Part:BBa_K3332099

RNAi sequence of phnF(0.97)-RNAi sequence of phnJ(0.69)

Encoding the siRNA squence which can silence the phnF and phnJ gene in E.coli BL21(DE3).Use BBa_K823005 to silence the phnF gene in E.coli BL21 (DE3).

Biology

         In E. coli, the phn system is precisely regulated. The protein phnF encoding 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 and 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 0.69 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

1. Agarose Gel Electrophoresis

        When we were building this circuit, enzyme-cut identification was used to certify the plasmid was correct. We used the EcoR I and Pst I to cut the plasmid, then we got the target separate fragment-823bp (lane 2).

Fig.1 The result of plasmid cut with enzyme EcoR I and Pst I. Plasmid: pSB1C3.

2. qPCR

        QPCR was used to determine the expression intensity of the target gene (phnJ & phnF). 16S gene was used as an internal reference.

Fig.2 The expression intensity of phnJ and phnF in the bacteria with RNAi plasmid.

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  INCOMPATIBLE 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
  
• 21
  INCOMPATIBLE WITH RFC[21]

  Illegal XhoI site found at 281
  Illegal XhoI site found at 712
  
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]