"
Experimental Layout
From 2010.igem.org
I.stansfield (Talk | contribs) |
|||
| Line 2: | Line 2: | ||
{{:Team:Aberdeen_Scotland/Title}} | {{:Team:Aberdeen_Scotland/Title}} | ||
<html> | <html> | ||
| - | <h1>Troubleshooting | + | <h1>Troubleshooting the CUP1p-[MS2-CFP] construct</h1> |
<h3>Aim</h3> | <h3>Aim</h3> | ||
| - | <p>Following the analysis of the two promoters using | + | <p>Following the analysis of the two promoters using CUP1p-GFP and GAL1p-GFP the next experiments planned would start to characterise the interactions of both constructs (CUP1p-[MS2-CFP] and GAL1p-[Npep-GFP]) and more specifically the mutual repression that would be taking place. Experiments using FACS analysis were set up in order to measure various levels of CFP and GFP depending on different conditions (i.e. different ranges of inducers, different ratios of pRS415 to pRS414 etc.). However the FACS machine was unable to detect any GFP or CFP in our calibration samples.</p> |
<h3>Hypothesis</h3> | <h3>Hypothesis</h3> | ||
<p>Our initial hypothesis was that the lack of GFP and CFP expression was due to experimental error during the set up of the cultures (this proved to be correct as far as pRS415 was concerned where the lack of expression was traced back to a faulty stock of inducing agent).<br><br> | <p>Our initial hypothesis was that the lack of GFP and CFP expression was due to experimental error during the set up of the cultures (this proved to be correct as far as pRS415 was concerned where the lack of expression was traced back to a faulty stock of inducing agent).<br><br> | ||
| Line 13: | Line 13: | ||
</p> | </p> | ||
<h3>Protocol</h3> | <h3>Protocol</h3> | ||
| - | <p>A series of experiments were set up in order to determine the functionality of various parts of | + | <p>A series of experiments were set up in order to determine the functionality of various parts of CUP1p-[MS2-CFP] with a view to repair the construct.<br><br></html> |
| - | [[1. Confirmation using microscope and fluorometer analysis that the | + | [[1. Confirmation using microscope and fluorometer analysis that the CUP1p-[MS2-CFP] construct was not expressing CFP]]<br> |
[[2. Confirming the CFP sequence is functional]] <br> | [[2. Confirming the CFP sequence is functional]] <br> | ||
[[3. N-GFP Swap Experiment]]<br> | [[3. N-GFP Swap Experiment]]<br> | ||
| - | [[4. Replacing the CUP1 promoter in | + | [[4. Replacing the CUP1 promoter in CUP1p-[MS2-CFP] with the CUP1-2 promoter from the CUP1p-GFP construct]]<br> |
<br><html> | <br><html> | ||
<h3>Conclusion</h3> | <h3>Conclusion</h3> | ||
<p>The first experiment did not detect any CFP fluorescent whilst the second experiment indicated that the CFP sequence used was accurate and in another vector resulted in fluorescence. The third experiment revealed that a fault lies with either the CUP1 promoter or/and the Bbox stem loop however the fourth experiment showed that the promoter did not seem to be contributing to the lack of expression.<br><br> | <p>The first experiment did not detect any CFP fluorescent whilst the second experiment indicated that the CFP sequence used was accurate and in another vector resulted in fluorescence. The third experiment revealed that a fault lies with either the CUP1 promoter or/and the Bbox stem loop however the fourth experiment showed that the promoter did not seem to be contributing to the lack of expression.<br><br> | ||
| - | Our data suggests that the reason why | + | Our data suggests that the reason why CUP1p-[MS2-CFP] is not producing any CFP is due to the presence of the Bbox Stem loop in the 5’UTR. Although Bbox stem loops have already be used in conjunction with the λ-N peptide as markers for mRNA, it is possible that it has never been placed in 5’UTR but is rather located to a 3’UTR. As a result we cannot be sure that the loop can be melted and could therefore be preventing the expression of the following proteins.<br><br> |
Our experiments however, do not rule out the possibility that the fusion of MS2 to CFP is defective and is resulting in an unstable protein that is being turned-over rapidly. It is also possible that the fusion is preventing the CFP portion from fluorescencing due to improper folding. | Our experiments however, do not rule out the possibility that the fusion of MS2 to CFP is defective and is resulting in an unstable protein that is being turned-over rapidly. It is also possible that the fusion is preventing the CFP portion from fluorescencing due to improper folding. | ||
</p> | </p> | ||
Revision as of 16:46, 17 October 2010
University of Aberdeen - ayeSwitch
Troubleshooting the CUP1p-[MS2-CFP] construct
Aim
Following the analysis of the two promoters using CUP1p-GFP and GAL1p-GFP the next experiments planned would start to characterise the interactions of both constructs (CUP1p-[MS2-CFP] and GAL1p-[Npep-GFP]) and more specifically the mutual repression that would be taking place. Experiments using FACS analysis were set up in order to measure various levels of CFP and GFP depending on different conditions (i.e. different ranges of inducers, different ratios of pRS415 to pRS414 etc.). However the FACS machine was unable to detect any GFP or CFP in our calibration samples.
Hypothesis
Our initial hypothesis was that the lack of GFP and CFP expression was due to experimental error during the set up of the cultures (this proved to be correct as far as pRS415 was concerned where the lack of expression was traced back to a faulty stock of inducing agent).
The second hypothesis put forward to explain the lack of CFP expression was that one of the parts that made up pRS414 was defective.
Protocol
A series of experiments were set up in order to determine the functionality of various parts of CUP1p-[MS2-CFP] with a view to repair the construct.
[[1. Confirmation using microscope and fluorometer analysis that the CUP1p-[MS2-CFP] construct was not expressing CFP]]
2. Confirming the CFP sequence is functional
3. N-GFP Swap Experiment
[[4. Replacing the CUP1 promoter in CUP1p-[MS2-CFP] with the CUP1-2 promoter from the CUP1p-GFP construct]]
Conclusion
The first experiment did not detect any CFP fluorescent whilst the second experiment indicated that the CFP sequence used was accurate and in another vector resulted in fluorescence. The third experiment revealed that a fault lies with either the CUP1 promoter or/and the Bbox stem loop however the fourth experiment showed that the promoter did not seem to be contributing to the lack of expression.
Our data suggests that the reason why CUP1p-[MS2-CFP] is not producing any CFP is due to the presence of the Bbox Stem loop in the 5’UTR. Although Bbox stem loops have already be used in conjunction with the λ-N peptide as markers for mRNA, it is possible that it has never been placed in 5’UTR but is rather located to a 3’UTR. As a result we cannot be sure that the loop can be melted and could therefore be preventing the expression of the following proteins.
Our experiments however, do not rule out the possibility that the fusion of MS2 to CFP is defective and is resulting in an unstable protein that is being turned-over rapidly. It is also possible that the fusion is preventing the CFP portion from fluorescencing due to improper folding.
