1
|
Ryan AK, Rahman S, Williams RM. An optical aptamer-based cytokine nanosensor detects macrophage activation by bacterial toxins. bioRxiv 2024:2024.04.05.588290. [PMID: 38617274 PMCID: PMC11014583 DOI: 10.1101/2024.04.05.588290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Overactive or dysregulated cytokine expression is hallmark of many acute and chronic inflammatory diseases. This is true for acute or chronic infection, neurodegenerative diseases, autoimmune diseases, cardiovascular disease, cancer, and others. Cytokines such as interleukin-6 (IL-6) are known therapeutic targets and biomarkers for such inflammatory diseases. Platforms for cytokine detection are therefore desirable tools for both research and clinical applications. Single-walled carbon nanotubes (SWCNT) are versatile nanomaterials with near-infrared fluorescence that can serve as transducers for optical sensors. When functionalized with an analyte-specific recognition element, SWCNT emission may become sensitive and selective towards the desired target. SWCNT-aptamer sensors are easily assembled, inexpensive, and biocompatible. In this work, we introduced a nanosensor design based on SWCNT and a DNA aptamer specific to IL-6. We first evaluated several SWCNT-aptamer constructs based on this simple direct complexation method, wherein the aptamer both solubilizes the SWCNT and confers sensitivity to IL-6. The sensor limit of detection, 105 ng/mL, lies in the relevant range for pathological IL-6 levels. Upon investigation of sensor kinetics, we found rapid response within seconds of antigen addition which continued over the course of three hours. We found that this sensor construct is stable, and the aptamer is not displaced from the nanotube surface during IL-6 detection. Finally, we investigated the ability of this sensor construct to detect macrophage activation caused by bacterial lipopolysaccharides (LPS) in an in vitro model of disease, finding rapid and sensitive detection of macrophage-expressed IL-6. We are confident further development of this sensor will have novel implications for diagnosis of acute and chronic inflammatory diseases, in addition to contributing to the understanding of the role of cytokines in these diseases.
Collapse
Affiliation(s)
- Amelia K. Ryan
- The City College of New York, Department of Biomedical Engineering, New York, NY 10031
| | - Syeda Rahman
- The City College of New York, Department of Biomedical Engineering, New York, NY 10031
| | - Ryan M. Williams
- The City College of New York, Department of Biomedical Engineering, New York, NY 10031
- PhD Program in Chemistry, Graduate Center, City University of New York, New York, NY 10016
| |
Collapse
|
2
|
Li Z, Lv Y, Duan X, Liu B, Zhao Y. Highly Uniform DNA Monolayers Generated by Freezing-Directed Assembly on Gold Surfaces Enable Robust Electrochemical Sensing in Whole Blood. Angew Chem Int Ed Engl 2023; 62:e202312975. [PMID: 37726209 DOI: 10.1002/anie.202312975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 09/21/2023]
Abstract
Assembling DNA on solid surfaces is fundamental to surface-based DNA technology. However, precise control over DNA conformation and organization at solid-liquid interfaces remains a challenge, resulting in limited stability and sensitivity in biosensing applications. We herein communicate a simple and robust method for creating highly uniform DNA monolayers on gold surfaces by a freeze-thawing process. Using Raman spectroscopy, fluorescent imaging, and square wave voltammetry, we demonstrate that thiolated DNA is concentrated and immobilized on gold surfaces with an upright conformation. Moreover, our results reveal that the freezing-induced DNA surfaces are more uniform, leading to improved DNA stability and target recognition. Lastly, we demonstrate the successful detection of a model drug in undiluted whole blood while mitigating the effects of biofouling. Our work not only provides a simple approach to tailor the DNA-gold surface for biosensors but also sheds light on the unique behavior of DNA oligonucleotides upon freezing on the liquid-solid interface.
Collapse
Affiliation(s)
- Zhenglian Li
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Yanguan Lv
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
- Department of Clinical Medical Laboratory, Affiliated Hospital of Yang Zhou University Medical College, Huai'an Maternal and Child Health Care Center, Huai'an, Jiangsu, 223002, P. R. China
| | - Xiaoman Duan
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Biwu Liu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| |
Collapse
|
3
|
Shafiei N, Mahmoodzadeh Hosseini H, Amani J, Mirhosseini SA, Jafary H. Screening and Identification of DNA Nanostructure Aptamer Using the SELEX Method for Detection of Epsilon Toxin. Iran J Pharm Res 2023; 22:e140505. [PMID: 38444705 PMCID: PMC10912870 DOI: 10.5812/ijpr-140505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 03/07/2024]
Abstract
Background Epsilon toxin (ETX), produced by Clostridium perfringens, is one of the most potent toxins known, with a lethal potency approaching that of botulinum neurotoxins. Epsilon toxin is responsible for enteritis. Therefore, the development of rapid and simple methods to detect ETX is imperative. Aptamers are single-stranded oligonucleotides that can bind tightly to specific target molecules with an affinity comparable to that of monoclonal antibodies (mAbs). DNA aptamers can serve as tools for the molecular identification of organisms, such as pathogen subspecies. Objectives This study aimed to isolate high-affinity single-stranded DNA (ssDNA) aptamers against ETX. Methods This study identified aptamers using the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method, enzyme-linked apta-sorbent assay (ELASA), and surface plasmon resonance (SPR) to determine the affinity and specificity of the newly obtained aptamers targeting ETX. Results Several aptamers obtained through the SELEX process were studied. Among them, 2 aptamers, ETX clone 3 (ETX3; dissociation constant (Kd = 8.4 ± 2.4E-9M) and ETX11 (Kd = 6.3 ± 1.3E-9M) had favorable specificity for ETX. The limits of detection were 0.21 and 0.08 μg/mL for ETX3 and ETX11, respectively.. Conclusions The discovered aptamers can be used in various aptamer-based rapid diagnostic tests for the detection of ETX.
