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RNA

Part:BBa_K1323007:Design

Designed by: Julia Manalil   Group: iGEM14_Waterloo   (2014-10-07)


SRNA Binding3.png


Targeting site of YFP.

sRNA 3 targets 28 bp downstream from the start codon of the YFP construct. This sequence has a binding energy of -30.3 kcal/mol as determined using DINAMelt software (http://mfold.rna.albany.edu/?q=DINAMelt/Two-state-melting). For effective binding, sRNA should have a binding energy between -30 kcal/mol to -40 kcal/mol (Yoo et al., 2013). We aligned the sRNA 3 sequence with other constructs and the ATCC 12228 genome to determine the highest binding energy for non-specific RNA binding, which is -13.03 kcal/mol. This shows that sRNA 3 binds more specifically to YFP and should not interfere with other gene expressions in our system.


sRNA (3): YFP-targeting molecule


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 142
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]