method in poison detection. In this work, aptamers targeting N-fluoroacetyl glycine as an analog of fluoroacetamide were selected by a specific systematic evolution of ligands by exponential enrichment (SELEX) strategy. The binding ability of the selected aptamers to fluoroacetamide was identified using surface plasmon resonance (SPR)-based assay. The estimated KD values in the low micromolar range showed a good affinity of these aptamers to the target. Our work verified that the SELEX strategy has the potential for developing aptamers targeted to small molecular toxicants and aptamers can be employed as new recognition elements instead of antibodies for poison detection.
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Affiliation(s)
- Fangqi Cao
- a Shanghai Key Laboratory of Crime Scene Evidence , Shanghai Research Institute of Criminal Science and Technology , Shanghai , China
| | - Xinwei Lu
- b Shanghai Key Laboratory of Crime Scene Evidence , Shanghai Institute of Forensic Science , Shanghai , China.,c State Key Laboratory of New Drug and Pharmaceutical Process , Shanghai Institute of Pharmaceutical Industry , Shanghai , China
| | - Xiaolong Hu
- b Shanghai Key Laboratory of Crime Scene Evidence , Shanghai Institute of Forensic Science , Shanghai , China
| | - Yurong Zhang
- b Shanghai Key Laboratory of Crime Scene Evidence , Shanghai Institute of Forensic Science , Shanghai , China
| | - Libo Zeng
- b Shanghai Key Laboratory of Crime Scene Evidence , Shanghai Institute of Forensic Science , Shanghai , China
| | - Liankang Chen
- b Shanghai Key Laboratory of Crime Scene Evidence , Shanghai Institute of Forensic Science , Shanghai , China
| | - Meiqi Sun
- c State Key Laboratory of New Drug and Pharmaceutical Process , Shanghai Institute of Pharmaceutical Industry , Shanghai , China
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Single-stranded DNA aptamers for functional probing of bacterial RNA polymerase. Methods Mol Biol 2015; 1276:165-83. [PMID: 25665563 DOI: 10.1007/978-1-4939-2392-2_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Bacterial RNA polymerase (RNAP) is the main regulatory hub of gene transcription. During transcription, RNAP interacts with the DNA template, RNA product, nucleotide substrates, metal cofactors, and regulatory molecules that bind to distinct RNAP sites to modulate its activity. RNAP is also inhibited by several known antibiotics and is a promising target for development of novel antibacterial compounds. Despite great progress in structural analysis of RNAP in recent years, many details of RNAP interactions with nucleic acids, regulatory molecules and antibiotics remain insufficiently understood. Aptamers that target various epitopes on the RNAP molecule represent a useful tool for functional analysis of transcription. Here, we describe protocols for selection of highly specific aptamers to different components of RNAP and their applications for analysis of RNAP-ligand interactions and RNAP inhibition.
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Liu X, Hua X, Fan Q, Chao J, Su S, Huang YQ, Wang L, Huang W. Thioflavin T as an Efficient G-Quadruplex Inducer for the Highly Sensitive Detection of Thrombin Using a New Föster Resonance Energy Transfer System. ACS APPLIED MATERIALS & INTERFACES 2015; 7:16458-16465. [PMID: 26173915 DOI: 10.1021/acsami.5b03662] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report a new Föster resonance energy transfer (FRET) system that uses a special dye, thioflavin T (ThT), as an energy acceptor and a water-soluble conjugated polymer (CP) with high fluorescence as an energy donor. A simple, label-free, and sensitive strategy for the detection of thrombin in buffer and in diluted serum was designed based on this new system using ThT as an efficient inducer of the G-quadruplex. The difference between the blank and the positive samples was amplified due to distinctive FRET signals because thrombin has little effect on the intercalation of ThT into the G-quadruplex. In the absence of the target, ThT induces the aptamer to form a G-quadruplex and intercalates into it with strong fluorescence. The electrostatic attractions between the negatively charged G-quadruplex and positively charged CP allow a short donor-acceptor distance, resulting in a high FRET signal. However, in the presence of the target, the aptamer forms a G-quadruplex-thrombin complex first, followed by the intercalation of ThT into the G-quadruplex. A long distance exists between the donor and acceptor due to the strong steric hindrance from the large-sized thrombin, which leads to a low FRET signal. Compared with previously reported strategies based on the FRET between the CP and dye, our strategy is label-free, and the sensitivity was improved by an order of magnitude. Our strategy also shows the advantages of being simple, rapid (about 50 min), sensitive, label-free, and low-cost in comparison to strategies based on the FRET between quantum dots and dyes.
