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HPAI H5N1-aptamer
Description
In 2012, Suenaga et al. selected an aptamer (8-3) from a completely random RNA pool that binds with high affinity (∼KD 170 pM) to the hemagglutinins (HAs) derived from HPAI H5N1 (A/H5N1/Vietnam/1194/2004 and A/H5N1/Indonesia/05/2005) and H7N7 (A/H7N7/Netherlands/219/2003) influenza A viruses. Aptamer 8-3 was analyzed further to assess its ability to interfere with HA–glycan interactions using our previously established SPR-based competitive assay[1].SELEX
In 2012, Suenaga et al. identified isolated 3 specific sequences for targeting HA in a 74nt sequence poolthrough 10 rounds of selection[1].
Detailed information are accessible on SELEX page.
Structure
8-3 was the aptamer sequence mainly studied in the article, which had a high affinity with HA of H5N1 and H7N7. The 2D structure of the figure is based on the article by ribodraw tool to draw[1].5'-GGAGCUCAGCCUUCACUGCGAGAUUGUUCUGACCGAGUUGCCUAGCAGGGCAACCGCUGGAACUUGAAGUCGGUAAUGCGAGCGGAAAGCCUUGGCACCACGGUCGGAUCCAC-3'
Ligand information
SELEX ligand
This entry represents the haemagglutinin-neuraminidase (HN) glycoprotein found in a variety of paramyxoviruses (negative-stranded RNA viruses), including Mumps virus, Human parainfluenza virus 3, and the avian pathogen Newcastle disease virus. It also includes hemagglutinin glycoproteins from Morbiliviruses, a genus belonging to the Paramyxoviridae family that includes the Measles virus. Morbiliviruses hemagglutinins have no neuraminidase activity.
HN is a multi-functional protein with three distinct functions: a receptor-binding (haemagglutinin) activity, a receptor-destroying (neuraminidase) activity, and a membrane fusion activity that fuses the viral envelope to the host cell membrane in order to infect the cell.-----from Pfam
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Hemagglutinins (HA) | Q5EP31 | IPR000665 | 20.86 kDa | GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSGRLVPR | 4N5Z | 2FK0_B |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| 8-3 | 5'-GGAGCUCAGCCUUCACUGCGAGAUUGUUCUGACCGAGUUGCCUAGCAGGGCAACCGCUGGAACUUGAAGUCGGUAAUGCGAGCGGAAAGCCUUGGCACCACGGUCGGAUCCAC-3' | A/H5N1/Vietnam/1194/2004 | 0.75 nM |
| 8-3 | 5'-GGAGCUCAGCCUUCACUGCGAGAUUGUUCUGACCGAGUUGCCUAGCAGGGCAACCGCUGGAACUUGAAGUCGGUAAUGCGAGCGGAAAGCCUUGGCACCACGGUCGGAUCCAC-3' | A/H5N1/Indonesia/05/2005 | 0.17 nM |
| 8-3 | 5'-GGAGCUCAGCCUUCACUGCGAGAUUGUUCUGACCGAGUUGCCUAGCAGGGCAACCGCUGGAACUUGAAGUCGGUAAUGCGAGCGGAAAGCCUUGGCACCACGGUCGGAUCCAC-3' | A/H7N7/Netherlands/219/2003 | 0.42 nM |
