Difference between revisions of "Part:BBa K4286107:Design"
 
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<partinfo>BBa_K4286107 short</partinfo>
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<partinfo>BBa_K4286107 SequenceAndFeatures</partinfo>
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===Design Notes===
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We have confirmed that this siRNA sequence has a good binding ability to Rhizoctonia solani. The intrinsic order of this sequence is sense RNAi fragment — loop —  antisense RNAi fragment. This sequence was assembled in the pET28a (+) plasmid containing the IPTG-inducible phage T7 promoter and subsequently transferred into RNase-deficient E. coli HT115 (DE3). In our project, shRNA will be industrially produced by E. coli on a large scale, and shRNA will be purified and sprayed on rice fields to inhibit Rhizoctonia solani.
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<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K4286203 SequenceAndFeatures</partinfo>
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===Functional Parameters===
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<partinfo>BBa_K4286203 parameters</partinfo>
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===Source===
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We input the CDS sequence of PG in the professional shRNA design webpage, and the RNAi fragment is automatically designed by the program. Our examination confirmed that the sense portion of this sequence perfectly matches the gene encoding PG of Rhizoctonia solani AG1-IA.
 
We input the CDS sequence of PG in the professional shRNA design webpage, and the RNAi fragment is automatically designed by the program. Our examination confirmed that the sense portion of this sequence perfectly matches the gene encoding PG of Rhizoctonia solani AG1-IA.
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===References===
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[1]Rao, T.B., Chopperla, R., Methre, R. et al. Pectin induced transcriptome of a Rhizoctonia solani strain causing sheath blight disease in rice reveals insights on key genes and RNAi machinery for development of pathogen derived resistance. Plant Mol Biol 100, 59–71 (2019). https://doi.org/10.1007/s11103-019-00843-9
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[2]Chen, X., Lili, L., Zhang, Y. et al. Functional analysis of polygalacturonase gene RsPG2 from Rhizoctonia solani, the pathogen of rice sheath blight. Eur J Plant Pathol 149, 491–502 (2017). https://doi.org/10.1007/s10658-017-1198-5

Latest revision as of 14:42, 3 October 2023


shRNA (PG)-1


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

We have confirmed that this siRNA sequence has a good binding ability to Rhizoctonia solani. The intrinsic order of this sequence is sense RNAi fragment — loop — antisense RNAi fragment. This sequence was assembled in the pET28a (+) plasmid containing the IPTG-inducible phage T7 promoter and subsequently transferred into RNase-deficient E. coli HT115 (DE3). In our project, shRNA will be industrially produced by E. coli on a large scale, and shRNA will be purified and sprayed on rice fields to inhibit Rhizoctonia solani.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 1946
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 1046
    Illegal NgoMIV site found at 1091
    Illegal NgoMIV site found at 1385
    Illegal NgoMIV site found at 1499
    Illegal AgeI site found at 2015
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 66
    Illegal BsaI site found at 1232
    Illegal BsaI.rc site found at 1109


Source

We input the CDS sequence of PG in the professional shRNA design webpage, and the RNAi fragment is automatically designed by the program. Our examination confirmed that the sense portion of this sequence perfectly matches the gene encoding PG of Rhizoctonia solani AG1-IA.


References

[1]Rao, T.B., Chopperla, R., Methre, R. et al. Pectin induced transcriptome of a Rhizoctonia solani strain causing sheath blight disease in rice reveals insights on key genes and RNAi machinery for development of pathogen derived resistance. Plant Mol Biol 100, 59–71 (2019). https://doi.org/10.1007/s11103-019-00843-9 [2]Chen, X., Lili, L., Zhang, Y. et al. Functional analysis of polygalacturonase gene RsPG2 from Rhizoctonia solani, the pathogen of rice sheath blight. Eur J Plant Pathol 149, 491–502 (2017). https://doi.org/10.1007/s10658-017-1198-5