1
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Lai H, Ming P, Wu M, Wang S, Sun D, Zhai H. An electrochemical aptasensor based on P-Ce-MOF@MWCNTs as signal amplification strategy for highly sensitive detection of zearalenone. Food Chem 2023; 423:136331. [PMID: 37182496 DOI: 10.1016/j.foodchem.2023.136331] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 04/22/2023] [Accepted: 05/05/2023] [Indexed: 05/16/2023]
Abstract
In this research, a signal-off electrochemical aptasensor with high sensitivity was constructed for trace detection of zearalenone (ZEN). Specifically, Ce-based metal-organic framework and multi-walled carbon nanotubes nanocomposite was functionalized with polyethyleneimine (P-Ce-MOF@MWCNTs) and served as sensing platform for its high surface area and excellent electrochemical active. Subsequently, toluidine blue (TB) was electrodeposited as the signal probe, and platinum@gold nanoparticles (Pt@Au) were dropped for the attachment of aptamer (ZEA). In the presence of ZEN, the ZEA would specifically recognize and combine with the target, causing a decrease of electrochemical signal from TB. Under the optimal conditions, the aptasensor exhibited good linear relationship for ZEN in a concentration range from 5.0 × 10-5 to 50.0 ng/mL, while the limit of detection (LOD, S/N = 3) and limit of quantitation (LOQ, S/N = 10) were 1.0 × 10-5 ng/mL and 2.9 × 10-5 ng/mL, respectively. Ultimately, the aptasensor was successfully applied into ZEN detection in semen coicis real samples.
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Affiliation(s)
- Haohong Lai
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Pingtao Ming
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Maoqiang Wu
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Shumei Wang
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Duanping Sun
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Haiyun Zhai
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou 510006, China.
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2
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Amundarain A, Pastor F, Prósper F, Agirre X. Aptamers, a New Therapeutic Opportunity for the Treatment of Multiple Myeloma. Cancers (Basel) 2022; 14:5471. [PMID: 36358889 PMCID: PMC9657029 DOI: 10.3390/cancers14215471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 08/30/2023] Open
Abstract
Multiple Myeloma (MM) remains an incurable disease due to high relapse rates and fast development of drug resistances. The introduction of monoclonal antibodies (mAb) has caused a paradigm shift in MM treatment, paving the way for targeted approaches with increased efficacy and reduced toxicities. Nevertheless, antibody-based therapies face several difficulties such as high immunogenicity, high production costs and limited conjugation capacity, which we believe could be overcome by the introduction of nucleic acid aptamers. Similar to antibodies, aptamers can bind to their targets with great affinity and specificity. However, their chemical nature reduces their immunogenicity and production costs, while it enables their conjugation to a wide variety of cargoes for their use as delivery agents. In this review, we summarize several aptamers that have been tested against MM specific targets with promising results, establishing the rationale for the further development of aptamer-based strategies against MM. In this direction, we believe that the study of novel plasma cell surface markers, the development of intracellular aptamers and further research on aptamers as building blocks for complex nanomedicines will lead to the generation of next-generation targeted approaches that will undoubtedly contribute to improve the management and life quality of MM patients.
