HIRRV aptamer

May 6, 2024 • Jiali Wang, Bo Fu

Description

In 2012, Aoki et al. 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, Aoki et al. used an ssDNA library containing approximately 5 × 10¹⁶ different sequences. After nine rounds of SELEX, they isolated 45 RNA aptamers. Four of these (H1, H2, H3, and H4) were found to 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 aptamer bind to Hirame rhabdovirus (HIRRV). H1 and H2 aptamer was named by Aoki et al^[1].

H1 aptamer: 5'-GGGCCAGGCAGCGAGGGUGUAUAGGUAUUGAAUCAAUUGUUUUAGCGUUGUCUUACCGACCACACGCGUCCGAGA-3'
H2 aptamer: 5'-GGGCCAGGCAGCGAGGGAACGCGAGCUUAGAUUUCGGAGAACAGUUUGUAAUUGUUCCGACCACACGCGUCCGAGA-3'

Ligand information

SELEX ligand

Some isolated sequences bind to the affinity of the protein^[1].

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

Structure 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

GenBase gene : the gene sequence in the GenBank database, crucial for genetic studies.

GenBase protein : the protein sequence in the GenBank database, crucial for genetic studies.

NCBI ID: a unique identifier by NCBI for biological entities in its databases.

Name	GenBase gene	GenBase protein	NCBI ID
Hirame rhabdovirus (HIRRV)	NC_005093.1	Hirame rhabdovirus	1980915

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)