RNA

Part:BBa_K581006:Design

Designed by: Qin Xiao   Group: iGEM11_Peking_S   (2011-09-26)

Pc+ptsG(wt)-GFP (ptsG(wt) 5' UTR fused with gfp)


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 7
    Illegal NheI site found at 30
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 790


Design Notes

This part is designed as the wild type of the ptsG's 5' untranslated region fused with gfp.

A 31-nt-long stretch in the 3’ region of SgrS is partially complementary to the translation initiation region of ptsG mRNA, and a 6 nt region overlapping the Shine-Dalgarno sequence of the target mRNA turns out to be crucial for SgrS’ function(Teppei Morita et.al).

Teppei Morita et.al’ s work suggest that two mutations (C85G and C87G) in ptsG mRNA could completely impair the ability of SgrS to downregulate its expression, while compensatory mutations of SgrS (G178C and G176C) restore the gene silencing ability.

Since such a specific repression effect is favored in our comparator device, we selected the ptsG/SgrS system as its foundation.

Source

Escherichia coli genome.

References

Kawamoto, H., Koide, Y., Morita, T., and Aiba, H. (2006). Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq. Molecular microbiology 61, 1013-1022.