Difference between revisions of "Part:BBa K2043006:Design"

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===Design Notes===
 
===Design Notes===
−
Fabric Binding Domain 1 was fused downstream in the 5' end of the original <i>catA</i> CDS <br>
+
Fabric Binding Domain 10 was fused downstream in the 5' end of the original <i>xylE</i> CDS <br>
−
A linker was introduced in the DNA sequence between FBD1 and the CDS of <i>catA</i> <br>
+
A linker was introduced in the DNA sequence between FBD10 and the CDS of <i>xylE</i> <br>
 
His-tag is added in the C-terminal for protein purification <br>
 
His-tag is added in the C-terminal for protein purification <br>
 
The sequence was codon optimized for <i>E. coli</i> and restriction sites for the restriction enzymes BpiI, BsaI and BsmBI were avoided. <br>
 
The sequence was codon optimized for <i>E. coli</i> and restriction sites for the restriction enzymes BpiI, BsaI and BsmBI were avoided. <br>
Line 19: Line 19:
  
 
===References===
 
===References===
 +
Boyer, S., Biswas, D., Soshee, A. K., Scaramozzino, N., Nizak, C., & Rivoire, O. (2016). Hierarchy and extremes in selections from pools of randomized proteins. Proceedings of the National Academy of Sciences, 201517813.
 +
 +
Cerdan, P., Rekik, M., & Harayama, S. (1995). Substrate Specificity Differences Between Two Catechol 2, 3‐Dioxygenases Encoded by the TOL and NAH Plasmids from Pseudomonas putida. European journal of biochemistry, 229(1), 113-118.
 +
 +
Jain, P., Soshee, A., Narayanan, S. S., Sharma, J., Girard, C., Dujardin, E., & Nizak, C. (2014). Selection of arginine-rich anti-gold antibodies engineered for plasmonic colloid self-assembly. The Journal of Physical Chemistry C, 118(26), 14502-14510.
 +
 +
Kobayashi, T., Ishida, T., Horiike, K., Takahara, Y., Numao, N., Nakazawa, A., ... & Nozaki, M. (1995). Overexpression of Pseudomonas putida catechol 2, 3-dioxygenase with high specific activity by genetically engineered Escherichia coli. Journal of biochemistry, 117(3), 614-622.
 +
 +
Soshee, A., Zürcher, S., Spencer, N. D., Halperin, A., & Nizak, C. (2013). General in vitro method to analyze the interactions of synthetic polymers with human antibody repertoires. Biomacromolecules, 15(1), 113-121.

Latest revision as of 16:39, 27 October 2016


xylE-FBD10 from Pseudomonas putida codon optimized for E. coli


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 703
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Fabric Binding Domain 10 was fused downstream in the 5' end of the original xylE CDS
A linker was introduced in the DNA sequence between FBD10 and the CDS of xylE
His-tag is added in the C-terminal for protein purification
The sequence was codon optimized for E. coli and restriction sites for the restriction enzymes BpiI, BsaI and BsmBI were avoided.
The sequence was confirmed by sequencing and no mutations were observed.
The construction was done by Golden Gate technique using BsaI as restriction enzyme to obtain the desired cohesive ends.

Source

Pseudomonas putida

References

Boyer, S., Biswas, D., Soshee, A. K., Scaramozzino, N., Nizak, C., & Rivoire, O. (2016). Hierarchy and extremes in selections from pools of randomized proteins. Proceedings of the National Academy of Sciences, 201517813.

Cerdan, P., Rekik, M., & Harayama, S. (1995). Substrate Specificity Differences Between Two Catechol 2, 3‐Dioxygenases Encoded by the TOL and NAH Plasmids from Pseudomonas putida. European journal of biochemistry, 229(1), 113-118.

Jain, P., Soshee, A., Narayanan, S. S., Sharma, J., Girard, C., Dujardin, E., & Nizak, C. (2014). Selection of arginine-rich anti-gold antibodies engineered for plasmonic colloid self-assembly. The Journal of Physical Chemistry C, 118(26), 14502-14510.

Kobayashi, T., Ishida, T., Horiike, K., Takahara, Y., Numao, N., Nakazawa, A., ... & Nozaki, M. (1995). Overexpression of Pseudomonas putida catechol 2, 3-dioxygenase with high specific activity by genetically engineered Escherichia coli. Journal of biochemistry, 117(3), 614-622.

Soshee, A., Zürcher, S., Spencer, N. D., Halperin, A., & Nizak, C. (2013). General in vitro method to analyze the interactions of synthetic polymers with human antibody repertoires. Biomacromolecules, 15(1), 113-121.