Difference between revisions of "Part:BBa K1076001:Design"

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===Design Notes===
 
===Design Notes===
  
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To design the upstream gene we used primers with Apa1(5') and NdeI(3') and to downsteam gene we used primers with NdeI(5') and BamH1(3')ends, this parts have Nde1 complementary site and they were ligate together. This method garantee generation of a deleted copy of the target gene using a two step assymmetric/crossover PCR amplification. The target in this case is the FadR.
  
 
===Source===
 
===Source===
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===References===
 
===References===
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 +
HEIDELBERG, John F. et al. Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis. Nature biotechnology, v. 20, n. 11, p. 1118-1123, 2002.
 +
 +
GORBY, Yuri A. et al. Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms.Proceedings of the National Academy of Sciences, v. 103, n. 30, p. 11358-11363, 2006.
 +
 +
SUKOVICH, David J. et al. Structure, function, and insights into the biosynthesis of a head-to-head hydrocarbon in Shewanella oneidensis strain MR-1. Applied and environmental microbiology, v. 76, n. 12, p. 3842-3849, 2010.
 +
 +
ROBINSON, Lee T. Fatty Acid Metabolic Engineering: Insights for Bacterial Hydrocarbon Production. 2012. Doctor tese UNIVERSITY OF MINNESOTA.
 +
 +
KAZAKOV, Alexey E. et al. Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. Journal of bacteriology, v. 191, n. 1, p. 52-64, 2009.
 +
 +
EVANS, W. Charles; FUCHS, G. Anaerobic degradation of aromatic compounds. Annual Reviews in Microbiology, v. 42, n. 1, p. 289-317, 1988.

Latest revision as of 23:30, 27 September 2013

Flanking genes for FadR deletion


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 768
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

To design the upstream gene we used primers with Apa1(5') and NdeI(3') and to downsteam gene we used primers with NdeI(5') and BamH1(3')ends, this parts have Nde1 complementary site and they were ligate together. This method garantee generation of a deleted copy of the target gene using a two step assymmetric/crossover PCR amplification. The target in this case is the FadR.

Source

It comes from amplified genomic sequence

References

HEIDELBERG, John F. et al. Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis. Nature biotechnology, v. 20, n. 11, p. 1118-1123, 2002.

GORBY, Yuri A. et al. Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms.Proceedings of the National Academy of Sciences, v. 103, n. 30, p. 11358-11363, 2006.

SUKOVICH, David J. et al. Structure, function, and insights into the biosynthesis of a head-to-head hydrocarbon in Shewanella oneidensis strain MR-1. Applied and environmental microbiology, v. 76, n. 12, p. 3842-3849, 2010.

ROBINSON, Lee T. Fatty Acid Metabolic Engineering: Insights for Bacterial Hydrocarbon Production. 2012. Doctor tese UNIVERSITY OF MINNESOTA.

KAZAKOV, Alexey E. et al. Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. Journal of bacteriology, v. 191, n. 1, p. 52-64, 2009.

EVANS, W. Charles; FUCHS, G. Anaerobic degradation of aromatic compounds. Annual Reviews in Microbiology, v. 42, n. 1, p. 289-317, 1988.