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NX-213 aptamer
Description
Louis S Green and Derek Jellinek et al. reported aptamers with affinity for VEGF in their article published in 1995[1].SELEX
In their work published in 1995, Louis S Green and Derek Jellinek et al. used SELEX to isolate RNA aptamer sequences with affinity for VEGF from a nucleic acid library containing about 6×1014 sequences 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 article by ribodraw tool to draw[1].5'-ACCCUGAUGGUAGACGCCGGGGUG-3'
Ligand information
SELEX ligand
VEGF active in angiogenesis, vasculogenesis and endothelial cell growth. Induces endothelial cell proliferation, promotes cell migration, inhibits apoptosis and induces permeabilization of blood vessels. Binds to the FLT1/VEGFR1 and KDR/VEGFR2 receptors, heparan sulfate and heparin. Binds to the NRP1/neuropilin-1 receptor. Binding to NRP1 initiates a signaling pathway needed for motor neuron axon guidance and cell body migration, including for the caudal migration of facial motor neurons from rhombomere 4 to rhombomere 6 during embryonic development (By similarity). Also binds the DEAR/FBXW7-AS1 receptor.-----From Uniprot
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| VEGF | P49767 | P49767 | 46.883 kDa | MHLLGFFSVACSLLAAALLPGPREAPAAAAAFESGLDLSDAEPDAGEATAYASKDLEEQLRSVSSVDELMTVLYPEYWKMYKCQLRKGGWQHNREQANLNSRTEETIKFAAAHYNTEILKSIDNEWRKTQCMPREVCIDVGKEFGVATNTFFKPPCVSVYRCGGCCNSEGLQCMNTSTSYLSKTLFEITVPLSQGPKPVTISFANHTSCRCMSKLDVYRQVHSIIRRSLPATLPQCQAANKTCPTNYMWNNHICRCLAQEDFMFSSDAGDDSTDGFHDICGPNKELDEETCQCVCRAGLRPASCGPHKELDRNSCQCVCKNKLFPSQCGANREFDENTCQCVCKRTCPRNQPLNPGKCACECTESPQKCLLKGKKFHHQTCSCYRRPCTNRQKACEPGFSYSEEVCRCVPSYWKRPQMS |
2X1X 4BSK |
7424 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| NX-213 | 5'-ACCCUGAUGGUAGACGCCGGGGUG-3' | NA | 0.14 ± 0.01 nM |
| NX-178 | 5'-ACCCUGAUGGUAGACGCCGGGGUG-3' | NA | 2.4 ± 0.5 nM |
| NX-191 | 5'-ACCCUGAUGGUAGACGCCGGGGUG-3' | NA | 250 ± 130 nM |
| NX-223 | 5'-ACCCUGAUGGUAGACGCCGGGGUG-3' | NA | 250 ± 100 nM |
| NX-224 | 5'-ACCCUGAUGGUAGACGCCGGGGUG-3' | NA | 320 ±70 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 |
|---|---|---|---|
| 2XV7-A | 12.6 | 1.5 | Vascular endothelial growth factor D |
| 1FZV-b | 10.9 | 3.0 | Placenta growth factor |
| 2GNN-C | 10.4 | 3.9 | Vascular endothelial growth factor homolog |
| 3MJK-A | 9.4 | 3.3 | Platelet-derived growth factor subunit A |
| 4NT5-A | 6.6 | 2.7 | Von willebrand factor |
| 5BPU-A | 6.0 | 3.4 | Norrin |
| 8END-A | 6.0 | 3.1 | Bursicon |
| 2ASK-A | 5.7 | 3.3 | Artemin |
| 4MQW-B | 5.5 | 2.1 | Glycoprotein hormones, alpha polypeptide |
| 8I2G-Y | 5.3 | 2.2 | Chimera of guanine nucleotide-binding protein g(s |
References
[1] Nuclease-resistant nucleic acid ligands to vascular permeability factor/vascular endothelial growth factor.Green, L. S., Jellinek, D., Bell, C., Beebe, L. A., Feistner, B. D., Gill, S. C., Jucker, F. M., & Janjić, N.
Chemistry & biology, 2(10), 683–695. (1995)