Difference between revisions of "Part:BBa K2165001:Design"

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	<partinfo>BBa_K2165001 SequenceAndFeatures</partinfo>		<partinfo>BBa_K2165001 SequenceAndFeatures</partinfo>
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	===Design Notes===		===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.	+	The VioD developed by the University of Washington's iGEM team have been codon optimized for yeast in hopes to improve the efficiency of its translation.
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−		+
	===Source===		===Source===
−	&#8203;VioC&#8203; &#8203;is&#8203; &#8203;originally&#8203; &#8203;from&#8203; &#8203;the&#8203; violacein&#8203; &#8203;metabolic pathway&#8203; &#8203;in&#8203; &#8203;Chromobacterium&#8203; &#8203;Violaceum&#8203;, a type of Proteobacteria. The original vioC sequence for the bacteria chassis was submitted by the Alberta team in 2013 as https://parts.igem.org/Part:BBa_K1161004 K1161004 and has been codon-optimized for use in yeast in this part.	+	The CDS contained in this BioBrick was designed by running the VioD 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.
−	===References===	+	===Characterization===
		+	[[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 VioD (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 "VioD" found in "cloning vector pET15b-vioD" with 100% quarry cover. Figure 1 shows an example of Violacein using the plasmid this biobrick was based from.

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Revision as of 13:01, 29 October 2016

Violacein D gene codon-optimized for S. Cerevisiae

Design Notes

The VioD developed by the University of Washington's iGEM team have been codon optimized for yeast in hopes to improve the efficiency of its translation.

Source

The CDS contained in this BioBrick was designed by running the VioD 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

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 VioD (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 "VioD" found in "cloning vector pET15b-vioD" with 100% quarry cover. Figure 1 shows an example of Violacein using the plasmid this biobrick was based from.