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14.12 aptamer
Description
Dan O'Connell and Andrea Koenig et al. reported aptamers with affinity for L-selectin in their article published in 1996[1].SELEX
In their work published in 1996, Dan O'Connell and Andrea Koenig et al. used SELEX to isolate RNA aptamer sequences with affinity for L-selectin from a nucleic acid library containing about 6×1014 sequences after 6 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'-UAACAACAAUCAAGGCGGGUUCACCGCCCCAGUAUGAGUA-3'
Ligand information
SELEX ligand
L-selectin is one of calcium-dependent lectin that mediates cell adhesion by binding to glycoproteins on neighboring cells. Mediates the adherence of lymphocytes to endothelial cells of high endothelial venules in peripheral lymph nodes. Promotes initial tethering and rolling of leukocytes in endothelia.-----From Uniprot
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| L-selectin | P14151 | IPR016348 | 42.187 kDa | MIFPWKCQSTQRDLWNIFKLWGWTMLCCDFLAHHGTDCWTYHYSEKPMNWQRARRFCRDNYTDLVAIQNKAEIEYLEKTLPFSRSYYWIGIRKIGGIWTWVGTNKSLTEEAENWGDGEPNNKKNKEDCVEIYIKRNKDAGKWNDDACHKLKAALCYTASCQPWSCSGHGECVEIINNYTCNCDVGYYGPQCQFVIQCEPLEAPELGTMDCTHPLGNFSFSSQCAFSCSEGTNLTGIEETTCGPFGNWSSPEPTCQVIQCEPLSAPDLGIMNCSHPLASFSFTSACTFICSEGTELIGKKKTICESSGIWSNPSPICQKLDKSFSMIKEGDYNPLFIPVAVMVTAFSGLAFIIWLARRLKKGKKSKRSMNDPY |
2LGF 3CFW 5VC1 |
6402 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| 14.12 aptamer | 5'-UAACAACAAUCAAGGCGGGUUCACCGCCCCAGUAUGAGUA-3' | L-selectin | 3 nM |
| 13.32 aptamer | 5'-CGCGUAUGUGUGAAAGCGUGUGCACGGAGGCGUCUACAAU-3' | L-selectin | 3 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 |
|---|---|---|---|
| 4C16-A | 21.3 | 3.5 | E-selectin |
| 2RIC-C | 16.9 | 1.6 | Pulmonary surfactant-associated protein D |
| 2VUV-A | 16.7 | 1.8 | Codakine |
| 5E4l-B | 16.2 | 6.7 | C-type mannose receptor 2 |
| 3KQG-A | 15.8 | 2.5 | C-type lectin domain family 4 member K |
| 7Y5N-A | 15.7 | 1.6 | Bone marrow proteoglycan |
| 1SL6-A | 15.6 | 3.0 | C-type lectin DC-signR |
| 6JK4-A | 15.5 | 1.9 | Type II antifreeze protein |
| 1QDD-A | 15.0 | 2.0 | Lithostathine |
| 3L9J-C | 15.0 | 2.2 | Tnfalpha |
References
[1] Calcium-dependent oligonucleotide antagonists specific for L-selectin.O'Connell, D., Koenig, A., Jennings, S., Hicke, B., Han, H. L., Fitzwater, T., Chang, Y. F., Varki, N., Parma, D., & Varki, A.
Proceedings of the National Academy of Sciences of the United States of America, 93(12), 5883–5887. (1996)