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Gastrointestinal cancer antigen 50-aptamer
Description
In 2018, Qing Pan and colleagues used SELEX (Systematic Evolution of Ligands by Exponential enrichment) technique to isolate high affinity RNA aptamers that bind to the CA50 protein[1].SELEX
In 2018, Qing Pan, Carmen O. K. Law , et al. isolated 6 specific sequences targeting gastrointestinal cancer biomarkers CEA and CA50 protein after 15 rounds of selection[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'-GGGUCGUGUCGGAUCCGUGAGUUUUUCGCGGCGAAGACAAGGCUCGAAGCUUCUAAGGUAACGAU-3'
Ligand information
SELEX ligand
Cancer antigen 50 (CA50) is a glycolipid that is similar to the tumor marker CA19-9; however, CA50 antibodies recognize both the fucosyl form of sialylated Lewis(a) carbohydrate moiety and sialylated Lewis(a) moiety.-----from Pfam| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Gastrointestinal cancer antigen 50 (CA50) | P16422 | PF00086 | 34.932 kDa | MAPPQVLAFGLLLAAATATFAAAQEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMNGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCNGTSMCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQNSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKAGVIAVIVVVVIAVVAGIVVLVISRKKRMAKYEKAEIKEMGEMHRELNA | 4MZV | 4072 |
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| CA50 A01 | 5'-GGGUCGUGUCGGAUCCGUGAGUUUUUCGCGGCGAAGACAAGGCUCGAAGCUUCUAAGGUAACGAU-3' | Gastrointestinal cancer antigen 50 | 38 nM |
| CA50 A02 | 5'-GGUUACCUUAGAAGCUUAGCUCGAAAGUGGGCUGGCGAUGUGUCCCGGGAUCCGACACGACCCUAUAGUGAGUCGUAUUA-3' | Homo sapien - CA50 | 30.7 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 |
|---|---|---|---|
| 4MZV-A | 40.2 | 0.0 | Epithelial cell adhesion molecule |
| 8D6M-A | 7.6 | 3.1 | Saxiphilin |
| 6FJW-A | 7.5 | 5.2 | Cas6 protein |
| 1ICF-J | 7.3 | 2.2 | Protein (cathepsin l: heavy chain) |
| 6FFY-A | 7.1 | 9.8 | Vps10 domain-containing receptor sorcs2 |
| 8KDB-A | 6.5 | 7.6 | Rna-directed rna polymerase l |
| 5YHF-A | 6.4 | 5.3 | Protein translocase subunit secdf |
| 3QJJ-A | 6.4 | 5.3 | Rna (5'-r(*gp*up*up*gp*ap*ap*ap*up*cp*ap*gp*a)-3') |
| 2QT7-B | 6.4 | 3.3 | Receptor-type tyrosine-protein phosphatase-like n |
| 2IA0-A | 6.4 | 12.8 | Putative hth-type transcriptional regulator pf086 |
References
[1] Novel RNA aptamers targeting gastrointestinal cancer biomarkers CEA, CA50 and CA72-4 with superior affinity and specificity.Pan, Q., Law, C. O., Yung, M. M., Han, K. C., Pon, Y. L., & Lau, T. C. K.
PLoS One, 13(10), e0198980. (2018)