Home
Database
Research
About us
Cancer antigen 72–4(CA72-4)-aptamer
Description
In 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 CA72-4 protein[1].SELEX
In 2018, Qing Pan, Carmen O. K. Law , et al. isolated 6 specific sequences targeting gastrointestinal cancer biomarkers CEA , CA50 and CA72-4 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'-GGGUCGUGUCGGAUCCUGCGAAGGGGGGCAGAGGUUUGACGCGAGAAAGCUUCUAAGGUAACGAU-3'
Ligand information
SELEX ligand
CA 72-4 is a mucin-glycoprotein present on the surface of many cell types such as ovarian, breast, colon, pancreatic cells, especially cancer cells.
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Cancer antigen 72–4(CA72-4) | P78358 | PF09341 | 17.992 kDa | MQAEGRGTGGSTGDADGPGGPGIPDGPGGNAGGPGEAGATGGRGPRGAGAARASGPGGGAPRGPHGGAASGLNGCCRCGARGPESRLLEFYLAMPFATPMEAELARRSLAQDAPPLPVPGVLLKEFTVSGNILTIRLTAADHRQLQLSISSCLQQLSLLMWITQCFLPVFLAQPPSGQRR | 1S9W | 1485 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| CA72-4 A01 | 5'-GGGUCGUGUCGGAUCCUGCGAAGGGGGGCAGAGGUUUGACGCGAGAAAGCUUCUAAGGUAACGAU-3' | Cancer antigen 72–4 | 52.7 nM |
| CA72-4 A02 | 5'-AUCGUUACCUUAGAAGCUUCCCAAAAAGGAUUGGGGCGUCUGCAUGACCGGAUCCGACACGACCCUAUAGUGAGUCGUAUUA-3' | Cancer antigen 72–4 | 71.2 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 |
|---|---|---|---|
| 2QRI-A | 28.4 | 1.5 | H-2 class i histocompatibility antigen k-b alpha |
| 3D2U-A | 23.4 | 2.7 | Ul18 protein |
| 7M72-A | 21.9 | 3.9 | Antigen-presenting glycoprotein cd1d1 |
| 1LQV-B | 17.0 | 2.5 | Endothelial protein c receptor |
| 4S0U-C | 16.2 | 3.0 | Nkg2-d type ii integral membrane protein |
| 1PQZ-A | 15.4 | 3.4 | Mcmv m144 |
| 3IT8-D | 14.3 | 6.3 | Tumor necrosis factor |
| 8VSP-A | 14.1 | 3.1 | Hla class ii histocompatibility antigen, dq alpha |
| 7XXA-E | 13.9 | 2.9 | Vp1; |
| 6YJP-C | 13.3 | 11.0 | Natural cytotoxicity triggering receptor 3 ligand |
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)