Difference between revisions of "Part:BBa K1323006:Design"
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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 sRNA2 binds more specifically to YFP and should not interfere with other gene expressions in our system. | ||
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<partinfo>BBa_K1323006 short</partinfo> | <partinfo>BBa_K1323006 short</partinfo> | ||
<partinfo>BBa_K1323006 SequenceAndFeatures</partinfo> | <partinfo>BBa_K1323006 SequenceAndFeatures</partinfo> | ||
Revision as of 20:05, 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 sRNA2 binds more specifically to YFP and should not interfere with other gene expressions in our system.
sRNA (2): YFP-targeting molecule
Assembly Compatibility:
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal XhoI site found at 142
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]