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Affiliation(s)
- Ane Amundarain
- Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 31008 Pamplona, Spain
| | - Fernando Pastor
- Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 31008 Pamplona, Spain
| | - Felipe Prósper
- Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 31008 Pamplona, Spain
- Hematology Department, Clínica Universidad de Navarra, CCUN, University of Navarra, 31008 Pamplona, Spain
| | - Xabier Agirre
- Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 31008 Pamplona, Spain
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3
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Farrel Côrtes M, Marli Bes T, Ribeiro Deo B, Barbosa dos Anjos B, Jimenez Galisteo A, Cerdeira Sabino E, Santos C, Figueiredo Costa S. Selection and Identification of a DNA Aptamer for Multidrug-Resistant Acinetobacter baumannii Using an In-House Cell-SELEX Methodology. Front Cell Infect Microbiol 2022; 12:818737. [PMID: 35846753 PMCID: PMC9280162 DOI: 10.3389/fcimb.2022.818737] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/29/2022] [Indexed: 11/21/2022] Open
Abstract
Infections caused by multidrug-resistant A. baumannii are a worldwide health concern with high mortality rates. Rapid identification of this infectious agent is critical as it can easily spread with difficult or no options for treatment. In this context, the development of reliable and economically viable detection and therapeutic methodologies are still challenging. One of the promising solutions is the development of nucleic acid aptamers capable of interacting with bacteria. These aptamers can be used for specific recognition of infectious agents as well as for blocking their functions. Cell-SELEX technology currently allows the selection and identification of aptamers and is flexible enough to target molecules present in an entire bacterial cell without their prior knowledge. However, the aptamer technology is still facing many challenges, such as the complexity of the screening process. Here, we describe the selection and identification of a new aptamer A01, using an in-house whole-cell SELEX-based methodology, against multi-resistant Acinetobacter baumannii, with rapid execution and low cost. In addition, this protocol allowed the identification of the aptamer A01 with the whole A. baumannii cell as a target. The aptamer A01 demonstrated a binding preference to A. baumannii when compared to K. pneumoniae, C. albicans, and S. aureus in fluorescence assays. Although the time-kill assay did not show an effect on bacterial growth, the potential bactericidal or bacteriostatic cannot be totally discarded. The new categorized aptamer (A01) displayed a significant binding affinity to MDR A. baumannii.
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Affiliation(s)
- Marina Farrel Côrtes
- Instituto de Medicina Tropical e Departamento de Moléstias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Taniela Marli Bes
- Instituto de Medicina Tropical e Departamento de Moléstias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Beatriz Ribeiro Deo
- Instituto de Medicina Tropical e Departamento de Moléstias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Beatriz Barbosa dos Anjos
- Instituto de Medicina Tropical e Departamento de Moléstias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Andrés Jimenez Galisteo
- Instituto de Medicina Tropical e Departamento de Moléstias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical e Departamento de Moléstias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Carlos Santos
- Biologia Molecular, Clinimol Diag Molecular, Sao Paulo, Brazil
| | - Silvia Figueiredo Costa
- Instituto de Medicina Tropical e Departamento de Moléstias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- *Correspondence: Silvia Figueiredo Costa,
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4
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Shoaib M, Shehzad A, Mukama O, Raza H, Niazi S, Khan IM, Ali B, Akhtar W, Wang Z. Selection of potential aptamers for specific growth stage detection of Yersinia enterocolitica. RSC Adv 2020; 10:24743-24752. [PMID: 35516186 PMCID: PMC9055141 DOI: 10.1039/d0ra00683a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/17/2020] [Indexed: 11/28/2022] Open
Abstract
Yersinia enterocolitica remains a threat to public health, and a sensitive detection method is a prerequisite due to its complicated diagnosis associated with slow growth. Recently, aptamer-based detection systems have played a vital role in the development of simple, rapid, sensitive, and specific detection methods. Herein, highly specific ssDNA aptamers were screened against Y. enterocolitica at the different growth stages by whole cell-SELEX. Cells at different growth stages were harvested and incubated with an ssDNA library to get an enriched pool of specific aptamer candidates. After the 10th round of SELEX, the enriched pool was sequenced and grouped into seven families based on homology and similarity of the secondary structure. Flow cytometry analysis revealed that the aptamers M1, M5, and M7 with K d values of 37.93 ± 7.88 nM, 74.96 ± 21.34 nM, and 73.02 ± 18.76 nM had the highest affinity and specificity to the target, respectively. The selected aptamers showed binding to the different growth stages of Y. enterocolitica with a significant increase in the gated fluorescence. Our aptamer selection strategy is convenient, and the developed aptamer can be useful for an accurate and reliable detection system.