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Spiridonova VA, Barinova KV, Glinkina KA, Melnichuk AV, Gainutdynov AA, Safenkova IV, Dzantiev BB. A family of DNA aptamers with varied duplex region length that forms complexes with thrombin and prothrombin. FEBS Lett 2015; 589:2043-9. [PMID: 26143256 DOI: 10.1016/j.febslet.2015.06.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 06/06/2015] [Accepted: 06/22/2015] [Indexed: 01/25/2023]
Abstract
Structural properties determine binding affinities of DNA aptamers specific to thrombin. Our paper is the first to focus on a family of eight G-quadruplex-based aptamers with varied duplex region length (from two to eight base pairs). We have shown that the duplex, which is not the main binding domain, greatly influences the interaction with thrombin and prothrombin. Furthermore, the affinity of an aptamer to thrombin and prothrombin increases (respectively from 2.7×10⁻⁸ M to 5.6×10⁻¹⁰ M and from 1.8×10⁻⁵ M to 7.1×10⁻⁹ M) with an increase in the number of nucleotide pairs in the duplex region.
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Affiliation(s)
- V A Spiridonova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - K V Barinova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - K A Glinkina
- Chemistry Department, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - A V Melnichuk
- Chemistry Department, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - A A Gainutdynov
- Chemistry Department, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - I V Safenkova
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - B B Dzantiev
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia.
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A Highlight of Recent Advances in Aptamer Technology and Its Application. Molecules 2015; 20:11959-80. [PMID: 26133761 PMCID: PMC6331864 DOI: 10.3390/molecules200711959] [Citation(s) in RCA: 204] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 01/10/2023] Open
Abstract
Aptamers and SELEX (systematic evolution of ligands by exponential enrichment) technology have gained increasing attention over the past 25 years. Despite their functional similarity to protein antibodies, oligonucleotide aptamers have many unique properties that are suitable for clinical applications and industrialization. Aptamers may be superior to antibodies in fields such as biomarker discovery, in vitro and in vivo diagnosis, precisely controlled drug release, and targeted therapy. However, aptamer commercialization has not occurred as quickly as expected, and few aptamer-based products have yet successfully entered clinical and industrial use. Thus, it is important to critically review some technical barriers of aptamer and SELEX technology per se that may impede aptamer development and application. To date, how to rapidly obtain aptamers with superior bioavailability over antibodies remains the key issue. In this review, we discuss different chemical and structural modification strategies aimed to enhance aptamer bioavailability. We also discuss improvements to SELEX process steps to shorten the selection period and improve the SELEX process success rate. Applications in which aptamers are particularly suited and perform differently or superior to antibodies are briefly introduced.
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Xi Z, Huang R, Li Z, He N, Wang T, Su E, Deng Y. Selection of HBsAg-Specific DNA Aptamers Based on Carboxylated Magnetic Nanoparticles and Their Application in the Rapid and Simple Detection of Hepatitis B Virus Infection. ACS APPLIED MATERIALS & INTERFACES 2015; 7:11215-23. [PMID: 25970703 DOI: 10.1021/acsami.5b01180] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides and can be selected from synthetic combinatorial libraries in vitro. They have a high binding affinity and specificity for their targets. Agarose gels, nitrocellulose membranes, and adsorptive microplates are often used as carriers to immobilize targets in the SELEX (systematic evolution of ligands by exponential enrichment) process, but the subsequent separation step is tedious and time-consuming. Therefore, we used magnetic nanoparticles (MNPs) as carriers to immobilize the target, hepatitis B surface antigen (HBsAg), which is convenient for fast magnetic separation. In this study, we first selected DNA aptamers against HBsAg by immobilizing HBsAg on the surface of carboxylated MNPs. The ssDNA library of each selection round was prepared by asymmetric PCR amplification for the next selection round. To obtain aptamer sequences, the final selected products were purified by gel electrophoresis, then cloned, and sequenced. DNA aptamers that specifically bind to HBsAg were successfully obtained after 13 selection rounds. The selected aptamers were used to construct a chemiluminescence aptasensor based on magnetic separation and immunoassay to detect HBsAg from pure protein or actual serum samples. There was a linear relationship between HBsAg concentration and chemiluminescent intensity in the range of 1-200 ng/mL. The aptasensor worked well even in the presence of interfering substances and was highly specific in the detection of HBsAg in serum samples, with a detection limit 0.1 ng/mL lower than the 0.5 ng/mL limit of an ELISA in use at the hospital. This aptasensor can contribute to better detection of hepatitis B virus infection.
