Difference between revisions of "Part:BBa K1323007:Design"

Latest revision as of 20:07, 17 October 2014

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]

@@ Line 2: / Line 2: @@
 [[File:sRNA Binding3.png]]
 Targeting site of YFP.
-sRNA 3 targets 28 bps downstream from the start codon of the YFP construct. This sequence has 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 binding energy between -30kcal/mol to -40kcal/mol (Yoo et al., 2013). We aligned sRNA 3 sequence with other constructs and ATCC 12228 genome to determine the highest binding energy for non-specific RNA binding, which is -13.03 kcal/mol. This shows that sRNA1 binds more specifically to YFP and should not interfere with other gene expressions in our system.
+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.
 <partinfo>BBa_K1323007 short</partinfo>
 <partinfo>BBa_K1323007 SequenceAndFeatures</partinfo>