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Affiliation(s)
- Muhammad Shoaib
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University Wuxi 214122 People's Republic of China
- National Institute of Food Science and Technology, FFNHS, University of Agriculture Faisalabad 38040 Pakistan
| | - Aamir Shehzad
- National Institute of Food Science and Technology, FFNHS, University of Agriculture Faisalabad 38040 Pakistan
- UniLaSalle, Univ. Artois, EA7519 - Transformations & Agro-ressources, Normandie Université F-76130 Mont-Saint-Aignan France
| | - Omar Mukama
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
- Department of Biology, College of Science and Technology, University of Rwanda Avenue de l'armée, P. O. Box: 3900 Kigali Rwanda
| | - Husnain Raza
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
- School of Food and Biological Engineering, Jiangsu University Zhenjiang Jiangsu 212013 People's Republic of China
- National Institute of Food Science and Technology, FFNHS, University of Agriculture Faisalabad 38040 Pakistan
| | - Sobia Niazi
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University Wuxi 214122 People's Republic of China
- National Institute of Food Science and Technology, FFNHS, University of Agriculture Faisalabad 38040 Pakistan
| | - Imran Mahmood Khan
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University Wuxi 214122 People's Republic of China
- National Institute of Food Science and Technology, FFNHS, University of Agriculture Faisalabad 38040 Pakistan
| | - Barkat Ali
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
| | - Wasim Akhtar
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University Wuxi 214122 People's Republic of China
- National Institute of Food Science and Technology, FFNHS, University of Agriculture Faisalabad 38040 Pakistan
| | - Zhouping Wang
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University Wuxi 214122 People's Republic of China
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5
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A sensitive and rapid bacterial antibiotic susceptibility test method by surface enhanced Raman spectroscopy. Braz J Microbiol 2020; 51:875-881. [PMID: 32347530 DOI: 10.1007/s42770-020-00282-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 04/17/2020] [Indexed: 02/07/2023] Open
Abstract
This study aims to develop a rapid bacterial antibiotic susceptibility test (AST) method by Bacteria-aptamer@AgNPs-surface enhanced Raman spectroscopy (SERS) and further evaluate the influence of different antibiotics on the Raman intensity of bacteria. The Raman intensity of Escherichia coli O157:H7 (E. coli O157:H7) and Staphylococcus aureus (S. aureus) in the presence of different concentrations of antibiotics in 2 h was detected by Bacteria-aptamer@AgNPs-SERS in this study. Our results found that the bacteria Raman signal peak at 735 cm-1 and the minimum inhibitory concentration (MIC) value was determined in 1 h according to Raman signals. In 2 h, the bacteria Raman signal growth at sub-MIC concentrations of four different kinds of antibiotics and the bacteria colony-forming unit (CFU) have similar enhancements. SERS utilizes special functions of rough metal surfaces and offers a huge enhancement of Raman intensities with reduced fluorescence backgrounds, which makes it an ultrasensitive tool of detection. This rapid AST method and the enhancement effect should be of value in search of new antibiotic drugs.
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6
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Loo JFC, Chien YH, Yin F, Kong SK, Ho HP, Yong KT. Upconversion and downconversion nanoparticles for biophotonics and nanomedicine. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.213042] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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7
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Komarova N, Kuznetsov A. Inside the Black Box: What Makes SELEX Better? Molecules 2019; 24:E3598. [PMID: 31591283 PMCID: PMC6804172 DOI: 10.3390/molecules24193598] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023] Open
Abstract
Aptamers are small oligonucleotides that are capable of binding specifically to a target, with impressive potential for analysis, diagnostics, and therapeutics applications. Aptamers are isolated from large nucleic acid combinatorial libraries using an iterative selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Since being implemented 30 years ago, the SELEX protocol has undergone many modifications and improvements, but it remains a laborious, time-consuming, and costly method, and the results are not always successful. Each step in the aptamer selection protocol can influence its results. This review discusses key technical points of the SELEX procedure and their influence on the outcome of aptamer selection.
