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HIRRV aptamer
Description
In 2012, Hwang SD, Midorikawa N, Punnarak P, et al. used selexed RNA aptamers (H1, H2, H3, and H4) targeting Hirome rhabdovirus (HIRRV) through an in vitro process called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). These RNA aptamers are able to specifically bind to HIRRV, and when used to treat Hirome natural embryo (HINAE) cells in contact with the virus, the appearance of cytopathic effect (CPE) is reduced compared to the control group that only treated the virus. This indicates that these RNA aptamers can inhibit the growth of HIRRV. In addition, by transforming RNA aptamer genes into Rhodovulum sulfidophilum and secreting these aptamers into the culture medium, the recombinant R Sulfidophilum may be a powerful tool for preventing HIRRV infection in the aquaculture industry[1].SELEX
In 2012, Hwang SD, Midorikawa N, Punnarak P, et al. used an ssDNA library containing approximately 5 × 1016 different sequences, and after nine rounds of SELEX, they sequenced 45 RNA aptamers and identified four RNA aptamers (H1, H2, H3, and H4) that could specifically bind to HIRRV[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figures are based on the article by ribodraw tool to draw. H1 and H2 aptamers bind to Hirame rhabdovirus (HIRRV)[1].H1 aptamer: 5'-GGGCCAGGCAGCGAGGGUGUAUAGGUAUUGAAUCAAUUGUUUUAGCGUUGUCUUACCGACCACACGCGUCCGAGA-3'
H2 aptamer: 5'-GGGCCAGGCAGCGAGGGAACGCGAGCUUAGAUUUCGGAGAACAGUUUGUAAUUGUUCCGACCACACGCGUCCGAGA-3'
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Ligand information
SELEX ligand
(Biology) any of the viruses belonging to the Rhabdoviradae family, which are composed of rod-shaped particles that can infect living organisms, and which include the viruses that cause rabies.-----From Wiki
| Name | GenBase gene | GenBase protein | NCBI ID |
|---|---|---|---|
| Hirame rhabdovirus (HIRRV) | NC_005093.1 | Hirame rhabdovirus | 1980915 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| H1 | 5'-GGGCCAGGCAGCGAGGGUGUAUAGGUAUUGAAUCAAUUGUUUUAGCGUUGUCUUACCGACCACACGCGUCCGAGA-3' | Hirame rhabdovirus (HIRRV) | NA |
| H2 | 5'-GGGCCAGGCAGCGAGGGAACGCGAGCUUAGAUUUCGGAGAACAGUUUGUAAUUGUUCCGACCACACGCGUCCGAGA-3' | Hirame rhabdovirus (HIRRV) | NA |
| H3 | 5'-GGGCCAGGCAGCGAGGUCCUAUACAGUGUGACCGGUUGAAAGUGGGUUCGUUGCCGACCACACGCGUCCGAGA-3' | Hirame rhabdovirus (HIRRV) | NA |
| H4 | 5'-GGGCCAGGCAGCGAGGGGUUAAGCCGGAUUGUAGACUGUAACAGGUAGAGCUGGCCCGACCACACGCGUCCGAGA-3' | Hirame rhabdovirus (HIRRV) | NA |
References
[1] Inhibition of Hirame rhabdovirus growth by RNA aptamers.Hwang, S. D., Midorikawa, N., Punnarak, P., Kikuchi, Y., Kondo, H., Hirono, I., & Aoki, T.
Journal of fish diseases, 35(12), 927–934. (2012)