Difference between revisions of "Part:BBa K5047023"

Latest revision as of 18:03, 30 September 2024

DNA encodes a shRNA binds to chitin synthase gene of V. velutina.

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 19915311-19930067 iVesVel2.1 genome GCF_912470025.1.

The specific target sequence spans from positions 19925844 to 19925869. This shRNA has been designed to keep GC content intermediate approx. 30 - 50% with 44% in this variant to avoid strong secondary structure. This sequence has off-targets in Vespa mandarinia one mismatch Vespa crabro one INDEL and Rhorus exstirpatorius one mismatch.

Upon testing in human embryonic kidney 293T cells using a luciferase assay, 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 reported that shRNAs based on the mir-17 and mir-25 loops exhibited the strongest target repression, approximately 10-fold stronger than the 9-nt loop.

This shRNA contains the optimized CCUCUCAACACUGG 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 101016jantiviral201002320. Through secondary structure analysis performed by ViennaRNA the free energy of the thermodynamic ensemble is -50.09 kcalmol. The frequency of the minimum free energy structure in the ensemble is 53.36%. The ensemble diversity is 0.68.

Sequence and Features

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]

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 <partinfo>BBa_K5047023 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 19915311-19930067 iVesVel2.1 genome GCF_912470025.1. The specific target sequence spans from positions 19925844 to 19925869. This shRNA has been designed to keep GC content intermediate approx. 30 - 50% with 44% in this variant to avoid strong secondary structure. This sequence has off-targets in Vespa mandarinia one mismatch Vespa crabro one INDEL and Rhorus exstirpatorius one mismatch.
+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 19915311-19930067 iVesVel2.1 genome GCF_912470025.1.
+The specific target sequence spans from positions 19925844 to 19925869. This shRNA has been designed to keep GC content intermediate approx. 30 - 50% with 44% in this variant to avoid strong secondary structure. This sequence has off-targets in Vespa mandarinia one mismatch Vespa crabro one INDEL and Rhorus exstirpatorius one mismatch.
+Upon testing in human embryonic kidney 293T cells using a luciferase assay, 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 reported that shRNAs based on the mir-17 and mir-25 loops exhibited the strongest target repression, approximately 10-fold stronger than the 9-nt loop.
 This shRNA contains the optimized CCUCUCAACACUGG 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 101016jantiviral201002320.
 Through secondary structure analysis performed by ViennaRNA the free energy of the thermodynamic ensemble is -50.09 kcalmol. The frequency of the minimum free energy structure in the ensemble is 53.36%. The ensemble diversity is 0.68.