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HCV aptamer
Description
In 2003, Vo NV, Oh JW, Lai MM used the SELEX method to select the aptamer with high compatibility for the Hepatitis C virus NS5B protein. They found that the aptamers can act as templates for HCV polymerase, but others can interfere with the activity of the viral enzyme. These findings suggest that these RNA aptamers may be useful for further characterization of the binding properties of NS5B, and with further modifications, may have potential therapeutic value[1].SELEX
In 2003, Vo NV, Oh JW, Lai MM utilized an RNA library estimated to contain 1012 (one hundred trillion) distinct RNA species. Following 20 rounds of screening, the highest affinity RNA enrichment was achieved between rounds 18 and 20. Through the SELEX process, a total of 37 selected ligands were obtained, categorized into eight groups (A-H) based on sequence homology[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. R20-43 aptamer and R20-15 aptamer bind to hepatitis C virus NS5B protein (HCV NS5B protein)[1].R20-43 aptamer: 5'-GGGAGCUCAGAAUAAACGCUCAAUGUAGAGACUUUUCGAAAAGCGUGUUCCCAAUGAGUCUAUGCAUGCAUGAGGCCCGGAUCCGGC-3'
R20-15 aptamer: 5'-GGGAGCUCAGAAUAAACGCUCAAUGUAGGCUAGUACCGACCUGCGUGCCUCGCUCCUUUUCAUGCAUGCAUGAGGCCCGGAUCCGGC-3'
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Ligand information
SELEX ligand
This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.-----From Pfam
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Hepatitis C virus NS5B protein (HCV NS5B protein) | P26663 | PF00998 | 58.978 kDa | SMSYTWTGALITPCAAEESKLPINALSNSLLRHHNMVYATTSRSAGLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGYGAKDVRNLSSKAVNHIHSVWKDLLEDTVTPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQVVMGSSYGFQYSPGQRVEFLVNTWKSKKNPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIKSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVK | 1CSJ | M58335 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| R20-43 | 5'-GGGAGCUCAGAAUAAACGCUCAAUGUAGAGACUUUUCGAAAAGCGUGUUCCCAAUGAGUCUAUGCAUGCAUGAGGCCCGGAUCCGGC-3' | HCV NS5B protein | (1.4 ± 0.3)* 104 (1/s) （dissociation rate constant） |
| R20-15 | 5'-GGGAGCUCAGAAUAAACGCUCAAUGUAGGCUAGUACCGACCUGCGUGCCUCGCUCCUUUUCAUGCAUGCAUGAGGCCCGGAUCCGGC-3' | HCV NS6B protein | (1.0 ± 0.1)* 104 (1/s) |
| R1-1 | 5'-GGGAGCUCAGAAUAAACGCUCAACUCCUAACCUCUCCGCAUGNGCUGUUACCUACACAGCUCAGCAUGCAUGAGGCCCGGAUCCGGC-3' | HCV NS7B protein | (100 ± 6)* 104 (1/s) |
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 |
|---|---|---|---|
| 3GNW-B | 51.7 | 1.1 | RNA-directed RNA polymerase |
| 5Y6R-A | 30.3 | 3.3 | Genome polyprotein |
| 4K6M-A | 27.2 | 3.1 | Polyprotein |
| 1SH0-B | 24.5 | 4.0 | RNA polymerase |
| 8WU3-B | 23.5 | 3.3 | RNA polymerase |
| 2IJD-1 | 23.0 | 3.5 | Picornain 3c, RNA-directed RNA polymerase |
| 5I61-A | 20.5 | 3.4 | Potential RNA-dependent RNA polymerase |
| 6OGZ-A | 18.4 | 4.0 | Rotavirus RNA-dependent RNA polymerase |
| 8GWE-A | 17.7 | 3.8 | RNA-directed RNA polymerase |
| 8H69-B | 17.6 | 3.9 | Cryo-EM structure of influenza RNA polymerase |
References
[1] Identification of RNA ligands that bind hepatitis C virus polymerase selectively and inhibit its RNA synthesis from the natural viral RNA templates.Vo, N. V., Oh, J. W., & Lai, M. M.
Virology, 307(2), 301–316. (2003)