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Affiliation(s)
- Zhijiang Xi
- †State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
- ‡School of Life and Science, Yangtze University, Jingzhou 434025, P. R. China
| | - Rongrong Huang
- †State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
| | - Zhiyang Li
- †State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
| | - Nongyue He
- †State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
- §Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Packaging and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Ting Wang
- †State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
| | - Enben Su
- †State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
- ∥Getein Biotechnology Co., Ltd., Nanjing 210000, P. R. China
| | - Yan Deng
- †State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
- §Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Packaging and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou 412007, P. R. China
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Abstract
Aptamers, as a novel class of molecular probes for diagnosis, imaging and targeting therapy, have attracted increasing attention in recent years. Aptamers are generated from libraries of single-stranded nucleic acids against different molecules via the "systematic evolution of ligands by exponential enrichment" (SELEX) method. SELEX is a repetitive process of a sequential selection procedure in which a DNA or RNA library pool is incubated separately with target and control molecules to select specific oligonucleotide aptamers with high affinities and specificities. Cell-SELEX is a modified version of the SELEX process in which whole living cells are used as targets for the aptamers. Dendritic cell (DC) targeting, as a new therapeutic approach, can improve the efficiency of immunotherapy in the treatment of allergies and cancers. DCs use various receptors to continuously induce adaptive immunity via capture and presentation of antigens to naïve T cells. DCs are considered as the best targets in modulating immune responses against cancer, autoimmunity, allergy and transplantation. Aptamers, as a new agent, can be applied in DC targeting. The purpose of this review is to present some general concepts of aptamer production and DC targeting by aptamer molecules.
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Affiliation(s)
- A Ganji
- a Student Research Committee , Mashhad University of Medical Sciences , Mashhad , Iran .,b Immunology Research Center, Medical School, Mashhad University of Medical Sciences , Mashhad , Iran , and
| | - A Varasteh
- c Allergy Research Center, Medical School, Mashhad University of Medical Sciences , Mashhad , Iran
| | - M Sankian
- b Immunology Research Center, Medical School, Mashhad University of Medical Sciences , Mashhad , Iran , and
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Ahirwar R, Nahar P. Screening and identification of a DNA aptamer to concanavalin A and its application in food analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:4104-11. [PMID: 25865304 DOI: 10.1021/acs.jafc.5b00784] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Herein, a novel aptamer that targets concanavalin A (Con A), a plant lectin, is isolated using systematic evolution of ligands by an exponential enrichment (SELEX) technique. Nine rounds of SELEX screening over an agarose spin column have resulted in enrichment of eight sequences having high affinity to Con A. The highest affinity sequence was selected as a potent aptamer and characterized it in detail. The evolved Con A aptamer (Con A-aptabody) is a 41 nt ssDNA that binds the Con A specifically with a dissociation constant of 172.7 ± 29.7 nM. In silico analyses predict the Con A-aptabody to form G-quadruplex due to its G-rich sequence (GGAAGGCGGAGGG). A detection method developed using Con A-aptabody is found to have a detection range of 10-750 ng/mL with limits of detection and quantification being 13.22 and 44.09 ng/mL, respectively. The utility of the method is demonstrated by analyzing jack bean (Canavalia ensiformis), kidney bean (Phaseolus vulgaris), wheat (Triticum spp.), mung bean (Vigna radiata), and lentil (Lens culinaris) for their Con A contents. Hence, the developed Con A-aptabody provides a useful substitute to Con A-antibody for food analysis and related applications.