Collapse
Affiliation(s)
- Nafiseh Shafiei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamideh Mahmoodzadeh Hosseini
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Jafar Amani
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Seyed Ali Mirhosseini
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hanieh Jafary
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| |
Collapse
|
4
|
Behbahani M, Mohabatkar H, Hosseini B. In silico design of quadruplex aptamers against the spike protein of SARS-CoV-2. Inform Med Unlocked 2021; 26:100757. [PMID: 34664030 PMCID: PMC8514331 DOI: 10.1016/j.imu.2021.100757] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022] Open
Abstract
Nucleic acid aptamers are short sequences of nucleic acid ligands that bind to a specific target molecule. Aptamers are experimentally nominated using the well-designed SELEX (systematic evolution of ligands by exponential enrichment) method. Here, we designed a new method for diagnosis and blocking SARS-CoV-2 based on G-quadruplex aptamer. This aptamer was developed against the receptor-binding domain (RBD) region of the spike protein. In the current study, ten quadruplex DNA aptamers entitled AP1, AP2, AP3, AP4, AP5, AP6, AP7, AP8, AP9, and AP10 were designed in silico and had high HADDOCK scores. One quadruplex aptamer sequence (AP1) was selected based on the interaction with RBD of SARS-CoV-2. Results showed that AP1 aptamer could be used as an agent in the diagnosis and therapy of SARS-CoV-2, although more works are still needed.
Collapse
Affiliation(s)
- Mandana Behbahani
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jareeb St., Isfahan, 81746-73441, Iran
| | - Hassan Mohabatkar
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jareeb St., Isfahan, 81746-73441, Iran
| | - Barumand Hosseini
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jareeb St., Isfahan, 81746-73441, Iran
| |
Collapse
|
5
|
Schmitz FRW, Valério A, de Oliveira D, Hotza D. An overview and future prospects on aptamers for food safety. Appl Microbiol Biotechnol 2020; 104:6929-6939. [PMID: 32588103 PMCID: PMC7315907 DOI: 10.1007/s00253-020-10747-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023]
Abstract
Introduction Many bacteria are responsible for infections in humans and plants, being found in vegetables, water, and medical devices. Most bacterial detection methods are time-consuming and take days to give the result. Aptamers are a promising alternative for a quick and reliable measurement technique to detect bacteria present in food products. Selected aptamers are DNA or RNA oligonucleotides that can bind with bacteria or other molecules with affinity and specificity for the target cells by the SELEX or cell-SELEX technique. This method is based on some rounds to remove the non-ligand oligonucleotides, leaving the aptamers specific to bind to the selected bacteria. Compared with conventional methodologies, the detection approach using aptamers is a rapid, low-cost form of analysis. Objective This review summarizes obtention methods and applications of aptamers in the food industry and biotechnology. Besides, different techniques with aptamers are presented, which enable more effective target detection. Conclusion Applications of aptamers as biosensors, or the association of aptamers with nanomaterials, may be employed in analyses by colorimetric, fluorescence, or electrical devices. Additionally, more efficient ways of sample preparation are presented, which can support food safety to provide human health, with a low-cost method for contaminant detection.Key points • Aptamers are promising for detecting contaminants outbreaks. • Studies are needed to identify aptamers for different targets. |
Collapse
Affiliation(s)
- Fernanda Raquel Wust Schmitz
- Department of Chemical Engineering and Food Engineering (EQA), Federal University of Santa Catarina (UFSC), Florianópolis, SC, 88040-900, Brazil
| | - Alexsandra Valério
- Department of Chemical Engineering and Food Engineering (EQA), Federal University of Santa Catarina (UFSC), Florianópolis, SC, 88040-900, Brazil
| | - Débora de Oliveira
- Department of Chemical Engineering and Food Engineering (EQA), Federal University of Santa Catarina (UFSC), Florianópolis, SC, 88040-900, Brazil.
| | - Dachamir Hotza
- Department of Chemical Engineering and Food Engineering (EQA), Federal University of Santa Catarina (UFSC), Florianópolis, SC, 88040-900, Brazil
| |
Collapse
|