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Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
| | - Alexander Kuznetsov
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
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8
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Diao D, Qiao N, Wu X, Li J, Lou X. An efficient method to evaluate experimental factor influence on in vitro binding of aptamers. Anal Biochem 2018; 556:7-15. [PMID: 29913134 DOI: 10.1016/j.ab.2018.06.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 12/11/2022]
Abstract
Nucleic acid-based aptamers are promising alternative to antibodies, however, their selection process (SELEX) is challenging. A number of simulations and few experiments have been reported offering insights into experimental factors (EFs) that govern the effectiveness of the selection process. Though useful, these previous studied were either lack of experimental confirmation, or considered limited EFs. A more efficient experimental method is highly desired. In this study, we developed a fast method that is capable to quantitatively probe the influence of multiple EFs. Based on the fact that the aptamer enrichment efficiency is highly affected by background binding, the binding ratio between the numbers of specific aptamer binders and nonspecific (unselected library) binders per bead was used to quantitatively evaluate EF effects. Taking thrombin and streptavidin as models, three previously studied EFs (surface coverage, buffer composition, and DNA concentration) and four never-studied ones (surface chemistry, heat treatment, elution methodology and pool purity) were investigated. The EFs greatly affected binding ratio (ranging from 0.03 ± 0.03 to 14.60 ± 2.30). The results were in good agreement with the literature, suggesting the good feasibility of our method. Our study provides guidance for the choice of EFs not only for aptamer selection, but also for binding evaluation of aptamers.
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Affiliation(s)
- Donglin Diao
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Na Qiao
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Xiao Wu
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Jiyuan Li
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China.
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9
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Kalra P, Dhiman A, Cho WC, Bruno JG, Sharma TK. Simple Methods and Rational Design for Enhancing Aptamer Sensitivity and Specificity. Front Mol Biosci 2018; 5:41. [PMID: 29868605 PMCID: PMC5966647 DOI: 10.3389/fmolb.2018.00041] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/13/2018] [Indexed: 12/27/2022] Open
Abstract
Aptamers are structured nucleic acid molecules that can bind to their targets with high affinity and specificity. However, conventional SELEX (Systematic Evolution of Ligands by EXponential enrichment) methods may not necessarily produce aptamers of desired affinity and specificity. Thus, to address these questions, this perspective is intended to suggest some approaches and tips along with novel selection methods to enhance evolution of aptamers. This perspective covers latest novel innovations as well as a broad range of well-established approaches to improve the individual binding parameters (aptamer affinity, avidity, specificity and/or selectivity) of aptamers during and/or post-SELEX. The advantages and limitations of individual aptamer selection methods and post-SELEX optimizations, along with rational approaches to overcome these limitations are elucidated in each case. Further the impact of chosen selection milieus, linker-systems, aptamer cocktails and detection modules utilized in conjunction with target-specific aptamers, on the overall assay performance are discussed in detail, each with its own advantages and limitations. The simple variations suggested are easily available for facile implementation during and/or post-SELEX to develop ultrasensitive and specific assays. Finally, success studies of established aptamer-based assays are discussed, highlighting how they utilized some of the suggested methodologies to develop commercially successful point-of-care diagnostic assays.