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Affiliation(s)
- Rajesh Ahirwar
- †CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
- ‡Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Pradip Nahar
- †CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
- ‡Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
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Neutralization of staphylococcal enterotoxin B by an aptamer antagonist. Antimicrob Agents Chemother 2015; 59:2072-7. [PMID: 25624325 DOI: 10.1128/aac.04414-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcal enterotoxin B (SEB) is a major virulence factor for staphylococcal toxic shock syndrome (TSS). SEB activates a large subset of the T lymphocytic population, releasing proinflammatory cytokines. Blocking SEB-initiated toxicity may be an effective strategy for treating TSS. Using a process known as systematic evolution of ligands by exponential enrichment (SELEX), we identified an aptamer that can antagonize SEB with nanomolar binding affinity (Kd = 64 nM). The aptamer antagonist effectively inhibits SEB-mediated proliferation and cytokine secretion in human peripheral blood mononuclear cells. Moreover, a PEGylated aptamer antagonist significantly reduced mortality in a "double-hit" mouse model of SEB-induced TSS, established via sensitization with d-galactosamine followed by SEB challenge. Therefore, our novel aptamer antagonist may offer potential therapeutic efficacy against SEB-mediated TSS.
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37
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Heilkenbrinker A, Reinemann C, Stoltenburg R, Walter JG, Jochums A, Stahl F, Zimmermann S, Strehlitz B, Scheper T. Identification of the target binding site of ethanolamine-binding aptamers and its exploitation for ethanolamine detection. Anal Chem 2014; 87:677-85. [PMID: 25435319 DOI: 10.1021/ac5034819] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Aptamers are promising recognition elements for sensitive and specific detection of small molecules. We have previously selected ssDNA aptamers for ethanolamine, one of the smallest aptamer targets so far. The work presented here focuses on the determination of the binding region within the aptamer structure and its exploitation for the development of an aptamer-based assay for detection of ethanolamine. Sequence analysis of the aptamers resulted in the identification of a G-rich consensus sequence, which was able to fold in a typical two- or three-layered G-quartet structure. Experiments with stepwise truncated variants of the aptamers revealed that the consensus sequence is responsible and sufficient for binding to the target. On the basis of the knowledge of the aptamers binding site, we developed an aptamer-based microarray assay relying on competition between ethanolamine and an oligonucleotide complementary to the consensus sequence. Competitive binding of ethanolamine and fluorescently labeled complementary oligonucleotides resulted in fluorescence intensities dependent on ethanolamine concentration with a limit of detection of 10 pM. This method enables detection of small molecules without any labeling of analytes. The competitive assay could potentially be transferred to other aptamers and thus provides a promising system for aptamer-based detection of diverse small molecules.
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Affiliation(s)
- Alexandra Heilkenbrinker
- Gottfried Wilhelm Leibniz Universität Hannover, Institut für Technische Chemie, Callinstr. 5, D-30167 Hannover, Germany
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Hünniger T, Wessels H, Fischer C, Paschke-Kratzin A, Fischer M. Just in time-selection: A rapid semiautomated SELEX of DNA aptamers using magnetic separation and BEAMing. Anal Chem 2014; 86:10940-7. [PMID: 25286022 DOI: 10.1021/ac503261b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A semiautomated two-step method for in vitro selection of DNA aptamers using magnetic separation and solid-phase emulsion polymerase chain reaction has been developed. The application of a magnetic separator allows the simultaneous processing of up to 12 SELEXs (systematic evolution of ligands by exponential enrichment) with different targets or buffer conditions. Using a magnetic separator and covalent target immobilization on magnetic beads, the selection process was simplified and the substeps of aptamer/target incubation, washing, and elution of the aptamers were merged into one automated procedure called "FISHing". Without further processing the resulting FISHing eluates are suitable for BEAMing (beads, emulsion, amplification, and magnetics), which includes the amplification by emPCR (emulsion polymerase chain reaction) and strand separation by the implementation of covalently immobilized reverse primers on magnetic beads. The novel selection process has been proved and validated by selecting and characterization of aptamers to the wine fining agent lysozyme.
