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Gastrointestinal carcinoembryonic antigen (CEA)-aptamer
Description
In 2015, Qing Pan and colleagues used SELEX (Systematic Evolution of Ligands by Exponential enrichment) technique to isolate high affinity RNA aptamers that bind to the CEA protein[1].SELEX
In 2015, 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'-GGGUCGUGUCGGAUCCAGGCACGACGCAUAGCCUUGGGAGCGAGGAAAGCUUCUAAGGUAACGAU-3'
Ligand information
SELEX ligand
Carcinoembryonic antigen (CEA) describes a set of highly-related glycoproteins involved in cell adhesion. CEA is normally produced in gastrointestinal tissue during fetal development, but the production stops before birth. Consequently, CEA is usually present at very low levels in the blood of healthy adults (about 2–4 ng/mL).-----from Pfam
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Carcinoembryonic antigen (CEA) | P06731 | PF13895 | 76.796 kDa | MESPSAPPHRWCIPWQRLLLTASLLTFWNPPTTAKLTIESTPFNVAEGKEVLLLVHNLPQHLFGYSWYKGERVDGNRQIIGYVIGTQQATPGPAYSGREIIYPNASLLIQNIIQNDTGFYTLHVIKSDLVNEEATGQFRVYPELPKPSISSNNSKPVEDKDAVAFTCEPETQDATYLWWVNNQSLPVSPRLQLSNGNRTLTLFNVTRNDTASYKCETQNPVSARRSDSVILNVLYGPDAPTISPLNTSYRSGENLNLSCHAASNPPAQYSWFVNGTFQQSTQELFIPNITVNNSGSYTCQAHNSDTGLNRTTVTTITVYAEPPKPFITSNNSNPVEDEDAVALTCEPEIQNTTYLWWVNNQSLPVSPRLQLSNDNRTLTLLSVTRNDVGPYECGIQNELSVDHSDPVILNVLYGPDDPTISPSYTYYRPGVNLSLSCHAASNPPAQYSWLIDGNIQQHTQELFISNITEKNSGLYTCQANNSASGHSRTTVKTITVSAELPKPSISSNNSKPVEDKDAVAFTCEPEAQNTTYLWWVNGQSLPVSPRLQLSNGNRTLTLFNVTRNDARAYVCGIQNSVSANRSDPVTLDVLYGPDTPIISPPDSSYLSGANLNLSCHSASNPSPQYSWRINGIPQQHTQVLFIAKITPNNNGTYACFVSNLATGRNNSIVKSITVSASGTSPGLSAGATVGIMIGVLVGVALI | 2QSQ | 1048 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| CEA A01 | 5'-GGGUCGUGUCGGAUCCAGGCACGACGCAUAGCCUUGGGAGCGAGGAAAGCUUCUAAGGUAACGAU-3' | Gastrointestinal carcinoembryonic antigen | 16.5 nM |
| CEA A02 | 5'-GGUUACCUUAGAAGCUUAACGGCAUGACCUAACCUGGAGGCGCAUCAGGAUCCGACACGACCCUAUAGUGAGUCGUAUUA-3' | Homo sapien - CEA | 156.0 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 |
|---|---|---|---|
| 1L6Z-A | 18.0 | 1.5 | Biliary glycoprotein c |
| 5A2F-A | 13.1 | 1.7 | Cd166 antigen |
| 2DRU-A | 13.0 | 2.0 | Chimera of cd48 antigen and t-cell surface antige |
| 4BFI-B | 12.8 | 2.2 | Cell surface glycoprotein cd200 receptor 1 |
| 7ZOZ-A | 12.4 | 1.8 | Sialic acid-binding ig-like lectin 15 |
| 3Q0H-A | 12.3 | 2.3 | T cell immunoreceptor with ig and itim domains |
| 1HNG-A | 12.1 | 2.1 | Cd2 |
| 4HJJ-H | 12.1 | 2.6 | Interleukin-18 |
| 5XPW-A | 12.0 | 2.1 | Amphioxus igvj-c2 |
| 5IMM-A | 12.0 | 2.3 | Nanobody |
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. (2015)