Part:BBa_K3338007:Design

Synthetic promoter_1 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 binding sites followed by three repetitions of randomly generated AP-1 binding sites in front of a CMV_min 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.