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A30 aptamer
Timeline
An aptamer called A30, which binds specifically to the HER3, was selected for the first time by the SELEX methodology[1]
Description
In 2003, Chen C.H and Chernis G.A had used the SELEX methodology to select RNA aptamers against the oligomeric state of the extracellular domains of HER3. One of the aptamers, A30, binds with high affinity to a limited number of binding sites in the oligomeric state of the extracellular domains of HER3[1].SELEX
In 2003, Chen C.H et al. chose to make a filter binding assay was used for the first eight rounds of selection.A gel-shift assay was used in the last seven rounds of selection. Then, the cDNA was PCR-amplified for the next round of selection. Finally, Individual clones were obtained by ligation of the PCR product into either pGEM4 or pGEM3Z vectors after digestion with EcoRI and BamHI[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[1].5'-GGGAAUUCCGCGUGUGCCAGCGAAAGUUGCGUAUGGGUCACAUCGCAGGCACAUGUCAUCUGGGCGGUCCGUUCGGGAUCCUC-3'
Ligand information
SELEX ligand
HER3 binds the neuregulin ligands, NRG1 and NRG2, and it relies on its heterodimerization partners for activity following ligand binding. The HER2-HER3 heterodimer constitutes a high affinity co-receptor capable of potent mitogenic signaling. HER3 participates in a signaling pathway involved in the proliferation, survival, adhesion, and motility of tumor cells.-----from Pfam
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| HER3ECD(the extracellular domains of HER3) | P21860 | CD05111 | 82 kDa | SEVGNSQAVCPGTLNGLSVTGDAENQYQTLYKLYERCEVVMGNLEIVLTGHNADLSFLQWVREVTGYVLVAMNEFSTLPLPNLRVVRGTQVYDGKFAIFVMLNYNTNSSHALRQLRLTQLTEILSGGVYIEKNDKLCHMDTIDWRDIVRDRDAEIVVKDNGRSCPPCHEVCKGRCWGPGSEDCQTLTKTICAPQCNGHCFGPNPNQCCHDECAGGCSGPQDTDCFACRHFNDSGACVPRCPQPLVYNKLTFQLEPNPHTKYQYGGVCVASCPHNFVVDQTSCVRACPPDKMEVDKNGLKMCEPCGGLCPKACEGTGSGSRFQTVDSSNIDGFVNCTKILGNLDFLITGLNGDPWHKIPALDPEKLNVFRTVREITGYLNIQSWPPHMHNFSVFSNLTTIGGRSLYNRGFSLLIMKNLNVTSLGFRSLKEISAGRIYISANRQLCYHHSLNWTKVLRGPTEERLDIKHNRPRRDCVAEGKVCDPLCSSGGCWGPGPGQCLSCRNYSRGGVCVTHCNFLNGEPREFAHEAECFSCHPECQPMEGTATCNGSGSDTCAQCAHFRDGPHCVSSCPHGVLGAKGPIYKYPDVQNECRPCHENCTQGCKGPELQDCLGQTLVLIGKT | 1M6B | AAQ24492.1 |
The aptamer bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| A30 aptamer | 5'-GGGAAUUCCGCGUGUGCCAGCGAAAGUUGCGUAUGGGUCACAUCGCAGGCACAUGUCAUCUGGGCGGUCCGUUCGGGAUCCUC-3' | HER3ECD(the extracellular domains of HER3) | 45 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 |
|---|---|---|---|
| 4KRP-A | 37.3 | 5.3 | Epidermal Growth Factor Receptor |
| 8PWH-E | 26.0 | 22.0 | Trastuzumab Fab Light Chain |
| 7S8V-B | 20.0 | 8.2 | Insulin-Like Growth Factor 1 Receptor |
| 8CLS-B | 18.9 | 13.9 | Insulin-Like Receptor |
| 1M9S-A | 6.0 | 5.0 | Internalin B |
| 7B8B-B | 5.7 | 5.5 | Polygalacturonase Adpg2 |
| 1HG8-A | 5.6 | 5.3 | Endopolygalacturonase |
| 7YA8-B | 5.3 | 4.5 | Ring-Type E3 Ubiquitin Transferase |
| 8TH8-C | 5.1 | 5.9 | Dynein Regulatory Complex Protein 1/2 N-Terminal |
| 7O17-A | 5.0 | 3.4 | Probable Abc Transporter Binding Protein Nosd |
References
[1] Inhibition of heregulin signaling by an aptamer that preferentially binds to the oligomeric form of human epidermal growth factor receptor-3.Chen CH, Chernis GA, Hoang VQ, Landgraf R.
Proc Natl Acad Sci U S A, 100(16):9226-31. (2003)
[2] Targeting EGFR/HER2/HER3 with a Three-in-One Aptamer-siRNA Chimera Confers Superior Activity against HER2+ Breast Cancer.
Yu X, Ghamande S, Liu H, Xue L, Zhao S, Tan W, Zhao L, Tang SC, Wu D, Korkaya H, Maihle NJ, Liu HY.
Mol Ther Nucleic Acids, 10:317-330. (2017)