Difference between revisions of "Part:BBa K1323006:Design"

 
 
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__NOTOC__
 
__NOTOC__
<partinfo>BBa_K1323006 short</partinfo>
 
  
<partinfo>BBa_K1323006 SequenceAndFeatures</partinfo>
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[[File:sRNA Binding2.png]]
  
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The targeting region of YFP.
  
===Design Notes===
 
TBA
 
  
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sRNA 2 targets 5’UTR directly downstream of Shine Dalgarno sequence of the YFP construct.  This 28 bp sequence has binding energy of -31.6 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 2 sequence with other constructs and the ATCC 12228 genome to determine the highest binding energy for non-specific RNA binding, which is -16.78 kcal/mol. This shows that sRNA 2 binds more specifically to YFP and should not interfere with other gene expressions in our system.
  
  
===Source===
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<partinfo>BBa_K1323006 short</partinfo>
  
TBA
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<partinfo>BBa_K1323006 SequenceAndFeatures</partinfo>
 
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===References===
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Latest revision as of 20:07, 17 October 2014


SRNA Binding2.png

The targeting region of YFP.


sRNA 2 targets 5’UTR directly downstream of Shine Dalgarno sequence of the YFP construct. This 28 bp sequence has binding energy of -31.6 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 2 sequence with other constructs and the ATCC 12228 genome to determine the highest binding energy for non-specific RNA binding, which is -16.78 kcal/mol. This shows that sRNA 2 binds more specifically to YFP and should not interfere with other gene expressions in our system.


sRNA (2): 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]