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Affiliation(s)
- Priya Kalra
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India.,Faculty of Pharmacy, Uttarakhand Technical University, Dehradun, India
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - John G Bruno
- Operational Technologies Corporation, San Antonio, TX, United States
| | - Tarun K Sharma
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, India.,AptaBharat Innovation Private Limited, Translational Health Science and Technology Institute Incubator, Faridabad, India
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10
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Zeninskaya NA, Kolesnikov AV, Ryabko AK, Shemyakin IG, Dyatlov IA, Kozyr AV. [Aptamers in the Treatment of Bacterial Infections: Problems and Prospects]. ACTA ACUST UNITED AC 2018; 71:350-8. [PMID: 29297663 DOI: 10.15690/vramn591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Aptamers are short single-stranded oligonucleotides which are selected via targeted chemical evolution in vitro to bind a molecular target of interest. The aptamer selection technology is designated as SELEX (Systematic evolution of ligands by exponential enrichment). SELEX enables isolation of oligonucleotide aptamers binding a wide range of targets of interest with little respect for their nature and molecular weight. A number of applications of aptamer selection were developed ranging from biosensor technologies to antitumor drug discovery. First aptamer-based pharmaceutical (Macugen) was approved by FDA for clinical use in 2004, and since then more than ten aptamer-based drugs undergo various phases of clinical trials. From the medicinal chemist’s point of view, aptamers represent a new class of molecules suitable for the development of new therapeutics. Due to the stability, relative synthesis simplicity, and development of advanced strategies of target specific molecular selection, aptamers attract increased attention of drug discovery community. Difficulties of the development of next-generation antibiotics basing on the conventional basis of combinatorial chemistry and high-throughput screening have also amplified the interest to aptamer-based therapeutic candidates. The present article reviews the investigations focused on the development of antibacterial aptamers and discusses the potential and current limitations of the use of this type of therapeutic molecules.
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11
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Darkoh C, Deaton M, DuPont HL. Nonantimicrobial drug targets for Clostridium difficile infections. Future Microbiol 2017; 12:975-985. [PMID: 28759258 DOI: 10.2217/fmb-2017-0024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile infection (CDI) is a major public health problem worldwide. Treatment has become complicated due to the emergence of strains with increased toxigenicity and sporulation rate, together with rampant antibiotics use that disrupts colonization resistance of the colonic microbiota. As a result, there is a critical need for nonantibiotic treatments. Therapies based on inhibiting the toxins, bacterial structures responsible for colonization, virulence and restoration of the gut microbiota are the most important nonantibiotic targets to combat CDI. This report outlines these targets and how they could become the focus of future therapeutic agents. Inhibiting colonization and virulence factors during CDI will disrupt pathogen persistence and decrease exposure to the inflammatory toxins, allowing the immune system to clear the infection.
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Affiliation(s)
- Charles Darkoh
- Department of Epidemiology, Human Genetics, & Environmental Sciences, Center For Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Microbiology & Infectious Diseases Program, Houston, TX 77030, USA
| | - Magdalena Deaton
- Department of Epidemiology, Human Genetics, & Environmental Sciences, Center For Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Herbert L DuPont
- Department of Epidemiology, Human Genetics, & Environmental Sciences, Center For Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA.,Baylor College of Medicine, Departments of Molecular Virology & Microbiology & Medicine, Houston, TX 77030, USA
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12
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Etzel M, Mörl M. Synthetic Riboswitches: From Plug and Pray toward Plug and Play. Biochemistry 2017; 56:1181-1198. [PMID: 28206750 DOI: 10.1021/acs.biochem.6b01218] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In synthetic biology, metabolic engineering, and gene therapy, there is a strong demand for orthogonal or externally controlled regulation of gene expression. Here, RNA-based regulatory devices represent a promising emerging alternative to proteins, allowing a fast and direct control of gene expression, as no synthesis of regulatory proteins is required. Besides programmable ribozyme elements controlling mRNA stability, regulatory RNA structures in untranslated regions are highly interesting for engineering approaches. Riboswitches are especially well suited, as they show a modular composition of sensor and response elements, allowing a free combination of different modules in a plug-and-play-like mode. The sensor or aptamer domain specifically interacts with a trigger molecule as a ligand, modulating the activity of the adjacent response domain that controls the expression of the genes located downstream, in most cases at the level of transcription or translation. In this review, we discuss the recent advances and strategies for designing such synthetic riboswitches based on natural or artificial components and readout systems, from trial-and-error approaches to rational design strategies. As the past several years have shown dramatic development in this fascinating field of research, we can give only a limited overview of the basic riboswitch design principles that is far from complete, and we apologize for not being able to consider every successful and interesting approach described in the literature.
