Difference between revisions of "Part:BBa K1323005:Design"
 
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[[File:sRNA Binding.png]]
 
[[File:sRNA Binding.png]]
  
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<partinfo>BBa_K1323005 short</partinfo>
 
  
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<partinfo>BBa_K1323005 SequenceAndFeatures</partinfo>
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The sRNA binding region.
  
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sRNA 1 targets the YFP gene starting at the end of its Shine-Dalgarno (SD) sequence. The SD region is determined by Yoo et al. (2013) to be the most effective binding region for mRNA silencing. This 26 bp sequence has binding energy of -27.6 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 1 sequence with other constructs and the ATCC 12228 genome to determine the highest binding energy for non-specific RNA binding, which is -21.18 kcal/mol. This shows that sRNA 1 binds more specifically to YFP and should not interfere with other gene expressions in our system.
  
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===Design Notes===
 
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TBA
 
  
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<partinfo>BBa_K1323005 short</partinfo>
  
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<partinfo>BBa_K1323005 SequenceAndFeatures</partinfo>
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===Source===
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TBA
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===References===
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Latest revision as of 19:30, 17 October 2014


SRNA Binding.png


The sRNA binding region.

sRNA 1 targets the YFP gene starting at the end of its Shine-Dalgarno (SD) sequence. The SD region is determined by Yoo et al. (2013) to be the most effective binding region for mRNA silencing. This 26 bp sequence has binding energy of -27.6 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 1 sequence with other constructs and the ATCC 12228 genome to determine the highest binding energy for non-specific RNA binding, which is -21.18 kcal/mol. This shows that sRNA 1 binds more specifically to YFP and should not interfere with other gene expressions in our system.


sRNA (1): 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 140
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]