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Affiliation(s)
- Tim Hünniger
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg , Grindelallee 117, 20146 Hamburg, Germany
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Zhou J, Rossi J. Cell-type-specific aptamer and aptamer-small interfering RNA conjugates for targeted human immunodeficiency virus type 1 therapy. J Investig Med 2014; 62:914-9. [PMID: 25118114 PMCID: PMC4172518 DOI: 10.1097/jim.0000000000000103] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Human immunodeficiency virus (HIV) is a virus that causes acquired immunodeficiency syndrome, a chronic and incurable disease of the human immune system. As the standard of care for the patients with HIV-1, current highly active antiretroviral treatment has been therapeutically effective in most patients; however, it is not curative, and highly active antiretroviral treatment is intolerable because of severe adverse effects. Therefore, nucleic acid-based therapeutics, such as antisense oligonucleotide, ribozyme, messenger RNA, RNA interference (RNAi)-based therapeutics, aptamer, and so on, have been actively developed as alternative or adjuvant agents for those chemical antiviral drugs to surmount those drawbacks. The combinatorial use of various antiviral nucleic acids could be more efficacious in blocking viral replication and preventing the emergence of resistant variants. In this regard, RNAi can function as a gene-specific therapeutic option for controlling HIV-1 replication. Another type of therapeutic nucleic acid--aptamers--shows promise as a new and potent class of anti-HIV agent and can additionally function as a cell-type-specific delivery vehicle for targeted RNAi. The combined use of small interfering RNA (siRNAs) and aptamers could effectively block viral replication and prevent the emergence of resistant variants. The present review offers a brief overview of the use of cell-type-specific aptamer and aptamer-siRNA conjugates' development in our group for the treatment of HIV-1. Their potentials for targeted delivering RNAi therapeutics (eg, siRNA) and suppressing HIV-1 replication in vitro and in humanized animal model will be highlighted here.
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Affiliation(s)
- Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010
| | - John Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010
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Zhang Z, Zhang J, Pei X, Zhang Q, Lu B, Zhang X, Liu J. An aptamer targets HBV core protein and suppresses HBV replication in HepG2.2.15 cells. Int J Mol Med 2014; 34:1423-9. [PMID: 25174447 DOI: 10.3892/ijmm.2014.1908] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 08/11/2014] [Indexed: 12/27/2022] Open
Abstract
Hepatitis B virus (HBV)-related hepatitis is a major health concern worldwide. As current anti-HBV therapies are limited, it is essential to develop new strategies. Aptamer, a newly developed adaptive molecule (single-strand DNA or RNA also known as nucleotide antibody), is a new strategy for clinical diagnosis and therapy due to its high affinity and specificity. In the present study, by systematic evolution of ligand by exponential enrichment (SELEX), aptamers were screened against the core protein of HBV (HBc) from a random ssDNA library. Quantitative PCR (qPCR) results showed that the binding proportions of the SELEX-enriched aptamer pools were increased with the SELEX rounds, until round seven. Thus, the pool of round seven was cloned. Following the sequence analysis of a total of 90 clones by Macaw software, five aptamer candidates were selected and their affinity to HBc was tested by dot blot. Apt.No.28, which had sequence replicates in the clones, was shown to have a high affinity. Furthermore, by agarose gel electrophoresis-capillary transfer-blotting and qPCR, Apt.No.28 was shown to inhibit the assembly of the nucleocapsid, reducing extracellular HBV DNA whose synthesis relied on the formation of the nucleocapsid, indicating its role in suppressing HBV replication. The results provided a new ideal targeting molecule and may facilitate the strategy for targeted therapy as well as drug development of HBV-related diseases.
