RNA

Part:BBa_K581005:Design

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

Pc+sgrS(wt)+Terminator (small RNA regulator, conjugate part of ptsG(wt))


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
    COMPATIBLE WITH RFC[1000]


Design Notes

This is the wild type of the small RNA SgrS.

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

E.coli K-12 strain.

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.