L-selectin aptamer

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Description

O'Connell, D. et al. reported aptamers with affinity for L-selectin in their article published in 1996. The 14.12 aptamer was named by O'Connell, D. et al. in the article[1].



SELEX

In their work published in 1996, O'Connell, D. 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. From the seventh round, the SELEX was branched and carried in parallel at 4℃ and 22℃[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 to draw. The figure shows the secondary structure prediction of the original aptamer sequence. This aptamer comprises a single stem-loop structure, with overhang sequences at both the 5' and 3' ends[1].

5'-UAACAACAAUCAAGGCGGGUUCACCGCCCCAGUAUGAGUA-3'

drawing

Ligand information

SELEX ligand

Some isolated sequences bind to the affinity of the protein[1].

Name Sequence Ligand Affinity
14.12 aptamer 5'-UAACAACAAUCAAGGCGGGUUCACCGCCCCAGUAUGAGUA-3' L-selectin 3 nM
13.32 aptamer 5'-CGCGUAUGUGUGAAAGCGUGUGCACGGAGGCGUCUACAAU-3' L-selectin 3 nM
drawing

Structure ligand

L-selectin is one of calcium-dependent lectin that mediates cell adhesion by binding to glycoproteins on neighboring cells. L-selectin mediates the adherence of lymphocytes to endothelial cells of high endothelial venules in peripheral lymph nodes and promotes initial tethering and rolling of leukocytes in endothelia. Interaction with SELPLG/PSGL1 and PODXL2 is required for promoting recruitment and rolling of leukocytes. This interaction is dependent on the sialyl Lewis X glycan modification of SELPLG and PODXL2, and tyrosine sulfation modifications of SELPLG.-----From Uniprot

UniProt ID: uniquely identifies protein sequences in the UniProt database, a resource for protein information.

Pfam: a widely recognised database of protein families and domains.

GenBank: maintained by NCBI(National Center for Biotechnology Information), is a database of nucleotide sequences from various organisms, vital for genetic and molecular biology research.

Mass: an intrinsic property of a body.

Name Uniprot ID Pfam Mass Protein sequence PDB ID GenBank
L-selectin P14151 IPR016348 42.187 kDa
...... MIFPWKCQSTQRDLWNIFKLWGWTMLCCDFLAHHGTDCWTYHYSEKPMNWQRARRFCRDNYTDLVAIQNKAEIEYLEKTLPFSRSYYWIGIRKIGGIWTWVGTNKSLTEEAENWGDGEPNNKKNKEDCVEIYIKRNKDAGKWNDDACHKLKAALCYTASCQPWSCSGHGECVEIINNYTCNCDVGYYGPQCQFVIQCEPLEAPELGTMDCTHPLGNFSFSSQCAFSCSEGTNLTGIEETTCGPFGNWSSPEPTCQVIQCEPLSAPDLGIMNCSHPLASFSFTSACTFICSEGTELIGKKKTICESSGIWSNPSPICQKLDKSFSMIKEGDYNPLFIPVAVMVTAFSGLAFIIWLARRLKKGKKSKRSMNDPY
2LGF
3CFW
5VC1 		6402

Similar compound(s)

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.

Dail server website: a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB).

Z-score: 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) is used to measure the degree to which atoms deviate from the alignment position.

PDB: PDB ID+ chain name.

PDB Z-socre RMSD (Å) Description
3CFW-A 30.8 0 Original chain
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)