Difference between revisions of "Part:BBa K4061045"
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Our mRFP1 antisense strand is also equipped with Spot42 AU rich region which is an Hfq binding spot. Hfq is a form of protein that is endogenous to E.coli and it is known to interact with AU-rich regions. The binding of Hfq to Spot42 will facilitate the interaction of the antisense fragment to its target.  
 
Our mRFP1 antisense strand is also equipped with Spot42 AU rich region which is an Hfq binding spot. Hfq is a form of protein that is endogenous to E.coli and it is known to interact with AU-rich regions. The binding of Hfq to Spot42 will facilitate the interaction of the antisense fragment to its target.  
  
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Since this mRFP1 antisense was designed to specifically downregulate mRFP1 that is controlled under OmpC promoter, we thus designed the mRFP1 antisense strand to bind to the last 10 nucleotides of the OmpC promoter. However, this can be customized according to the context of your project as long as it follows the rule of thumb of this antisense fragment. That is, to design an antisense strand that binds to the 1st 20 nucleotides of the mRFP1, the RBS, and the -10 region of the promoter.  
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Since this mRFP1 antisense was designed to specifically downregulate mRFP1 that is controlled under OmpC promoter, we thus designed the mRFP1 antisense strand to bind to the last -10 region of the OmpF promoter. However, this can be customized according to the context of your project as long as it follows the rule of thumb of this antisense fragment. That is, to design an antisense strand that binds to the 1st 20 nucleotides of the mRFP1, the RBS, and the -10 region of the promoter.  
  
 
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Revision as of 01:57, 1 October 2021


mRFP1 antisense to downregulate mRFP1 (BBa_E1010)

This mRFP1 antisense part is able to downregulate the expression of mRFP1 (BBa_E1010) at the translational level. Upon binding of the antisense mRNA to the coding mRNA, the double-stranded mRNA will be degraded by RNase H which is endogenous to E.coli. We designed the mRFP1 antisense particularly so that it binds with the first 20 nucleotides of the mRFP1, the RBS (BBa_B0034), and the last 10 nucleotides sequence of the promoter (BBa_R0082). Therefore, due to the binding of the antisense mRNA to the coding mRNA, the ribosome will not be able to bind to the ribosome binding site. Thus the translation of the mRFP1 gene will be inhibited.

Our mRFP1 antisense strand is also equipped with Spot42 AU rich region which is an Hfq binding spot. Hfq is a form of protein that is endogenous to E.coli and it is known to interact with AU-rich regions. The binding of Hfq to Spot42 will facilitate the interaction of the antisense fragment to its target.

Since this mRFP1 antisense was designed to specifically downregulate mRFP1 that is controlled under OmpC promoter, we thus designed the mRFP1 antisense strand to bind to the last -10 region of the OmpF promoter. However, this can be customized according to the context of your project as long as it follows the rule of thumb of this antisense fragment. That is, to design an antisense strand that binds to the 1st 20 nucleotides of the mRFP1, the RBS, and the -10 region of the promoter.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 49
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]