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3Dpol-aptamer
Description
In 2006, Ellingham, M., & Stonehouse, N. J. report the selection and characterization of RNA aptamers to the 3D RdRp, a key part of the FMDV replication complex. This is the first report of aptamer selection to any protein of this economically important animal pathogen. They have characterized three aptamers (F38, F47, and F52) that inhibit the in vitro activity of the enzyme with IC50 values of 15.8 nM, 10.6 nM, and 16.4 nM, respectively. One aptamer retains this inhibitory ability when truncated to a 32mer (F47tr) with an IC50 of 10.2 nM[2].SELEX
In 2006, Ellingham, M., & Stonehouse, N. J. undertaken Fifteen rounds of selection using a degenerate library of ∼1015 sequences, consisting of an N30 random region flanked by primer sequences for amplification and in vitro transcription. As expected, the selected pool displayed increased affinity for 3Dpol compared with the naive RNA population as assessed by electrophoretic mobility shift assays . Fifty-two cDNA clones were prepared from the round 15 selected pool, of which 25 were selected at random for detailed analysis and sequencing . Selection resulted in some of the aptamers incorporating N30 regions smaller than the original 30 nucleotides. The greatest reductions were seen with aptamers F4, F6, F12, and F38[2].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figures is based on the prediction results of the RNA fold website by ribodraw tool to draw[2].F47-aptamer: 5'-GGGAAGGGAUCCAAUCUACAAAUUCGUUAACAGAAAACCUCAGUUGCUGGGUUGUUUCACUGCAAACUUGACAAAGCUA-3'
F47tr-aptamer: 5'-GGGUUAACAGAAAACCUCAGUUGCUGGGUUGU-3'
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Ligand information
SELEX ligand
RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to typical DNA-dependent RNA polymerases, which all organisms use to catalyze the transcription of RNA from a DNA template.-----from Wikipedia
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| 3Dpol | O14227 | PF00680 | 53.97 kDa | GLIVDTRDVEERVHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNEGVVLDEVIFSKHKGDTKMSAEDKALFRRCAADYASRLHSVLGTANAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIDFENGTVGPEVEAALKLMEKREYKFACQTFLKDEIRPMEKVRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRFGTHFAQYRNVWDVDYSAFDANHCSDAMNIMFEEVFRTEFGFHPNAEWILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHYEGVELDTYTMISYGDDIVVASDYDLDFEALKPHFKSLGQTITPADKSDKGFVLGHSITDVTFLKRHFHMDYGTGFYKPVMASKTLEAILSFARRGTIQEKLISVAGLAVHSGPDEYRRLFEPFQGLFEIPSYRSLYLRWVNAVCGDAAALEHHHHHH | 8C2P | BBB93554.1 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| F47-aptamer | 5'-GGGAAGGGAUCCAAUCUACAAAUUCGUUAACAGAAAACCUCAGUUGCUGGGUUGUUUCACUGCAAACUUGACAAAGCUA-3' | 3Dpol | 18 nM |
| F47tr-aptamer | 5'-GGGUUAACAGAAAACCUCAGUUGCUGGGUUGU-3' | 3Dpol | 14 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 |
|---|---|---|---|
| 2IJD-1 | 42.5 | 1.9 | Picornain 3c, rna-directed rna polymerase |
| 1SH0-B | 33.2 | 2.7 | Picornain 3c, rna-directed rna polymerase |
| 5Y6R-A | 25.7 | 3.2 | Genome polyprotein |
| 8WU3-B | 24.9 | 3.2 | Rna polymerase |
| 8IIC-B | 24.4 | 2.6 | Polymerase polyprotein |
| 4K6M-A | 23.9 | 3.0 | Rna-directed rna polymerase |
| 3GNW-B | 23.6 | 3.3 | Potential rna-dependent rna polymerase |
| 5I61-A | 21.6 | 2.9 | Rna-directed rna polymerase |
| 8GWE-A | 20.5 | 3.0 | Rna-directed rna polymerase |
| 1HHS-A | 16.6 | 3.5 | Rna-directed rna polymerase |
References
[1] Structure of foot-and-mouth disease virus RNA-dependent RNA polymerase and its complex with a template-primer RNA.Ferrer-Orta,& Verdaguer, N.
The Journal of biological chemistry, 279(45), 47212–47221. (2004)
[2] Selection and characterization of RNA aptamers to the RNA-dependent RNA polymerase from foot-and-mouth disease virus.
Ellingham, M., & Stonehouse, N. J.
RNA (New York, N.Y.), 12(11), 1970–1979. (2006)