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Affiliation(s)
- Zuowei Zhang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Jun Zhang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Xiaoyu Pei
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Qi Zhang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Bin Lu
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Xiaojiao Zhang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Jie Liu
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
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Davlieva M, Donarski J, Wang J, Shamoo Y, Nikonowicz EP. Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis. Nucleic Acids Res 2014; 42:10795-808. [PMID: 25140011 PMCID: PMC4176348 DOI: 10.1093/nar/gku743] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Several protein-targeted RNA aptamers have been identified for a variety of applications and although the affinities of numerous protein-aptamer complexes have been determined, the structural details of these complexes have not been widely explored. We examined the structural accommodation of an RNA aptamer that binds bacterial r-protein S8. The core of the primary binding site for S8 on helix 21 of 16S rRNA contains a pair of conserved base triples that mold the sugar-phosphate backbone to S8. The aptamer, which does not contain the conserved sequence motif, is specific for the rRNA binding site of S8. The protein-free RNA aptamer adopts a helical structure with multiple non-canonical base pairs. Surprisingly, binding of S8 leads to a dramatic change in the RNA conformation that restores the signature S8 recognition fold through a novel combination of nucleobase interactions. Nucleotides within the non-canonical core rearrange to create a G-(G-C) triple and a U-(A-U)-U quartet. Although native-like S8-RNA interactions are present in the aptamer-S8 complex, the topology of the aptamer RNA differs from that of the helix 21-S8 complex. This is the first example of an RNA aptamer that adopts substantially different secondary structures in the free and protein-bound states and highlights the remarkable plasticity of RNA secondary structure.
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Affiliation(s)
- Milya Davlieva
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
| | - James Donarski
- Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - Jiachen Wang
- Department of Physics, East China Normal University, 200062 Shanghai, P. R. China
| | - Yousif Shamoo
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
| | - Edward P Nikonowicz
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
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Nucleic acid aptamers: research tools in disease diagnostics and therapeutics. BIOMED RESEARCH INTERNATIONAL 2014; 2014:540451. [PMID: 25050359 PMCID: PMC4090538 DOI: 10.1155/2014/540451] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/18/2014] [Indexed: 12/20/2022]
Abstract
Aptamers are short sequences of nucleic acid (DNA or RNA) or peptide molecules which adopt a conformation and bind cognate ligands with high affinity and specificity in a manner akin to antibody-antigen interactions. It has been globally acknowledged that aptamers promise a plethora of diagnostic and therapeutic applications. Although use of nucleic acid aptamers as targeted therapeutics or mediators of targeted drug delivery is a relatively new avenue of research, one aptamer-based drug “Macugen” is FDA approved and a series of aptamer-based drugs are in clinical pipelines. The present review discusses the aspects of design, unique properties, applications, and development of different aptamers to aid in cancer diagnosis, prevention, and/or treatment under defined conditions.
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Cell-type-specific, Aptamer-functionalized Agents for Targeted Disease Therapy. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e169. [PMID: 24936916 PMCID: PMC4078761 DOI: 10.1038/mtna.2014.21] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 05/05/2014] [Indexed: 02/07/2023]
Abstract
One hundred years ago, Dr. Paul Ehrlich popularized the "magic bullet" concept for cancer therapy in which an ideal therapeutic agent would only kill the specific tumor cells it targeted. Since then, "targeted therapy" that specifically targets the molecular defects responsible for a patient's condition has become a long-standing goal for treating human disease. However, safe and efficient drug delivery during the treatment of cancer and infectious disease remains a major challenge for clinical translation and the development of new therapies. The advent of SELEX technology has inspired many groundbreaking studies that successfully adapted cell-specific aptamers for targeted delivery of active drug substances in both in vitro and in vivo models. By covalently linking or physically functionalizing the cell-specific aptamers with therapeutic agents, such as siRNA, microRNA, chemotherapeutics or toxins, or delivery vehicles, such as organic or inorganic nanocarriers, the targeted cells and tissues can be specifically recognized and the therapeutic compounds internalized, thereby improving the local concentration of the drug and its therapeutic efficacy. Currently, many cell-type-specific aptamers have been developed that can target distinct diseases or tissues in a cell-type-specific manner. In this review, we discuss recent advances in the use of cell-specific aptamers for targeted disease therapy, as well as conjugation strategies and challenges.
