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ps11-20 aptamer
Description
Sulay Jhaveri and Brad Olwin et al. reported aptamers with affinity for bFGF in their article published in 1998[1].SELEX
In their work published in 1998, Sulay Jhaveri and Brad Olwin et al. used SELEX to isolate RNA aptamer sequences with affinity for bFGF from a nucleic acid library containing about 5×1012 sequences with after 11 rounds of selection process[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figure is based on the prediction results of the RNA fold website by ribodraw tool to draw[1].5'-GGGAAUGGAUCCACAUCUACGAAUUCAAUCCCAAUGGCUUGAACUGCCAACGAACGUUCACUGCAGACUUGACGAAGCUU-3'
Ligand information
SELEX ligand
Growth factor active in angiogenesis, and endothelial cell growth, stimulating their proliferation and migration and also has effects on the permeability of blood vessels. May function in angiogenesis of the venous and lymphatic vascular systems during embryogenesis, and also in the maintenance of differentiated lymphatic endothelium in adults. Binds and activates KDR/VEGFR2 and FLT4/VEGFR3 receptors.-----From Uniprot
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| bFGF (basic fibroblast growth factor) | P09038 | PF00167 | 30.77 kDa | MVGVGGGDVEDVTPRPGGCQISGRGARGCNGIPGAAAWEAALPRRRPRRHPSVNPRSRAAGSPRTRGRRTEERPSGSRLGDRGRGRALPGGRLGGRGRGRAPERVGGRGRGRGTAAPRAAPAARGSRPGPAGTMAAGSITTLPALPEDGGSGAFPPGHFKDPKRLYCKNGGFFLRIHPDGRVDGVREKSDPHIKLQLQAEERGVVSIKGVCANRYLAMKEDGRLLASKCVTDECFFFERLESNNYNTYRSRKYTSWYVALKRTGQYKLGSKTGPGQKAILFLPMSAKS | 1BAS | 2247 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| ps11-20 aptamer | 5'-GGGAAUGGAUCCACAUCUACGAAUUCAAUCCCAAUGGCUUGAACUGCCAACGAACGUUCACUGCAGACUUGACGAAGCUU-3' | bFGF | 1.8 ± 0.8 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 |
|---|---|---|---|
| 1G82-A | 23.7 | 1.1 | Fibroblast growth factor 9 |
| 3A07-B | 18.2 | 1.5 | Actinohivin |
| 1UPS-A | 17.6 | 1.9 | Glcnac-alpha-1,4-gal-releasing endo-beta- |
| 2VSE-A | 17.3 | 1.7 | Mosquitocidal toxin |
| 6LF2-B | 17.1 | 1.8 | Sevil |
| 8BAD-B | 16.8 | 1.8 | Binary toxin a-like protein |
| 1W3A-A | 16.7 | 1.9 | Hemolytic lectin lsla |
| 6IFB-B | 16.6 | 1.8 | Lectin |
| 4PC4-C | 16.4 | 2.0 | 30k lipoprotein |
| 2IHO-A | 16.4 | 1.9 | Lectin |
References
[1] In vitro selection of phosphorothiolated aptamers.Jhaveri, S., Olwin, B., & Ellington, A. D.
Bioorganic & medicinal chemistry letters, 8(17), 2285–2290. (1998)