Difference between revisions of "Part:BBa K2165000:Design"
Line 14: Line 14:
  
 
===Characterization===
 
===Characterization===
−
[[File:BBa_K2165000_Violcultures.png|thumb|left|200px|Constituatively active VioABCDE yeast in synthetic media, along with a positive control (regular yeast) and a negative control (no yeast)]]
+
[[File:BBa_K2165000_Violcultures.png|thumb|left|200px|Figure 1: Constituatively active VioABCDE yeast in synthetic media, along with a positive control (regular yeast) and a negative control (no yeast)]] Though typical biobrick characeterization involves in-vitro data, this is unavailabe due to the lack of an available chassis containing the three enzymes necessary to produce the substrate for VioC (VioA, VioB, and VioE). Because of the nature of this biobrick, it is reasonable to look at information from other sources to see the expected results. A protein BLAST shows that the sequence in this biobrick codes for "VioC" found in "cloning vector pET15b-vioC" with 100% quarry cover. Figure 1 shows an example of Violacein using the plasmid this biobrick was based from.

Revision as of 04:06, 29 October 2016


Violacein C gene codon-optimized for S. Cerevisiae


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 101


Design Notes

The online codon-optimization tool offered by Integrated DNA Technologies (https://www.idtdna.com/CodonOpt) was used to codon-optimize this sequence for use in yeast. Combinations containing RFC[10] illegal restriction sites were actively avoided.

Source

The CDS contained in this BioBrick was designed by running the VioC gene sent to the University of Washington by the [http://dueberlab.berkeley.edu/ Dueber Laboratory] at University of California-Berkley through IDT's Codon Optimization Tool for S. cerevisiae. A biobrick standard assembly prefix and suffix was added before the it was ordered as a geneblock through IDT.

Characterization

Figure 1: Constituatively active VioABCDE yeast in synthetic media, along with a positive control (regular yeast) and a negative control (no yeast)
Though typical biobrick characeterization involves in-vitro data, this is unavailabe due to the lack of an available chassis containing the three enzymes necessary to produce the substrate for VioC (VioA, VioB, and VioE). Because of the nature of this biobrick, it is reasonable to look at information from other sources to see the expected results. A protein BLAST shows that the sequence in this biobrick codes for "VioC" found in "cloning vector pET15b-vioC" with 100% quarry cover. Figure 1 shows an example of Violacein using the plasmid this biobrick was based from.