Team:TUDelft/Color testing

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==Results==
==Results==
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After we had our first succesful PCR on the genes of ''E. coli'' with ''Taq'' polymerase ([https://2008.igem.org/TUDelft/19_August_2008 Lab notebook August 19th]) we tried to repeat it using ''Pfx'' polymerase, but this didn't work (results not shown). In the end we decided to repeat the experiment with ''Taq'' polymerase as the desired sequences were not very long, thus the chance for mutations due to the lack of proofreading of ''Taq'' polymerase was small. In the end the sequences will be verified through DNA sequencing.  
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After we had our first succesful PCR on the genes of ''E. coli'' with ''Taq'' polymerase ([https://2008.igem.org/TUDelft/19_August_2008 Lab notebook August 19th]) we tried to repeat it using ''Pfx'' polymerase, but this didn't work ([https://2008.igem.org/TUDelft/4_September_2008 Lab notebook September 4th]). In the end we decided to repeat the experiment with ''Taq'' polymerase as the desired sequences were not very long, thus the chance for mutations due to the lack of proofreading of ''Taq'' polymerase was small. In the end the sequences will be verified through DNA sequencing. The gel of this PCR is displayed in figure 1.  
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Image:gelTUDelft2.jpg|thumb|250px|left|Figure 1:Gradient of atoB, click picture to enlarge]]
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[[Image:TUDelftgelcut090908.jpg|thumb|250px|left|Figure 1: ''Taq'' polymerase PCR of atoB, idi and ispA]]
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Image:gelTUDelft1.jpg|thumb|250px|right|Figure 2:Gradient of idi and ispA, click picture to enlarge]]
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The first gradient PCR have been performed on the genes, the ''E. coli'' genes all worked correctly (see lab notebook entry of [https://2008.igem.org/TUDelft/19_August_2008 August 19th]), while still some work has to be done on the ''S. cerevisiae'' primers ([https://2008.igem.org/TUDelft/20_August_2008 August 20th]). The next step will be to PCR the ''E. coli'' genes again, with the ideal annealing temperature, using ''Pfx'' polymerase instead of ''Taq''. The ''Pfx'' enzyme has proofreading and so is less likely to make a mistake within the genes. The gradient PCR on ''S. cerevisiae'' cDNA will be repeated and optimized.
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{{Template:TUDelftiGEM2008_sidebar}}

Revision as of 15:32, 29 October 2008

Contents

Color pathway testing

Correct genes testing

The first indication of whether obtaining of the genes was a succes, is the correct size of DNA product on a gel. DNA sequencing will provide final certainty of the correct genes.

Correct activity testing

The ultimate proof of activity of the pathway would obviously be a colored Escherichia coli colony. However, to identify individual working enzymes, we'd need specific enzymatic assays. Furthermore this is useful, as some enzymatic assays could yield parameters for the modeling guys. Due to a lack of time, we've not looked any further into these assays.

Results

After we had our first succesful PCR on the genes of E. coli with Taq polymerase (Lab notebook August 19th) we tried to repeat it using Pfx polymerase, but this didn't work (Lab notebook September 4th). In the end we decided to repeat the experiment with Taq polymerase as the desired sequences were not very long, thus the chance for mutations due to the lack of proofreading of Taq polymerase was small. In the end the sequences will be verified through DNA sequencing. The gel of this PCR is displayed in figure 1.

Figure 1: Taq polymerase PCR of atoB, idi and ispA
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