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11-1.41 aptamer
Description
Rebekah R. White and Siqing Shan et al. reported aptamers with affinity for angiopoietin-2 in their article published in 2003[1].SELEX
In their work published in 2003, Rebekah R. White and Siqing Shan et al. used SELEX to isolate RNA aptamer sequences with affinity for angiopoietin-2 from a nucleic acid library containing about 1014 80-nucleotides-long 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'-GAGGACGAUGCGGACUAGCCUCAUACUCCGAUGUGCCCCUC-3'
Ligand information
SELEX ligand
Angiopoietin-2 binds to TEK/TIE2, competing for the ANGPT1 binding site, and modulating ANGPT1 signaling. Can induce tyrosine phosphorylation of TEK/TIE2 in the absence of ANGPT1. In the absence of angiogenic inducers, such as VEGF, ANGPT2-mediated loosening of cell-matrix contacts may induce endothelial cell apoptosis with consequent vascular regression. In concert with VEGF, it may facilitate endothelial cell migration and proliferation, thus serving as a permissive angiogenic signal.-----From Uniprot
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Ang2 (Angiopoietin-2) | O15123 | PF00147 | 56.919 kDa | MWQIVFFTLSCDLVLAAAYNNFRKSMDSIGKKQYQVQHGSCSYTFLLPEMDNCRSSSSPYVSNAVQRDAPLEYDDSVQRLQVLENIMENNTQWLMKLENYIQDNMKKEMVEIQQNAVQNQTAVMIEIGTNLLNQTAEQTRKLTDVEAQVLNQTTRLELQLLEHSLSTNKLEKQILDQTSEINKLQDKNSFLEKKVLAMEDKHIIQLQSIKEEKDQLQVLVSKQNSIIEELEKKIVTATVNNSVLQKQQHDLMETVNNLLTMMSTSNSAKDPTVAKEEQISFRDCAEVFKSGHTTNGIYTLTFPNSTEEIKAYCDMEAGGGGWTIIQRREDGSVDFQRTWKEYKVGFGNPSGEYWLGNEFVSQLTNQQRYVLKIHLKDWEGNEAYSLYEHFYLSSEELNYRIHLKGLTGTAGKISSISQPGNDFSTKDGDNDKCICKCSQMLTGGWWFDACGPSNLNGMYYPQRQNTNKFNGIKWYYWKGSGYSLKATTMMIRPADF | 2GY7 | 285 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| 11-1.41 aptamer | 5'-GAGGACGAUGCGGACUAGCCUCAUACUCCGAUGUGCCCCUC-3' | Angiopoietin-2 | 2.2 nM |
| 11-1 aptamer | 5'-GGGAGGACGATGCGGACUAGCCUCAUCAGCUCAUGUGCCCCUCCGCCUGGAUCACCAGACGACTCGCTGAGGATCCGAGA-3' | Angiopoietin-2 | 3.1 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 |
|---|---|---|---|
| 4K0V-A | 57.5 | 0.9 | Tek tyrosine kinase variant |
| 2V5Y-A | 10.2 | 13.2 | Receptor-type tyrosine-protein phosphatase Mu |
| 2ID5-B | 9.8 | 11.0 | Leucine rich repeat neuronal 6A |
| 3TF7-C | 9.5 | 6.7 | H2-ld SBM2 |
| 8BXR-A | 9.5 | 2.1 | Ritin |
| 6RUL-A | 9.4 | 1.9 | GFP-lama-F98 a GFP enhancer nanobody with Cpdhfr |
| 3B43-A | 9.3 | 17.6 | Titin |
| 8ES7-B | 9.1 | 9.3 | T-cell surface glycoprotein Cd3 zeta chain |
| 8ES8-A | 9.1 | 3.9 | T-cell surface glycoprotein Cd3 zeta chain |
| 3SO5-B | 9.1 | 2.6 | Leucine-rich repeats and immunoglobulin-like doma |
References
[1] Inhibition of rat corneal angiogenesis by a nuclease-resistant RNA aptamer specific for angiopoietin-2.White, R. R., Shan, S., Rusconi, C. P., Shetty, G., Dewhirst, M. W., Kontos, C. D., & Sullenger, B. A.
Proceedings of the National Academy of Sciences of the United States of America, 100(9), 5028–5033. (2003)