Difference between revisions of "Part:BBa K3332098"
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Encoding the siRNA squence which can silence the phnF and phnJ gene in E.coli BL21(DE3).Use K823005 to silence the phnF gene in E.coli BL21 (DE3). | Encoding the siRNA squence which can silence the phnF and phnJ gene in E.coli BL21(DE3).Use K823005 to silence the phnF gene in E.coli BL21 (DE3). | ||
| − | + | ===Biology=== | |
| − | ===Usage and | + | In ''E. coli'', the phn system is precisely regulated. PhnF gene encoding protein can directly inhibit the expression of other genes in the phn system. But this is obviously disadvantageous for our experiment. At the same time, C-P lyase is actually composed of expression products of genes other than phnJ, so there is site competition between endogenous phnJ and exogenously transformed phnJ. In order to avoid the effects of endogenous phnF and phnJ, we need a way to silence these two genes. We determined to silence genes using RNAi. |
| + | RNAi design can use TACE system. In the TACE system, a gene loop for transferring the DNA sequence corresponding to the siRNA, where the GGA Cassette can be replaced by the sequence encoding the siRNA according to the GGA assembly standard. OmpA 5`-UTR can protect siRNA from degradation, Hfq binding sequence can improve the binding efficiency of siRNA and target mRNA. | ||
| + | Using the siRNA design software provided by Team: Bielefeld-CeBiTec in iGEM2018: siRCon, the siRNA sequence design for endogenous phnF and phnJ in ''E. coli'' BL21(DE3) was used for RNAi. The number 0.97 and 0.94 means the silence probability (up to 1.0). | ||
| + | ===Usage=== | ||
| + | The plasmid with this sequence was transformed into ''E. coli'' DH5α & ''E. coli'' BL21(DE3), and the correct recombinant one was confirmed by chloramphenicol, enzyme-cut identification and sequencing. We used this part to characterize the influence of our RNAi sequence toward target sequences. | ||
| + | ===Characterization=== | ||
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Revision as of 06:15, 25 October 2020
RNAi sequence of phnF(0.97)-RNAi sequence of phnJ(0.94)
Encoding the siRNA squence which can silence the phnF and phnJ gene in E.coli BL21(DE3).Use K823005 to silence the phnF gene in E.coli BL21 (DE3).
Biology
In E. coli, the phn system is precisely regulated. PhnF gene encoding protein can directly inhibit the expression of other genes in the phn system. But this is obviously disadvantageous for our experiment. At the same time, C-P lyase is actually composed of expression products of genes other than phnJ, so there is site competition between endogenous phnJ and exogenously transformed phnJ. In order to avoid the effects of endogenous phnF and phnJ, we need a way to silence these two genes. We determined to silence genes using RNAi. RNAi design can use TACE system. In the TACE system, a gene loop for transferring the DNA sequence corresponding to the siRNA, where the GGA Cassette can be replaced by the sequence encoding the siRNA according to the GGA assembly standard. OmpA 5`-UTR can protect siRNA from degradation, Hfq binding sequence can improve the binding efficiency of siRNA and target mRNA. Using the siRNA design software provided by Team: Bielefeld-CeBiTec in iGEM2018: siRCon, the siRNA sequence design for endogenous phnF and phnJ in E. coli BL21(DE3) was used for RNAi. The number 0.97 and 0.94 means the silence probability (up to 1.0).
Usage
The plasmid with this sequence was transformed into E. coli DH5α & E. coli BL21(DE3), and the correct recombinant one was confirmed by chloramphenicol, enzyme-cut identification and sequencing. We used this part to characterize the influence of our RNAi sequence toward target sequences.
Characterization
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12INCOMPATIBLE WITH RFC[12]Illegal NheI site found at 7
Illegal NheI site found at 30
Illegal NheI site found at 438
Illegal NheI site found at 461 - 21INCOMPATIBLE WITH RFC[21]Illegal XhoI site found at 281
Illegal XhoI site found at 712 - 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]