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Kosikowska P, Lesner A. Inhibitors of cathepsin G: a patent review (2005 to present). Expert Opin Ther Pat 2013; 23:1611-24. [PMID: 24079661 DOI: 10.1517/13543776.2013.835397] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Cathepsin G (CatG) is a neutral proteinase originating from human neutrophils. It displays a unique dual specificity (trypsin- and chymotrypsin-like); thus, its enzymatic activity is difficult to control. CatG is involved in the pathophysiology of several serious human diseases, such as chronic obstructive pulmonary disease (COPD), Crohn's disease, rheumatoid arthritis, cystic fibrosis and other conditions clinically manifested by excessive inflammatory reactions. For mentioned reasons, CatG was considered as good molecular target for the development of novel drugs. However, none of them have yet entered the market as novel therapeutic agents. AREAS COVERED This article presents an in-depth and detailed analysis of the therapeutic potential of CatG inhibitors based on a review of patent applications and academic publishing disclosed in patents and patent applications (1991 - 2012), with several exceptions for inhibitors retrieved from academic articles. EXPERT OPINION Among the discussed inhibitors of CatG, examples corresponding to derivatives of β-ketophosphonic acids, aminoalkylphosphonic esters and boswellic acids (BAs) could be regarded as the most promising. The most promising one seems to be analogues of compounds of Nature's origin (peptidic and BA derivates). Nevertheless, nothing is currently known about the clinical disposition of any of the CatG inhibitors discovered so far. This latter point suggests that there is still a lot of work to do in the design of stable, pharmacologically active compounds able to specifically regulate the in vivo activity of cathepsin G.
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Affiliation(s)
- Paulina Kosikowska
- University of Gdansk, Department of Bioorganic Chemistry , Wita Stwosza 63, 80-952 Gdansk , Poland +48585235095 ; +48585235472 ;
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Perturbation of discrete sites on a single protein domain with RNA aptamers: targeting of different sides of the TATA-binding protein (TBP). Biosci Biotechnol Biochem 2013; 77:1739-46. [PMID: 23924740 DOI: 10.1271/bbb.130296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Control of interactions among proteins is critical in the treatment of diseases, but the specificity required is not easily incorporated into small molecules. Macromolecules could be more suitable as antagonists in this situation, and RNA aptamers have become particularly promising. Here we describe a novel selection procedure for RNA aptamers against a protein that constitutes a single structural domain, the Drosophila TATA-binding protein (TBP). In addition to the conventional filter partitioning method with free TBP as target, we performed another experiment, in which the TATA-bound form of TBP was targeted. Aptamers generated by both selections were able to bind specifically to TBP, but the two groups showed characteristics which were clearly different in terms of their capability to compete with TATA-DNA, their effects on the TATA-bound form of TBP, and their effects on in vitro transcription. The method used to generate these two groups of aptamers can be used with other targets to direct aptamer specificity to discrete sites on the surface of a protein.
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Meyer M, Scheper T, Walter JG. Aptamers: versatile probes for flow cytometry. Appl Microbiol Biotechnol 2013; 97:7097-109. [PMID: 23838792 DOI: 10.1007/s00253-013-5070-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/17/2013] [Accepted: 06/17/2013] [Indexed: 12/21/2022]
Abstract
Aptamers are nucleic acid oligomers with distinct conformational shapes that allow them to bind targets with high affinity and specificity. Aptamers are selected from a random oligonucleotide library by their capability to bind a certain molecular target. A variety of targets ranging from small molecules like amino acids to complex targets and whole cells have been used to select aptamers. These characteristics and the ability to create specific aptamers against virtually any cell type in a process termed "systematic evolution by exponential enrichment" make them interesting tools for flow cytometry. In this contribution, we review the application of aptamers as probes for flow cytometry, especially cell-phenotyping and detection of various cancer cell lines and virus-infected cells and pathogens. We also discuss the potential of aptamers combined with nanoparticles such as quantum dots for the generation of new multivalent detector molecules with enhanced affinity and sensitivity. With regard to recent advancements in aptamer selection and the decreasing costs for oligonucleotide synthesis, aptamers may rise as potent competitors for antibodies as molecular probes in flow cytometry.
