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- W2479720692 abstract "Single-stranded DNA and RNA aptamers are able to bind to specific target molecules with high affinity and are widely used in many routine molecular-diagnostic laboratories. Developing methods for direct detection of specific targets using aptamers could be challenging. As a central protease of hemostasis, thrombin is widely used as targeted molecule for testing new analytical approaches. To develop an electrochemical method for the detection of thrombin, our collaborator uses osmium tetroxide, 2,2' bipyridine as an electrochemical tag that can be detected at an electrode surface. However, conjugation of the osmium to thrombin can potentially change the binding interface, diminishing the binding affinity of the aptamer to the thrombin analyte. To gain insight into the molecular basis of the thrombin-aptamer interaction, we investigated systems of hydrated thrombin and osmium-thrombin in the presence of DNA aptamer with 29 nucleotides. In particular, we conducted both canonical simulations and umbrella sampling with exchange of umbrellas to calculate the binding energy of the aptamer with thrombin and osmium-thrombin. We found that the orientations of thrombin-aptatmer complex rapidly relax from native conformation into another more energetically favourable conformations. Our results also indicate that, as a result of conjugating osmium complex to thrombin, the binding affinity of aptamer for osmium-thrombin conjugate significantly decreased in relation to thrombin/aptamer system. Therefore, we redesigned aptamers to regain the lost affinity for the osmium-thrombin conjugate to accommodate the osmium tags. We then calculate and compare the binding free energy of computer-optimized aptamers in the present of thrombin and osmium-thrombin conjugate. Overall, our results reveal in atomistic detail a variety of redesigned aptamers that may have enhanced binding affinity for osmium-thrombin conjugate. Our next step is to validate our computer-optimized aptamers in the presence of thrombin and osmium-thrombin using experimental methods." @default.
- W2479720692 created "2016-08-23" @default.
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- W2479720692 date "2016-02-01" @default.
- W2479720692 modified "2023-09-30" @default.
- W2479720692 title "Designing an Electrochemically Labelled Thrombin DNA Aptamer using Molecular Dynamics Simulations" @default.
- W2479720692 doi "https://doi.org/10.1016/j.bpj.2015.11.3029" @default.
- W2479720692 hasPublicationYear "2016" @default.
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