Difference between revisions of "Part:BBa K2909002:Design"
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===Design Notes===
 
===Design Notes===
 
The coding sequence was first codon optimized for C. reinhardtii by reverse translating its protein sequence using a software that takes into account the codon usage of C. reinhardtii.<br>
 
The coding sequence was first codon optimized for C. reinhardtii by reverse translating its protein sequence using a software that takes into account the codon usage of C. reinhardtii.<br>
−
The sequence was then standardized to fit the B3-B4 position of the C. reinhardtii MoClo Kit by adding BbsI recognition sites and fusion sites on both ends.
+
The sequence was then standardized in the Phytobrick standard to fit the B3-B4 position of the C. reinhardtii MoClo Kit by adding BbsI recognition sites and fusion sites on both ends.<br>
−
 
+
The stop codon was removed to allow for tagging at the C-terminal position, the stop codon being provided by the part on the position B5.
−
 
+
  
 
===Source===
 
===Source===
  
−
Predicted sequence from the E. guineensis genome sequencing.
+
Predicted sequence from the E. guineensis genome sequencing.<br>
 +
NCBI Reference Sequence: XM_010908457.2<br>
 +
https://www.ncbi.nlm.nih.gov/nuccore/1130625520
  
 
===References===
 
===References===
  
−
Dussert, S. et al. Comparative Transcriptome Analysis of Three Oil Palm Fruit and Seed Tissues That Differ in Oil Content and Fatty Acid Composition. PLANT PHYSIOLOGY 162, 1337–1358 (2013).
+
<ol>
 +
<li> Dussert, S. et al. Comparative Transcriptome Analysis of Three Oil Palm Fruit and Seed Tissues That Differ in Oil Content and Fatty Acid Composition. PLANT PHYSIOLOGY 162, 1337–1358 (2013). </li>
 +
<li> Crozet, P. et al. Birth of a Photosynthetic Chassis: A MoClo Toolkit Enabling Synthetic Biology in the Microalga Chlamydomonas reinhardtii. ACS Synth. Biol. 7, 2074–2086 (2018). </li>
 +
<li> 1.Weber, E., Engler, C., Gruetzner, R., Werner, S. & Marillonnet, S. A Modular Cloning System for Standardized Assembly of Multigene Constructs. PLoS ONE 6, e16765 (2011).</li>
 +
</ol>

Latest revision as of 08:36, 30 August 2019


LPAAT-A-B3-B4 E. guineensis codon optimized for C. reinhardtii


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 474
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 474
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 316
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 474
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 474
    Illegal NgoMIV site found at 204
    Illegal NgoMIV site found at 1029
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

The coding sequence was first codon optimized for C. reinhardtii by reverse translating its protein sequence using a software that takes into account the codon usage of C. reinhardtii.
The sequence was then standardized in the Phytobrick standard to fit the B3-B4 position of the C. reinhardtii MoClo Kit by adding BbsI recognition sites and fusion sites on both ends.
The stop codon was removed to allow for tagging at the C-terminal position, the stop codon being provided by the part on the position B5.

Source

Predicted sequence from the E. guineensis genome sequencing.
NCBI Reference Sequence: XM_010908457.2
https://www.ncbi.nlm.nih.gov/nuccore/1130625520

References

  1. Dussert, S. et al. Comparative Transcriptome Analysis of Three Oil Palm Fruit and Seed Tissues That Differ in Oil Content and Fatty Acid Composition. PLANT PHYSIOLOGY 162, 1337–1358 (2013).
  2. Crozet, P. et al. Birth of a Photosynthetic Chassis: A MoClo Toolkit Enabling Synthetic Biology in the Microalga Chlamydomonas reinhardtii. ACS Synth. Biol. 7, 2074–2086 (2018).
  3. 1.Weber, E., Engler, C., Gruetzner, R., Werner, S. & Marillonnet, S. A Modular Cloning System for Standardized Assembly of Multigene Constructs. PLoS ONE 6, e16765 (2011).