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Affiliation(s)
- Michael Meyer
- Institut für Technische Chemie, Leibniz Universität Hannover, Callinstr. 5, 30167 Hannover, Germany
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Shum KT, Zhou J, Rossi JJ. Nucleic Acid Aptamers as Potential Therapeutic and Diagnostic Agents for Lymphoma. ACTA ACUST UNITED AC 2013; 4:872-890. [PMID: 25057429 PMCID: PMC4104705 DOI: 10.4236/jct.2013.44099] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Lymphomas are cancers that arise from white blood cells and usually present as solid tumors. Treatment of lymphoma often involves chemotherapy, and can also include radiotherapy and/or bone marrow transplantation. There is an un-questioned need for more effective therapies and diagnostic tool for lymphoma. Aptamers are single stranded DNA or RNA oligonucleotides whose three-dimensional structures are dictated by their sequences. The immense diversity in function and structure of nucleic acids enable numerous aptamers to be generated through an iterative in vitro selection technique known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Aptamers have several biochemical properties that make them attractive tools for use as potential diagnostic and pharmacologic agents. Isolated aptamers may directly inhibit the function of target proteins, or they can also be formulated for use as delivery agents for other therapeutic or imaging cargoes. More complex aptamer identification methods, using whole cancer cells (Cell-SELEX), may identify novel targets and aptamers to affect them. This review focuses on recent advances in the use of nucleic acid aptamers as diagnostic and therapeutic agents and as targeted delivery carriers that are relevant to lymphoma. Some representative examples are also discussed.
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Affiliation(s)
- Ka-To Shum
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA ; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
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Abstract
Therapeutic strategies designed to treat HIV infection with combinations of antiviral drugs have proven to be the best approach for slowing the progression to AIDS. Despite the great success of highly active antiretroviral therapy (HAART), drug resistance and toxicity issues still remain a concern for some individuals. Therefore, alternative therapeutic strategies need to be developed to overcome these limitations. Nucleic acid-based therapeutics have been considered as an alternative to the currently used antivirals. In this regard, RNA interference (RNAi) can function as a gene-specific therapeutic option for controlling HIV-1 replication. Another type of therapeutic nucleic acid - aptamers - shows promise as a new and potent class of anti-HIV agent and can additionally function as a cell-type-specific delivery vehicle for targeted RNAi. The combined use of small interfering RNA (siRNAs) and aptamers could effectively block viral replication and prevent the emergence of resistant variants. In this review, we recapitulate recent progress and the therapeutic potential of aptamer-siRNA conjugates in the treatment of HIV infection.
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Affiliation(s)
- Jiehua Zhou
- Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, City of Hope, Duarte, CA, USA
| | - John J. Rossi
- Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, City of Hope, Duarte, CA, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, City of Hope, Duarte, CA, USA
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Haberland A, Wallukat G, Schimke I. Aptamer binding and neutralization of β1-adrenoceptor autoantibodies: basics and a vision of its future in cardiomyopathy treatment. Trends Cardiovasc Med 2012; 21:177-82. [PMID: 22814426 DOI: 10.1016/j.tcm.2012.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Autoantibodies directed against the second extracellular receptor loop of the β(1) receptor (β(1)-ECII-AABs) that belong to the superfamily of G protein-coupled receptors have been frequently found in patients with idiopathic dilated cardiomyopathy, Chagas' cardiomyopathy, and peripartum cardiomyopathy and have been clearly evidenced to be related to disease pathogenesis. Consequently, specific proteins or peptides used as binders in immunoapheresis or as in vivo neutralizers of β(1)-ECII-AABs have been suggested for patient treatment. Aptamers, which are target specifically selected short single- or double-stranded RNA or DNA sequences, are a recently introduced new molecule class applicable to bind and neutralize diverse molecule species, including antibodies. This article reviews selection technologies and characteristics of aptamers with respect to a single-stranded DNA aptamer recently identified as having a very high affinity against β(1)-ECII-AABs. The potential of this aptamer for the elimination of β(1)-ECII-AABs and in vivo neutralization is critically analyzed in view of its potential for future use in cardiomyopathy treatment.
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Affiliation(s)
- Annekathrin Haberland
- Pathobiochemie und Medizinische Chemie, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
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Yin BC, Ye BC, Wang H, Zhu Z, Tan W. Colorimetric logic gates based on aptamer-crosslinked hydrogels. Chem Commun (Camb) 2011; 48:1248-50. [PMID: 22158758 DOI: 10.1039/c1cc15639j] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a novel molecular logic gate system based on the incorporation of aptamer-crosslinked hydrogels. Modified gold nanoparticles are used as the output signal, which is visible to the naked eye. This system is designed for AND and OR operations using two chemicals as stimulus inputs.
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Affiliation(s)
- Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai 200237, P.R. China
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