Difference between revisions of "Part:BBa K371000:Design"
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In the previous literature，most of research work on pdu BMC(or pdu MCP) focus on ''Citrobacter Freundii'' and ''Salmonella enterica''. Taking all of the factors together, we choose ''Citrobacter Freundii'' as the orgin of gene in our project. Because the whole genome of ''Citrobacter Freundii'' has not been decoded yet, we use the reference sequence sent to NCBI by Martin J.Warren group(GenBank: AM498294.1).By seraching the restriction enzyme site in  pduJK(11457-11732), we found a '''PstI''' site inside pduJ. And in order to make the part compatible with the RFC53(A noval BioBrick assembly standard designed to facilitate protein fusion) for the following experiment. We also search the EarI, SacI ,SapI and BglII site inside pduJK. There is also a EarI site in pduK.
 
In the previous literature，most of research work on pdu BMC(or pdu MCP) focus on ''Citrobacter Freundii'' and ''Salmonella enterica''. Taking all of the factors together, we choose ''Citrobacter Freundii'' as the orgin of gene in our project. Because the whole genome of ''Citrobacter Freundii'' has not been decoded yet, we use the reference sequence sent to NCBI by Martin J.Warren group(GenBank: AM498294.1).By seraching the restriction enzyme site in  pduJK(11457-11732), we found a '''PstI''' site inside pduJ. And in order to make the part compatible with the RFC53(A noval BioBrick assembly standard designed to facilitate protein fusion) for the following experiment. We also search the EarI, SacI ,SapI and BglII site inside pduJK. There is also a EarI site in pduK.
  
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We got the ''Citrobacter Freundii'' from NBRC(NBRC NO.12681). We isolate the whole genome of ''Citrobacter Freundii''. Then we use this genoe as template and mutate the PstI and PstI site by over lapping PCR. Here is a rough illustration of our mutation workflow.
+
We got the ''Citrobacter Freundii'' from NBRC(NBRC NO.12681). We isolate the whole genome of ''Citrobacter Freundii''. Then we use this genoe as template and mutate the PstI sites by over lapping PCR. Here is a rough illustration of our mutation workflow.
  
 
[[Image:PduJK_mutation_PCR.png|800px]]
 
[[Image:PduJK_mutation_PCR.png|800px]]

Revision as of 06:10, 31 October 2010

Design Notes

In the previous literature，most of research work on pdu BMC(or pdu MCP) focus on Citrobacter Freundii and Salmonella enterica. Taking all of the factors together, we choose Citrobacter Freundii as the orgin of gene in our project. Because the whole genome of Citrobacter Freundii has not been decoded yet, we use the reference sequence sent to NCBI by Martin J.Warren group(GenBank: AM498294.1).By seraching the restriction enzyme site in pduJK(11457-11732), we found a PstI site inside pduJ. And in order to make the part compatible with the RFC53(A noval BioBrick assembly standard designed to facilitate protein fusion) for the following experiment. We also search the EarI, SacI ,SapI and BglII site inside pduJK. There is also a EarI site in pduK.

We got the Citrobacter Freundii from NBRC(NBRC NO.12681). We isolate the whole genome of Citrobacter Freundii. Then we use this genoe as template and mutate the PstI sites by over lapping PCR. Here is a rough illustration of our mutation workflow.

PduJK mutation PCR.png

Six primer used in mutation PCR:

pduJ 1-pduJ 190

f1: 5'-GTTT TCTAGAG CCACAGGAGAAAAGCAGTATGAATAACG-3'

r2:5'-CGCTTGCTGCTGCGCTTCC-3'

pduJ 190-pduK 318

f3: 5'-GGAAGCGCAGCAGCAAGCG-3'

r4:5'-GGTCCTCAGGGATTTCTTCATGTGGT-3'

pduK 318-pduK 471

f5: 5'-ACCACATGAAGAAATCCCTGAGGACC-3' 26

r6:5'-GTTT CTGCAGCGGCCGCTACTAGTA TCACGCTTCACCTCGTTTGCC-3'

The sequence results of pduJK are different from the sequence we found on Genebank. Some silent mutation locate in the sequence with no special spacial rule. We suspect that the strain we used is not same with the papar, maybe even belong to different strain of Citrobacter Freundii. However the proterin sequence alignment between the result of Martin J.Warren group, the proterin sequence of pduJK in Salmonella enterica and ours shows that the 'mutation' locate in the nonconserved site. Thus we decide to continue our experement with the gene pduJK.