| 8-3 | 5'-GGAGCUCAGCCUUCACUGCGAGAUUGUUCUGACCGAGUUGCCUAGCAGGGCAACCGCUGGAACUUGAAGUCGGUAAUGCGAGCGGAAAGCCUUGGCACCACGGUCGGAUCCAC-3' | A/H9N2/Hongkong/1073/99 | 260 nM |
| 8-3 | 5'-GGAGCUCAGCCUUCACUGCGAGAUUGUUCUGACCGAGUUGCCUAGCAGGGCAACCGCUGGAACUUGAAGUCGGUAAUGCGAGCGGAAAGCCUUGGCACCACGGUCGGAUCCAC-3' | A/H1N1/California/04/2009 | 170 nM |
| 8-1 | 5'-GGAGCUCAGCCUUCACUGCCUGUUAGAGUUUCCUAAAAGCGAACUGGCGCCCUCGUCAGCAUCUGGCAGACGAGUGGAGACGGACUAACCACAGGCACCACGGUCGGAUCCAC-3' | A/H5N1/Vietnam/1194/2004 | 2.6 μM |
| 8-1 | 5'-GGAGCUCAGCCUUCACUGCCUGUUAGAGUUUCCUAAAAGCGAACUGGCGCCCUCGUCAGCAUCUGGCAGACGAGUGGAGACGGACUAACCACAGGCACCACGGUCGGAUCCAC-3' | A/H5N1/Indonesia/05/2005 | 23 nM |
| 8-1 | 5'-GGAGCUCAGCCUUCACUGCCUGUUAGAGUUUCCUAAAAGCGAACUGGCGCCCUCGUCAGCAUCUGGCAGACGAGUGGAGACGGACUAACCACAGGCACCACGGUCGGAUCCAC-3' | A/H7N7/Netherlands/219/2003 | 7 nM |
| 8-10 | 5'-GGAGCUCAGCCUUCACUGCGGUGACCGGAGGAAUACGCGGACGGAGAAAGGGUUGGCCUCGUGGAUGGCGGAUACCCGUCCAGGGAUCUUCUAGGCACCACGGUCGGAUCCAC-3' | A/H5N1/Vietnam/1194/2004 | 93 nM |
| 8-10 | 5'-GGAGCUCAGCCUUCACUGCGGUGACCGGAGGAAUACGCGGACGGAGAAAGGGUUGGCCUCGUGGAUGGCGGAUACCCGUCCAGGGAUCUUCUAGGCACCACGGUCGGAUCCAC-3' | A/H5N1/Indonesia/05/2005 | 320 nM |
| 8-10 | 5'-GGAGCUCAGCCUUCACUGCGGUGACCGGAGGAAUACGCGGACGGAGAAAGGGUUGGCCUCGUGGAUGGCGGAUACCCGUCCAGGGAUCUUCUAGGCACCACGGUCGGAUCCAC-3' | A/H7N7/Netherlands/219/2003 | 21 nM |
Similar compound
We used the Dail server website to compare the structural similarities of ligand proteins, and chose the top 10 in terms of similarity for presentation. The Dali server is a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB). Z-score is a standard score that is converted from an original score. The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious. RMSD(Root Mean Square Deviation) value is used to measure the degree to which atoms deviate from the alignment position.
| PDB | Z-socre | RMSD | Description |
|---|---|---|---|
| 4F23-A | 11.9 | 2.0 | Hemagglutinin |
| 1FLC-B | 6.7 | 4.1 | Haemagglutinin-esterase-fusion glycoprotein |
| 5E5W-B | 6.5 | 4.4 | Hemagglutinin-esterase |
| 8TH8-A | 5.5 | 6.5 | Dynein regulatory complex protein 1/2 N-terminal |
| 8AFZ-B | 5.3 | 7.2 | Sorting nexin-1 |
| 8CR1-C | 5.2 | 5.1 | Atpase asna1 |
| 6VM0-A | 5.0 | 3.6 | Glycine receptor subunit alphaz1 |
| 5IP0-D | 4.9 | 7.9 | Pha granule-associated protein |
| 8EK4-B | 4.9 | 4.4 | Ice-binding protein tip-99A |
| 3FX7-B | 4.8 | 4.8 | Putative uncharacterized protein |
References
[1] An aptamer that binds efficiently to the hemagglutinins of highly pathogenic avian influenza viruses (H5N1 and H7N7) and inhibits hemagglutinin-glycan interactions.Suenaga, E., & Kumar, PK.
Acta Biomaterialia,10(3):1314-23. (2014)