Difference between revisions of "Part:BBa K5047006"

Revision as of 11:44, 30 September 2024

DNA sequence encodes a shRNA that does bind to the chitin synthase gene of V. velutina.

Sequence and Features

Assembly Compatibility:

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 __NOTOC__
 <partinfo>BBa_K5047006 short</partinfo>
 <!-- This DNA sequence encodes a short hairpin RNA (shRNA) designed to target a specific region within the chitin synthase gene of the Asian hornet (Vespa velutina). The target region is located on an exon common to all isoforms of the chitin synthase gene (GeneID: 124951980, Genbank: XM_047501172.1), within the genomic coordinates NC_062188.1:19,915,311-19,930,067 (iVesVel2.1 genome, GCF_912470025.1). The specific target sequence spans from positions 19’925’853 to 19’925’878. This shRNA has been designed to keep GC content intermediate (approx. 30 - 50%, with 48% in this variant) to avoid strong secondary structure. Additionally, this shRNA is the variant with the lowest number of potential off-target interactions compared to TS2 (BBa_XXXXX), TS3 (BBa_XXXXX) and TS4 (BBa_XXXXX). This sequence has off-targets in Vespa mandarinia and Vespa crabro with one mismatch only.
-This shRNA contains the optimized UGAUAUGUGCA loop (Schopman, Nick C T et al. “Optimization of shRNA inhibitors by variation of the terminal loop sequence.” Antiviral research vol. 86,2 (2010): 204-11. doi:10.1016/j.antiviral.2010.02.320).
-Through secondary structure analysis performed by ViennaRNA, the free energy of the thermodynamic ensemble is -50.39 kcal/mol. The frequency of the minimum free energy structure in the ensemble is 52.98%. The ensemble diversity is 0.70.
 ===Usage and Biology===