Difference between revisions of "Part:BBa K3338002:Design"
Jonas Scholz (Talk | contribs) (→Source) |
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===Source=== | ===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 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-κ 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. | + | 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 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-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 <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
- 10COMPATIBLE WITH RFC[10]
- 12INCOMPATIBLE WITH RFC[12]Illegal NheI site found at 1
Illegal NotI site found at 58 - 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE 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.