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J18 aptamer
Description
In 2009, Na Li et al. used the SELEX method to isolate the aptamer with high compatibility for the Epithelial Growth Factor Receptor (EGFR). The anti-EGFR aptamer J18 was extended at its 3′ end with either 5′-UUGUGUUGGUCCUAAAUGCAAAUG-3′ (Aptamer J18.A′) or with 5′-UAAGUAGAAGUGGUGAUGAUCGGU-3′ (Aptamer J18.B′). Some 10 nM extended J18 aptamers were hybridized with an equal amount of the fluorescein-labeled template. Nucleic acids were heated to 70 °C for 3 min in binding buffer, and cooled to 25 °C at 1 °C/s[1].SELEX
In 2009, Na Li et al. assayed aptamer J18 against Epithelial Growth Factor Receptor (EGFR) by flow cytometry[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.5'-GGCGCUCCGACCUUAGUCUCUGCAAGAUAAACCGUGCUAUUGACCACCCUCAACACACUUAUUUAAUGUAUUGAACGGACCUACGAACCGUGUAGCACAGCAGA-3'
Ligand information
SELEX ligand
The epidermal growth factor receptor (EGFR; ErbB-1; HER1 in humans) is a transmembrane protein that is a receptor for members of the epidermal growth factor family (EGF family) of extracellular protein ligands. The epidermal growth factor receptor is a member of the ErbB family of receptors, a subfamily of four closely related receptor tyrosine kinases: EGFR (ErbB-1), HER2/neu (ErbB-2), Her 3 (ErbB-3) and Her 4 (ErbB-4). In many cancer types, mutations affecting EGFR expression or activity could result in cancer.-----From Wiki
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Epithelial Growth Factor Receptor (EGFR) | P00533 | IPR050122 | 134.30 kDa | MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGEENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKIPSIATGMVGALLLLLVVALGIGLFMRRRHIVRKRTLRRLLQERELVEPLTPSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGFFSSPSTSRTPLLSSLSATSNNSTVACIDRNGLQSCPIKEDSFLQRYSSDPTGALTEDSIDDTFLPVPEYINQSVPKRPAGSVQNPVYHNQPLNPAPSRDPHYQDPHSTAVGNPEYLNTVQPTCVNSTFDSPAHWAQKGSHQISLDNPDYQQDFFPKEAKPNGIFKGSTAENAEYLRVAPQSSEFIGA | 3G5X | 1956 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| J18 | 5'-GGCGCUCCGACCUUAGUCUCUGCAAGAUAAACCGUGCUAUUGACCACCCUCAACACACUUAUUUAAUGUAUUGAACGGACCUACGAACCGUGUAGCACAGCAGA-3' | Epithelial Growth Factor Receptor (EGFR) | 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 |
|---|---|---|---|
| 3ZE2-F | 29.2 | 0.8 | Integrin alpha-iib |
| 2VDO-L | 28.9 | 1.4 | Integrin alpha-iib |
| 7U9V-L | 28.9 | 1.0 | Integrin alpha-iib |
| 2VDQ-L | 28.9 | 1.4 | Integrin alpha-iib |
| 2VDR-L | 28.9 | 1.4 | Integrin alpha-iib |
| 3NID-L | 28.9 | 1.1 | Integrin alpha-iib |
| 7TD8-L | 28.9 | 1.0 | Integrin alpha-iib |
| 7UDH-L | 28.9 | 1.0 | Integrin alpha-iib heavy chain |
| 2VDP-L | 28.9 | 1.4 | Integrin alpha-iib |
| 7L8P-L | 28.9 | 1.0 | Isoform 3 of integrin alpha-iib |
References
[1] Technical and biological issues relevant to cell typing with aptamers.Li, N., Ebright, J. N., Stovall, G. M., Chen, X., Nguyen, H. H., Singh, A., Syrett, A., & Ellington, A. D.
Journal of proteome research, 8(5), 2438–2448. (2009)