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

Latest revision as of 20:07, 17 October 2014

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]

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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 sRNA2 binds more specifically to YFP and should not interfere with other gene expressions in our system.
+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.
 <partinfo>BBa_K1323006 short</partinfo>
 <partinfo>BBa_K1323006 SequenceAndFeatures</partinfo>