Difference between revisions of "Team:HK SKHLPSS/Results"

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     <h2>Gel Electrophoresis</h2>
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     <h2>1. Gel electrophoresis (Collaborated with HKU)</h2>
 
     <p>
 
     <p>
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       This graph is our result. We have done this test so that we can see the size of DNA strands. We can see that if the DNA strand move slower, it has a larger size. If the DNA strand move faster, it has a smaller size. We also can see that on lane 10, which included all DNA strands, is staying highest. It shows that our design of nano-cube worked and they are successful to integrate because it moves slowly and the position is high.  
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       With the help of HKU team, we are able to get the gel electrophoresis to analyze whether our design was actually assembled. As seen in the first gel result. All 8 oligos come together as the shift observed in last lane.
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    </p>
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 +
    <p>
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      To further prove our nano-cube is formed as per our design, we conducted another gel electrophoresis, with each of the samples containing two oligos which should not be binded together. As shown above, each of the samples, except of the nano-cube, contains two distinct bands, indicating that these two oligos did not binded together, which further proves our design. 
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    </p>
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    <p>
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      Also, the band for the target could not be found when nano-cube and target were placed together (the last lane), indicating that the target should be successfully binded with the nano-cube. 
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    </p>
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    <p>
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      All in all,these two gel results suggested that our nano-cube should be formed as per our design.
 
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     <h2>DNA Peroxidase Assay Result</h2>
 
     <h2>DNA Peroxidase Assay Result</h2>
 
     <p>
 
     <p>
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       These two graphs are our results. In the first graph, it shows that the nano-cube gave a very high signal of absorbance at 0.85 on its own .The presence of target shows a low signal at 0.75. Then, we conduct another experiment with different concentrations of target. The second graph shows the relationship between the reduction of the absorbance and the concentration of the target strand. We found that the higher the concentration of the target was, the lower the signal was. Reduction in absorbance is directly proportional to the concentration of target showing that the presence of the target actually reduced the signal! Although it is out of our expectation, it’s suggesting that we have accidentally discovered its signal off ability. We deduced the cube is very flexible and will easily be closed by the split quadruplex sequences and we deduced that the presence of target might just prohibit the cube to close.
+
       These two graphs are our results. In the first graph, it showed that the nano-cube gave a very high signal of absorbance at 0.85 on its own.The presence of target showed a low signal at 0.75. Then, we conducted another experiment with different concentrations of target. The second graph shows the relationship between the reduction of the absorbance and the concentration of the target strand. We found that the higher the concentration of the target was, the lower the signal was. Reduction in absorbance is directly proportional to the concentration of target, showing that the presence of the target actually reduced the signal. Although it is out of our expectation, it is suggesting that we have accidentally discovered its signal off ability. We deduced the cube is very flexible and will easily be closed by the split quadruplex sequences and we deduced that the presence of target might just prohibit the cube to close.
 
     </p>
 
     </p>
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 +
    <p>
 +
      The limit of detection (LOD) was calculated to check for the lowest concentration of H3N2 virus DNA this nano-cube could be able to detect. The LOD was calculated as 199.74nM, or 39.9%. H3N2 virus can be detected when concentration of the virus is higher than limit of detection.
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     <h2>mRNA Peroxidase Assay Result</h2>
 
     <h2>mRNA Peroxidase Assay Result</h2>
 
     <p>
 
     <p>
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Upon successful of DNA peroxidase assay, we used RNA of the H3N2 virus to conduct an in-vitro test. The steps for this test were similar to DNA peroxidase assay, except DNA of H3N2 virus is replaced by RNA.  The results are shown below.   
 
     </p>
 
     </p>
 +
 +
    <p>
 +
The above graph showed the relationship between the reduction of the absorbance and the concentration of target RNA  strand. The result suggested that the reduction in absorbance is directly proportional to the concentration of target RNA strand, which is the same with the result of DNA peroxidase assay. This showed that our nano-cube could not only detect for the DNA strand but also RNA strand. It proves that this nano-cube is suitable to detect virus in which their genetic material are stored as RNA instead of DNA. 
 +
    </p>
 +
 +
    <p>
 +
The LOD was calculated again to check for the lowest concentration of H3N2 virus RNA this nano-cube could be able to detect. The LOD was calculated as 137.885nM, or 27.6%. H3N2 virus can be detected when concentration of the virus is higher than limit of detection. Obviously, RNA has a much lower limit of detection than DNA.
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{{HK_SKHLPSS_FOOTER}}
 
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Revision as of 04:04, 30 October 2017

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Results

1. Gel electrophoresis (Collaborated with HKU)

With the help of HKU team, we are able to get the gel electrophoresis to analyze whether our design was actually assembled. As seen in the first gel result. All 8 oligos come together as the shift observed in last lane.

To further prove our nano-cube is formed as per our design, we conducted another gel electrophoresis, with each of the samples containing two oligos which should not be binded together. As shown above, each of the samples, except of the nano-cube, contains two distinct bands, indicating that these two oligos did not binded together, which further proves our design.

Also, the band for the target could not be found when nano-cube and target were placed together (the last lane), indicating that the target should be successfully binded with the nano-cube.

All in all,these two gel results suggested that our nano-cube should be formed as per our design.

DNA Peroxidase Assay Result

These two graphs are our results. In the first graph, it showed that the nano-cube gave a very high signal of absorbance at 0.85 on its own.The presence of target showed a low signal at 0.75. Then, we conducted another experiment with different concentrations of target. The second graph shows the relationship between the reduction of the absorbance and the concentration of the target strand. We found that the higher the concentration of the target was, the lower the signal was. Reduction in absorbance is directly proportional to the concentration of target, showing that the presence of the target actually reduced the signal. Although it is out of our expectation, it is suggesting that we have accidentally discovered its signal off ability. We deduced the cube is very flexible and will easily be closed by the split quadruplex sequences and we deduced that the presence of target might just prohibit the cube to close.

The limit of detection (LOD) was calculated to check for the lowest concentration of H3N2 virus DNA this nano-cube could be able to detect. The LOD was calculated as 199.74nM, or 39.9%. H3N2 virus can be detected when concentration of the virus is higher than limit of detection.

mRNA Peroxidase Assay Result

Upon successful of DNA peroxidase assay, we used RNA of the H3N2 virus to conduct an in-vitro test. The steps for this test were similar to DNA peroxidase assay, except DNA of H3N2 virus is replaced by RNA. The results are shown below.

The above graph showed the relationship between the reduction of the absorbance and the concentration of target RNA strand. The result suggested that the reduction in absorbance is directly proportional to the concentration of target RNA strand, which is the same with the result of DNA peroxidase assay. This showed that our nano-cube could not only detect for the DNA strand but also RNA strand. It proves that this nano-cube is suitable to detect virus in which their genetic material are stored as RNA instead of DNA.

The LOD was calculated again to check for the lowest concentration of H3N2 virus RNA this nano-cube could be able to detect. The LOD was calculated as 137.885nM, or 27.6%. H3N2 virus can be detected when concentration of the virus is higher than limit of detection. Obviously, RNA has a much lower limit of detection than DNA.

Cloning


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