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Abstract Staphylococcus aureusis a major foodborne bacterial pathogen. Early detection ofS. aureusis crucial to prevent infections and ensure food quality. The iron‐regulated surface determinant protein A (IsdA) ofS. aureusis a unique surface protein necessary for sourcing vital iron from host cells for the survival and colonization of the bacteria. The function, structure, and location of the IsdA protein make it an important protein for biosensing applications relating to the pathogen. Here, we report an in‐silico approach to develop and validate high‐affinity binding aptamers for the IsdA protein detection using custom‐designed in‐silico tools and single‐molecule Fluorescence Resonance Energy Transfer (smFRET) measurements. We utilized in‐silico oligonucleotide screening methods and metadynamics‐based methods to generate 10 aptamer candidates and characterized them based on the Dissociation Free Energy (DFE) of the IsdA‐aptamer complexes. Three of the aptamer candidates were shortlisted for smFRET experimental analysis of binding properties. Limits of detection in the low picomolar range were observed for the aptamers, and the results correlated well with the DFE calculations, indicating the potential of the in‐silico approach to support aptamer discovery. This study showcases a computational SELEX method in combination with single‐molecule binding studies deciphering effective aptamers againstS. aureus IsdA, protein. The established approach demonstrates the ability to expedite aptamer discovery that has the potential to cut costs and predict binding efficacy. The application can be extended to designing aptamers for various protein targets, enhancing molecular recognition, and facilitating the development of high‐affinity aptamers for multiple uses.
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Recent Advances in Nanomaterial-Based Aptasensors in Medical Diagnosis and Therapy
Rapid and accurate diagnosis of various biomarkers associated with medical conditions including early detection of viruses and bacteria with highly sensitive biosensors is currently a research priority. Aptamer is a chemically derived recognition molecule capable of detecting and binding small molecules with high specificity and its fast preparation time, cost effectiveness, ease of modification, stability at high temperature and pH are some of the advantages it has over traditional detection methods such as High Performance Liquid Chromatography (HPLC), Enzyme-linked Immunosorbent Assay (ELISA), Polymerase Chain Reaction (PCR). Higher sensitivity and selectivity can further be achieved via coupling of aptamers with nanomaterials and these conjugates called “aptasensors” are receiving greater attention in early diagnosis and therapy. This review will highlight the selection protocol of aptamers based on Traditional Systematic Evolution of Ligands by EXponential enrichment (SELEX) and the various types of modified SELEX. We further identify both the advantages and drawbacks associated with the modified version of SELEX. Furthermore, we describe the current advances in aptasensor development and the quality of signal types, which are dependent on surface area and other specific properties of the selected nanomaterials, are also reviewed.
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- PAR ID:
- 10290364
- Date Published:
- Journal Name:
- Nanomaterials
- Volume:
- 11
- Issue:
- 4
- ISSN:
- 2079-4991
- Page Range / eLocation ID:
- 932
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3390/nano11040932