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Affiliation(s)
- Maja Etzel
- Institute for Biochemistry, Leipzig University , Brüderstrasse 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University , Brüderstrasse 34, 04103 Leipzig, Germany
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13
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Citartan M, Ch'ng ES, Rozhdestvensky TS, Tang TH. Aptamers as the ‘capturing’ agents in aptamer-based capture assays. Microchem J 2016. [DOI: 10.1016/j.microc.2016.04.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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14
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Hamula CLA, Peng H, Wang Z, Tyrrell GJ, Li XF, Le XC. An improved SELEX technique for selection of DNA aptamers binding to M-type 11 of Streptococcus pyogenes. Methods 2015; 97:51-7. [PMID: 26678795 DOI: 10.1016/j.ymeth.2015.12.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 12/26/2022] Open
Abstract
Streptococcus pyogenes is a clinically important pathogen consisting of various serotypes determined by different M proteins expressed on the cell surface. The M type is therefore a useful marker to monitor the spread of invasive S. pyogenes in a population. Serotyping and nucleic acid amplification/sequencing methods for the identification of M types are laborious, inconsistent, and usually confined to reference laboratories. The primary objective of this work is to develop a technique that enables generation of aptamers binding to specific M-types of S. pyogenes. We describe here an in vitro technique that directly used live bacterial cells and the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) strategy. Live S. pyogenes cells were incubated with DNA libraries consisting of 40-nucleotides randomized sequences. Those sequences that bound to the cells were separated, amplified using polymerase chain reaction (PCR), purified using gel electrophoresis, and served as the input DNA pool for the next round of SELEX selection. A specially designed forward primer containing extended polyA20/5Sp9 facilitated gel electrophoresis purification of ssDNA after PCR amplification. A counter-selection step using non-target cells was introduced to improve selectivity. DNA libraries of different starting sequence diversity (10(16) and 10(14)) were compared. Aptamer pools from each round of selection were tested for their binding to the target and non-target cells using flow cytometry. Selected aptamer pools were then cloned and sequenced. Individual aptamer sequences were screened on the basis of their binding to the 10 M-types that were used as targets. Aptamer pools obtained from SELEX rounds 5-8 showed high affinity to the target S. pyogenes cells. Tests against non-target Streptococcus bovis, Streptococcus pneumoniae, and Enterococcus species demonstrated selectivity of these aptamers for binding to S. pyogenes. Several aptamer sequences were found to bind preferentially to the M11 M-type of S. pyogenes. Estimated binding dissociation constants (Kd) were in the low nanomolar range for the M11 specific sequences; for example, sequence E-CA20 had a Kd of 7±1 nM. These affinities are comparable to those of a monoclonal antibody. The improved bacterial cell-SELEX technique is successful in generating aptamers selective for S. pyogenes and some of its M-types. These aptamers are potentially useful for detecting S. pyogenes, achieving binding profiles of the various M-types, and developing new M-typing technologies for non-specialized laboratories or point-of-care testing.
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Affiliation(s)
- Camille L A Hamula
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2G3, Canada; Mount Sinai Hospital, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York City, NY 10029, USA
| | - Hanyong Peng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Zhixin Wang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Gregory J Tyrrell
- The Provincial Laboratory for Public Health for Alberta, Walter Mackenzie Health Sciences Centre, Edmonton, Alberta T6G 2J2, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, 2B3.12 Walter Mackenzie Health Sciences Centre, Edmonton, Alberta T6G 2B7, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2G3, Canada.
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2G3, Canada.
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A Quarter Century of In Vitro Selection. J Mol Evol 2015; 81:137-9. [PMID: 26597944 DOI: 10.1007/s00239-015-9723-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/18/2015] [Indexed: 01/16/2023]
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