Difference between revisions of "Part:BBa K3798005"

Latest revision as of 12:11, 21 October 2021

ssDNA, our best aptamer for Ag+ ion 2

Silver is one of the most wasted precious metals that can be found in effluents, streams and even food. As our project is to develop a precious metal recycling platform, we chose Ag+ as the demonstration ion of this phase of the project. Aptamers are oligonucleotides that can bind targeted molecules with its secondary structures, in our project, Ag+ ion. BBa_K3798005 is a Ag+ aptamer obtained from a previous paper[1], and this particular aptamer had shown outstanding abilities efficiency and satbility in Ag+ ion capture.

Usage and Biology

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

Characterization

Binding efficiency and stability

Fig.1 Remaining Ag+ ion concentration of the solution after treated by different types of aptamers.

As can see above aptamer 3 and 4 has the best binding efficiency with Aptamer 3 having a higher binding ability (the remaining ion concentration of Aptamer 3 is 86ug/L lower than that of Aptamer 4) and Aptamer 4 having better stability when binding (smaller error bounds). Because having 90% of binding efficiency is enough for our use and having higher binding stability means that the treated effluents would have a more consistent results that is essential for industrial use, Aptamer 4 was chosen to be subject of further experiments.

Reusability

In this experiment, we were going to test the reusability of Ag+ aptamer by doing the experiment in previous section four times. Each time the aptamer had bound to the silver ions, the aptamers are separated and the supernatant are reserved for examination. Then the aptamers are heated at 55 degrees Celsius for ten minutes, and cooled for the next trial.

Fig.2 The binding efficiency of aptamer to silver ions in four reusing trials.

According to the result, the binding efficiency to silver ions in four reusing trials remained nearly the same. Thus, the reusability of Ag+ aptamer is extremely high and has no significant change in its binding efficiency for at least four times of reuse. Furthermore, because our samples were delayed for three days from testing during the experimenting process, and we still maintained a stable efficiency, it is proven that our platform can be viable for long periods of time.

Complete system test

Our last experiment is testing the binding efficiency of our whole system to Ag+. Every sections of the system(Bacterial cellulose, CBD-SA, Ag+ Aptamer) were connected together and tested with the same process as we did in aptamer selection experiment.

Fig.3 The concentration of silver ions remain after binding with the whole system.

As can see from the graph, the concentration of silver ions in the control group is only 0.66μg/L, much lower than our other control groups. We believe it was because fusion protein and cellulose also have the some ability of binding to silver ions. However, we can still find that the system works, because the experiment groups have a lower silver ion remaining, with the exact binding efficiency of 69.70%.

Reference

1. Shen, F., Mao, S., Mathivanan, J., Wu, Y., Chandrasekaran, A., & Liu, H. et al. (2020). Short DNA Oligonucleotide as a Ag+ Binding Detector. ACS Omega, 5(44), 28565-28570. doi: 10.1021/acsomega.0c03372

@@ Line 18: / Line 18: @@
 As can see above aptamer 3 and 4 has the best binding efficiency with Aptamer 3 having a higher binding ability (the remaining ion concentration of Aptamer 3 is 86ug/L lower than that of Aptamer 4) and Aptamer 4 having better stability when binding (smaller error bounds).
 Because having 90% of binding efficiency is enough for our use and having higher binding stability means that the treated effluents would have a more consistent results that is essential for industrial use, Aptamer 4 was chosen to be subject of further experiments.
+==Reusability==
+In this experiment, we were going to test the reusability of Ag+ aptamer by doing the experiment in previous section four times. Each time the aptamer had bound to the silver ions, the aptamers are separated and the supernatant are reserved for examination. Then the aptamers are heated at 55 degrees Celsius for ten minutes, and cooled for the next trial.
+[[File:T--SHSBNU_China--silver ion 2.png|600px|thumb|center]]
+<p  class="figure-description"><b><center>Fig.2 The binding efficiency of aptamer to silver ions in four reusing trials. </center></b></p >
+According to the result, the binding efficiency to silver ions in four reusing trials remained nearly the same. Thus, the reusability of Ag+ aptamer is extremely high and has no significant change in its binding efficiency for at least four times of reuse. Furthermore, because our samples were delayed for three days from testing during the experimenting process, and we still maintained a stable efficiency, it is proven that our platform can be viable for long periods of time.
+==Complete system test==
+Our last experiment is testing the binding efficiency of our whole system to Ag+. Every sections of the system(Bacterial cellulose, CBD-SA, Ag+ Aptamer) were connected together and tested with the same process as we did in aptamer selection experiment.
+[[File:T--SHSBNU_China--silver ion 3.png|600px|thumb|center]]
+<p  class="figure-description"><b><center>Fig.3 The concentration of silver ions remain after binding with the whole system. </center></b></p >
+As can see from the graph, the concentration of silver ions in the control group is only 0.66μg/L, much lower than our other control groups. We believe it was because fusion protein and cellulose also have the some ability of binding to silver ions. However, we can still find that the system works, because the experiment groups have a lower silver ion remaining, with the exact binding efficiency of 69.70%.
 ===Reference===