RNA

Part:BBa_K2379003:Design

Designed by: Ramit B   Group: iGEM17_SVCE_CHENNAI   (2017-10-01)


RNA pHmeter with biobrick scar site


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 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 118


Design Notes

In order to retain its functionality, the secondary structure of the RNA pHmeter must be maintained which is destroyed by the replacement of the natural scar site with the biobrick one. Hence we have tried to alter the sequence such that its predicted secondary structure is conserved. The structures of the wild-type and modified RNA pHmeter as predicted by RNA VIENNA FOLD are shown below.

Wild Type

320px-T--SVCE_CHENNAI--WILDTYPE.png

BioBrick Type

320px-T--SVCE_CHENNAI--BIOBRICK.png

Source

[Escherichia coli UMN026 (strain: UMN026)] Genbank Gene ID: 7159109

References

1. Nechooshtan, G., Elgrably-Weiss, M., Sheaffer, A.,Westhof, E., & Altuvia, S. A pH-responsive riboregulator.Genes Dev. 23, 2650–2662 (2009).

2. Nechooshtan, G., Elgrably-Weiss, M., & Altuvia, S.Changes in transcriptional pausing modify the folding dynamics of the pH-responsive RNA element. Nucleic Acids research. 42(1), 622-630 (2013)

3. Bingham, R., Karen, H., Joan S. Alkaline induction of a Novel Gene Locus, alx, in Escherichia coli. Journal of Bacteriology. 172(4), 2184-2186(1990)