Difference between revisions of "Part:BBa K4201012:Design"

 
 
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===Design Notes===
 
===Design Notes===
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Design Considerations
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[[File:RUBY pathway.png|200px|thumb|right|Biosynthesis starts with Tyrosine and is converted into betalain with three enzymes: CYP76AD1, DODA, and Glucosyl Trasnferase. CYP76AD1 converts Tyrosine into L-DOPA. CYP76AD1 can continue to convert L-DOPA into cyclo-DOPA. DODA will convert L-DOPA into Betalamic Acid. Both cyclo-DOPA and Betalamic Acid react non-enzymatically to form Betanidin. The Glucosyl transferase will convert this into Betalain<sup>1</sup>.]]
  
  
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Codon optimization for Glycine max (soybean) is a unique design consideration for all of CU Boulder’s coding sequences including our RUBY. Codon optimization is the intentional use of specific codons for specific amino acids, dependent on what tRNAs are most abundant in the organism. While codon optimization is a common consideration for synthetic biologists, our sequences are unique for iGEM because they are intended for expression in soybeans.
  
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===Source===
 
  
−
Source
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===Source===
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The RUBY sequence contains CYP76AD1, DODA, and Glucosyltransferase coding sequences<sup>1</sup>. All of our DNA fragments are obtained via de novo synthesis by iGEM sponsors Twist Bioscience and Integrated DNA technologies.
  
 
===References===
 
===References===
 +
1. He, Y., Zhang, T., Sun, H., Zhan, H. & Zhao, Y. A reporter for noninvasively monitoring gene expression and plant transformation. Hortic. Res. 7, 152 (2020).
 +
<br>2. Gandía-Herrero, F. & García-Carmona, F. Biosynthesis of betalains: yellow and violet plant pigments. Trends Plant Sci. 18, 334–343 (2013).

Latest revision as of 01:17, 12 October 2022


RUBY


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 3745
    Illegal BamHI site found at 2394
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 330
    Illegal NgoMIV site found at 909
    Illegal NgoMIV site found at 2622
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 1
    Illegal BsaI.rc site found at 3968


Design Notes

Biosynthesis starts with Tyrosine and is converted into betalain with three enzymes: CYP76AD1, DODA, and Glucosyl Trasnferase. CYP76AD1 converts Tyrosine into L-DOPA. CYP76AD1 can continue to convert L-DOPA into cyclo-DOPA. DODA will convert L-DOPA into Betalamic Acid. Both cyclo-DOPA and Betalamic Acid react non-enzymatically to form Betanidin. The Glucosyl transferase will convert this into Betalain1.


Codon optimization for Glycine max (soybean) is a unique design consideration for all of CU Boulder’s coding sequences including our RUBY. Codon optimization is the intentional use of specific codons for specific amino acids, dependent on what tRNAs are most abundant in the organism. While codon optimization is a common consideration for synthetic biologists, our sequences are unique for iGEM because they are intended for expression in soybeans.


Source

The RUBY sequence contains CYP76AD1, DODA, and Glucosyltransferase coding sequences1. All of our DNA fragments are obtained via de novo synthesis by iGEM sponsors Twist Bioscience and Integrated DNA technologies.

References

1. He, Y., Zhang, T., Sun, H., Zhan, H. & Zhao, Y. A reporter for noninvasively monitoring gene expression and plant transformation. Hortic. Res. 7, 152 (2020).
2. Gandía-Herrero, F. & García-Carmona, F. Biosynthesis of betalains: yellow and violet plant pigments. Trends Plant Sci. 18, 334–343 (2013).