Coding

Part:BBa_M36251:Design

Designed by: Evan Masutani, Erica Lieberman   Group: Stanford BIOE44 - S11   (2011-12-09)
Revision as of 09:46, 11 December 2011 by EricaKL (Talk | contribs) (→‎References)

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AlkS Transcription Factor


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 262
    Illegal EcoRI site found at 475
    Illegal PstI site found at 991
    Illegal PstI site found at 1615
    Illegal PstI site found at 2023
    Illegal PstI site found at 2299
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 262
    Illegal EcoRI site found at 475
    Illegal PstI site found at 991
    Illegal PstI site found at 1615
    Illegal PstI site found at 2023
    Illegal PstI site found at 2299
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 262
    Illegal EcoRI site found at 475
    Illegal BglII site found at 1976
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 262
    Illegal EcoRI site found at 475
    Illegal PstI site found at 991
    Illegal PstI site found at 1615
    Illegal PstI site found at 2023
    Illegal PstI site found at 2299
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 262
    Illegal EcoRI site found at 475
    Illegal PstI site found at 991
    Illegal PstI site found at 1615
    Illegal PstI site found at 2023
    Illegal PstI site found at 2299
    Illegal NgoMIV site found at 729
    Illegal NgoMIV site found at 951
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

We derived our AlkS gene from GenBank’s database. Since we did not want our cells to overproduce AlkS, our group decided to randomize codon usage. We ran through the 883 amino acid sequence of AlkS through the Optimizer web program in order to randomize codon usage. To minimize repeats in AlkS, we used the GENE DESIGNER software to find repeats and replaced the relevant codons. We are currently unsure whether this part works correctly--when used in conjunction with its promoter PalkB (BBa_M36250), a PoPS signal appears to be constitutively generated. Such being the case, we are not sure whether AlkS is being produced at all, since BBa_M36250 may currently operate independently of AlkS.

Source

Smits, T.H., M. Rothlisberger, B. Witholt, and J.B. Van Beilen. "HTH-type Transcriptional Regulator AlkS." GenBank. NCBI, 27 July 2011. Web. 28 Oct. 2011. <http://www.ncbi.nlm.nih.gov/protein/Q9L4M7.1>.

van Beilen,J.B., Panke,S., Lucchini,S., Franchini,A.G., Rothlisberger,M. and Witholt,B. "Analysis of Pseudomonas putida alkane-degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes." GenBank. NCBI, 27 July 2011. Web. 28 Oct. 2011. <http://www.ncbi.nlm.nih.gov/protein/Q9L4M7.1>.

References

Smits, T.H., M. Rothlisberger, B. Witholt, and J.B. Van Beilen. "HTH-type Transcriptional Regulator AlkS." GenBank. NCBI, 27 July 2011. Web. 28 Oct. 2011. <http://www.ncbi.nlm.nih.gov/protein/Q9L4M7.1>.

"Codon Optimization Program from EnCor Biotechnology, Inc." EnCor Biotechnology Inc. 2011. Web. 11 Dec. 2011. <http://www.encorbio.com/protocols/Codon.htm>.