Difference between revisions of "Part:BBa K4061045"

Latest revision as of 13:03, 12 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_K4061000). 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 OmpF promoter and BBa_B0034 as the RBS, we thus designed the mRFP1 antisense strand to bind to the -10 region of the OmpF promoter and the RBS. 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]

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 <partinfo>BBa_K4061045 short</partinfo>
-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.
+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_K4061000). 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 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 last 10 nucleotides of the promoter.
+Since this mRFP1 antisense was designed to specifically downregulate mRFP1 that is controlled under OmpF promoter and BBa_B0034 as the RBS, we thus designed the mRFP1 antisense strand to bind to the -10 region of the OmpF promoter and the RBS. 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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