Difference between revisions of "Part:BBa K115001:Design"

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===Design Notes===
 
===Design Notes===
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The secondary structure is important to the function of these regions, but part of the wt secondary structure is destroyed by the scar. We've tried to alter the sequence so the predicted structure (through mfold and those kind of servers) is sort of conserved, but temperature sensitivity still has to be tested. If it doesn't work, possible solution might be the addition of a larger conserved part of the wt, which implies a small part of wt protein sequence as well.
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The secondary structure is important to the function of an RNA thermometer, but part of the secondary structure is destroyed by the introduction of the scar. We've tried to alter the sequence so that the predicted secondary structure is conserved. More information on the design of this part can be found [http://2008.igem.org/Team:TUDelft/Temperature_design here].
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The figure shows the secondary structure of the wild type RNA thermometer, as predicted by RNAfold, on the left. On the right the predicted secondary structure of this part, after ligation to a protein coding part, is shown. Notice that the 3' prime including the scar and the start codon do not belong to this part. The light blue nucleotides show the mutations that were needed to regain the original secondary structure after introduction of the scar.
  
 
[[Image:BBa_K115001.png | 600px]]
 
[[Image:BBa_K115001.png | 600px]]
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===Source===
 
===Source===
  
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This sequence is taken from the Bradirhizobium Japonicum (BA000040.) as the 5'UTR (ROSE) of a heat shock protein.
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This sequence is taken from the ''Bradirhizobium Japonicum'' ([http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=272 NC_004463]) as the 5'UTR ROSE RNA thermometer of a heat shock protein.
  
 
===References===
 
===References===
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* Saheli Chowdhury, Christophe Maris, Frédéric H-T Allain, and Franz Narberhaus. Molecular basis for temperature sensing by an RNA thermometer. ''The EMBO Journal'', 25:2487–2497, 2006. [http://www.ncbi.nlm.nih.gov/pubmed/16710302 PMID:16710302]

Latest revision as of 07:58, 29 October 2008

RNA thermometer (ROSE)


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]


Design Notes

The secondary structure is important to the function of an RNA thermometer, but part of the secondary structure is destroyed by the introduction of the scar. We've tried to alter the sequence so that the predicted secondary structure is conserved. More information on the design of this part can be found [http://2008.igem.org/Team:TUDelft/Temperature_design here].

The figure shows the secondary structure of the wild type RNA thermometer, as predicted by RNAfold, on the left. On the right the predicted secondary structure of this part, after ligation to a protein coding part, is shown. Notice that the 3' prime including the scar and the start codon do not belong to this part. The light blue nucleotides show the mutations that were needed to regain the original secondary structure after introduction of the scar.

BBa K115001.png

Source

This sequence is taken from the Bradirhizobium Japonicum ([http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=272 NC_004463]) as the 5'UTR ROSE RNA thermometer of a heat shock protein.

References

  • Saheli Chowdhury, Christophe Maris, Frédéric H-T Allain, and Franz Narberhaus. Molecular basis for temperature sensing by an RNA thermometer. The EMBO Journal, 25:2487–2497, 2006. [http://www.ncbi.nlm.nih.gov/pubmed/16710302 PMID:16710302]