Binding Characteristics Study of DNA based Aptamers for <i>E. coli</i> O157:H7
<i>E. coli</i> O157:H7 is a pathogenic bacterium producing verotoxins that could lead to serious complications such as hemolytic uremia syndrome. Fast detection of such pathogens is important. For rapid detection, aptamers are quickly gaining traction as alternative biorecognition molecu...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-01-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/26/1/204 |
| _version_ | 1797542554990804992 |
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| author | Saika Siddiqui Jie Yuan |
| author_facet | Saika Siddiqui Jie Yuan |
| author_sort | Saika Siddiqui |
| collection | DOAJ |
| description | <i>E. coli</i> O157:H7 is a pathogenic bacterium producing verotoxins that could lead to serious complications such as hemolytic uremia syndrome. Fast detection of such pathogens is important. For rapid detection, aptamers are quickly gaining traction as alternative biorecognition molecules besides conventional antibodies. Several DNA aptamers have been selected for <i>E. coli</i> O157:H7. Nonetheless, there has not been a comparative study of the binding characteristics of these aptamers. In this work, we present a comprehensive analysis of binding characteristics including binding affinity (K<sub>d</sub>) and binding capacity (B<sub>max</sub>) of DNA-based aptamers for <i>E. coli</i> O157:H7 using qPCR. Our results show that aptamer E18R has the highest binding capacity to <i>E. coli</i> 157:H7 and the highest specificity over non-pathogenic <i>E. coli</i> strains K12 and DH5α. Our study also finds that the common biotin-tag modification at 5′ end typically changes the binding capacity significantly. For most of the selected aptamers, the binding capacity after a biotin-tag modification decreases. There exists a discrepancy in the binding capability between the selected aptamer and the aptamer used for detection. Our study also shows that a lower concentration of Mg<sup>2+</sup> ions in the binding buffer leads to a decrease in the binding capacity of E17F and E18R, while it does not affect the binding capacity of S1 and EcoR1. |
| first_indexed | 2024-03-10T13:32:14Z |
| format | Article |
| id | doaj.art-b94149e9507f451db17bded5d0533882 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T13:32:14Z |
| publishDate | 2021-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-b94149e9507f451db17bded5d05338822023-11-21T07:54:34ZengMDPI AGMolecules1420-30492021-01-0126120410.3390/molecules26010204Binding Characteristics Study of DNA based Aptamers for <i>E. coli</i> O157:H7Saika Siddiqui0Jie Yuan1Department of Bioengineering, Hong Kong University of Science and Technology, Kowloon, Hong KongDepartment of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Kowloon, Hong Kong<i>E. coli</i> O157:H7 is a pathogenic bacterium producing verotoxins that could lead to serious complications such as hemolytic uremia syndrome. Fast detection of such pathogens is important. For rapid detection, aptamers are quickly gaining traction as alternative biorecognition molecules besides conventional antibodies. Several DNA aptamers have been selected for <i>E. coli</i> O157:H7. Nonetheless, there has not been a comparative study of the binding characteristics of these aptamers. In this work, we present a comprehensive analysis of binding characteristics including binding affinity (K<sub>d</sub>) and binding capacity (B<sub>max</sub>) of DNA-based aptamers for <i>E. coli</i> O157:H7 using qPCR. Our results show that aptamer E18R has the highest binding capacity to <i>E. coli</i> 157:H7 and the highest specificity over non-pathogenic <i>E. coli</i> strains K12 and DH5α. Our study also finds that the common biotin-tag modification at 5′ end typically changes the binding capacity significantly. For most of the selected aptamers, the binding capacity after a biotin-tag modification decreases. There exists a discrepancy in the binding capability between the selected aptamer and the aptamer used for detection. Our study also shows that a lower concentration of Mg<sup>2+</sup> ions in the binding buffer leads to a decrease in the binding capacity of E17F and E18R, while it does not affect the binding capacity of S1 and EcoR1.https://www.mdpi.com/1420-3049/26/1/204DNA aptamers<i>E. coli</i> O157:H7 detectionaptamer binding characteristicsbiotin modificationionic buffer strength |
| spellingShingle | Saika Siddiqui Jie Yuan Binding Characteristics Study of DNA based Aptamers for <i>E. coli</i> O157:H7 Molecules DNA aptamers <i>E. coli</i> O157:H7 detection aptamer binding characteristics biotin modification ionic buffer strength |
| title | Binding Characteristics Study of DNA based Aptamers for <i>E. coli</i> O157:H7 |
| title_full | Binding Characteristics Study of DNA based Aptamers for <i>E. coli</i> O157:H7 |
| title_fullStr | Binding Characteristics Study of DNA based Aptamers for <i>E. coli</i> O157:H7 |
| title_full_unstemmed | Binding Characteristics Study of DNA based Aptamers for <i>E. coli</i> O157:H7 |
| title_short | Binding Characteristics Study of DNA based Aptamers for <i>E. coli</i> O157:H7 |
| title_sort | binding characteristics study of dna based aptamers for i e coli i o157 h7 |
| topic | DNA aptamers <i>E. coli</i> O157:H7 detection aptamer binding characteristics biotin modification ionic buffer strength |
| url | https://www.mdpi.com/1420-3049/26/1/204 |
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