Difference between revisions of "Part:BBa K4046903:Design"
 
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===Design Notes===
 
===Design Notes===
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This composite part is one of several that the Duke iGEM intends to test for use in a biosensor for the oncometabolite D-2-HG. A schematic for the operation of our system is shown below.
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<i>dhdO</i> sequences were designed and optimized for binding to the <i>DhdR</i> protein. Furthermore, a promoter, Kozak sequence, and a terminator were added.
  
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[[File:T--Duke--DhdrSchematic.png|600 px]]
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===Source===
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This includes identified binding site for the <i>DhdR</i> gene, as described by Xiao et al, 2021. This gene was synthesized commercially from the published sequence (IDT). The <i>DhdR</i> gene is a transcriptional repression factor that is derived from the bacteria <i>Achromobacter denitrificans</i>. The <i>dhdO</i> binding sites were designed and modified to improve binding behavior of the DhdR protein to the sequence.  
  
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<b><font size="+1">Figure 1: This figure outlines the mechanism of the interaction between the DhdR allosteric transcription factor and the <i>dhdO</i> binding site.</font></b>
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mCherry is a fluorescent gene product derived from the DsRed gene of mushrooms corals in the <i> Discosoma </i> family. This gene was obtained directly through assembly into the pcDNA5 plasmid (Thermo Fischer, V103320), which contained the <i> mCherry </i> gene. In normal function, mCherry is a red fluorescence protein.
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This plasmid will be tested together with another construct expressing the protein DhdR, which is a transcriptional repression factor isolated from the bacteria <i>Achromobacter denitrificans</i>. In a wild-type environment, without the presence of DhdR, we expect normal expression of the reporter protein. However, when DhdR is present, it will bind to the <i>dhdO</i> binding site, allosterically blocking the transcription of our reporter gene. When D-2-HG is elevated, particularly in <i>IDH1</i> mutant cells, it binds to DhdR, releasing it from the binding site.
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[[File:T--Duke--T--Duke--DhdO0 curve.png|600 px]]
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<b><font size="+1">Figure 2: This figure outlines the energetics of the interaction between the DhdR allosteric transcription factor and the <i>dhdO</i> binding site.</font></b>
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This allows for transcription of the downstream reporter protein sequence, resulting in brighter expression that is visible in our <i>in vivo</i> droplet system. Since D-2-HG levels are elevated due to the <i>IDH1</i> mutation, we expect that there will be an increase in fluorescence or luminescence due to the release of the allosteric transcription factor caused by the binding of the upregulated oncometabolite. When we perform drug screening assays on our completed co-culture system, we will associate decreased fluorescence or luminescence with lower levels of D-2-HG, which is associated with a variety of downstream metabolic impacts.
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Literature sources indicate that repressor binding can be affected by variables like the number of repeats of the binding site present, as well as the presence of spacer sequences in between repeats of the binding sequence. Because of these variations, we intend to test several different combinations to see which functions the best. By optimizing the binding site and promoter combination, we hope to establish a reporter system that allows for precise quantification of D-2-HG levels over a large dynamic range.
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===Source===
+
  
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This gene was synthesized commercially from the published sequence (IDT). The <i>DhdR</i> gene is a transcriptional repression factor that is derived from the bacteria <i>Achromobacter denitrificans</i>. The <i>dhdO</i> binding sites were designed and modified to improve binding behavior of the DhdR protein to the sequence.
 
 
hUBC is a constitutive reporter that is associated with the ubiquitin c gene in humans. This gene was obtained through a FUGW-GFP plasmid, generously donated by the Gersbach lab at Duke University. In normal function, the hUBC promoter allows for high levels of expression of associated gene products.
 
hUBC is a constitutive reporter that is associated with the ubiquitin c gene in humans. This gene was obtained through a FUGW-GFP plasmid, generously donated by the Gersbach lab at Duke University. In normal function, the hUBC promoter allows for high levels of expression of associated gene products.
  
 
===References===
 
===References===
 
Xiao, D., Zhang, W., Guo, X., Liu, Y., Hu, C., Guo, S., Kang, Z., Xu, X., Ma, C., Gao, C., & Xu, P. (2021). A D-2-hydroxyglutarate biosensor based on specific transcriptional regulator DHDR. https://doi.org/10.1101/2021.02.18.430539
 
Xiao, D., Zhang, W., Guo, X., Liu, Y., Hu, C., Guo, S., Kang, Z., Xu, X., Ma, C., Gao, C., & Xu, P. (2021). A D-2-hydroxyglutarate biosensor based on specific transcriptional regulator DHDR. https://doi.org/10.1101/2021.02.18.430539

Latest revision as of 03:15, 22 October 2021


hUBC - BS #1 - BS #1 - BS #1 - Kozak - mCherry - bghA


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 835
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 835
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 835
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 835
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

dhdO sequences were designed and optimized for binding to the DhdR protein. Furthermore, a promoter, Kozak sequence, and a terminator were added.

Source

This includes identified binding site for the DhdR gene, as described by Xiao et al, 2021. This gene was synthesized commercially from the published sequence (IDT). The DhdR gene is a transcriptional repression factor that is derived from the bacteria Achromobacter denitrificans. The dhdO binding sites were designed and modified to improve binding behavior of the DhdR protein to the sequence.

mCherry is a fluorescent gene product derived from the DsRed gene of mushrooms corals in the Discosoma family. This gene was obtained directly through assembly into the pcDNA5 plasmid (Thermo Fischer, V103320), which contained the mCherry gene. In normal function, mCherry is a red fluorescence protein.

hUBC is a constitutive reporter that is associated with the ubiquitin c gene in humans. This gene was obtained through a FUGW-GFP plasmid, generously donated by the Gersbach lab at Duke University. In normal function, the hUBC promoter allows for high levels of expression of associated gene products.

References

Xiao, D., Zhang, W., Guo, X., Liu, Y., Hu, C., Guo, S., Kang, Z., Xu, X., Ma, C., Gao, C., & Xu, P. (2021). A D-2-hydroxyglutarate biosensor based on specific transcriptional regulator DHDR. https://doi.org/10.1101/2021.02.18.430539