Difference between revisions of "Part:BBa K3338002:Design"
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===Source===
 
===Source===
  
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The sequence of the promoter was designed using a self-made MATLAB tool creating three repetitions of randomly generated NF-&#954;B/AP1 binding sites in front of a CMV<sub>min</sub> promoter which only contains the TATA-box and the Initiator-Sequence of the original CMV-promoter. As a consensus sequence for NF-&#954;B/AP1 binding sites “GGGRNYYYCC” and for AP1 binding sites “TGAXTCA” was used, where Y is C or T, R is A or G, X is C or G and N is any base (Chen <i>et al.</i> 1998, Alam and Den 1992). It was synthesized by IDT.
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The sequence of the promoter was designed using a self-made MATLAB tool creating three repetitions of randomly generated NF-&#954;B/AP1 binding sites in front of a CMV<sub>min</sub> promoter which only contains the TATA-box and the Initiator-Sequence of the original CMV-promoter. As a consensus sequence for NF-&#954;B binding sites “GGGRNYYYCC” and for AP1 binding sites “TGAXTCA” was used, where Y is C or T, R is A or G, X is C or G and N is any base (Chen <i>et al.</i> 1998, Alam and Den 1992). It was synthesized by IDT.
  
 
===References===
 
===References===

Latest revision as of 15:36, 22 October 2020


Synthetic promoter_2 with NF-κB and AP1 binding sites


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 1
    Illegal NotI site found at 58
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Although the sequence contains repeating transcription factor binding sites, it can be easily synthesized using standard gene synthesis approaches. This is due to the randomly generated transcription factor binding sites.

Source

The sequence of the promoter was designed using a self-made MATLAB tool creating three repetitions of randomly generated NF-κB/AP1 binding sites in front of a CMVmin promoter which only contains the TATA-box and the Initiator-Sequence of the original CMV-promoter. As a consensus sequence for NF-κB binding sites “GGGRNYYYCC” and for AP1 binding sites “TGAXTCA” was used, where Y is C or T, R is A or G, X is C or G and N is any base (Chen et al. 1998, Alam and Den 1992). It was synthesized by IDT.

References

Chen, F. E., Huang, D. B., Chen, Y. Q., & Ghosh, G. (1998). Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA. Nature, 391(6665), 410–413.

Alam, J., & Den, Z. (1992). Distal AP-1 binding sites mediate basal level enhancement and TPA induction of the mouse heme oxygenase-1 gene. The Journal of biological chemistry, 267(30), 21894–21900.