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HER2 aptamer
Description
In 2015, Moosavian, S. A. et al. isolate RNA aptamers that specifically bind to HER2 overexpressing TUBO cell line. Among them TSA14 aptamer had the most affinity for target cells. Different experiments showed that the interaction of TSA14 aptamer with TUBO cells is mediated by binding to the extracellular domain of HER2[1].SELEX
The random library was synthesized by DNA synthesizer (PolyGen) and purified by gel purification. This library was amplified using forward primer and reverse primer. RNA library was transcribed from the PCR product using DuraScribe T7 transcription kit (Epicentre Technologies). After purification, the RNA library was added to 300 µl binding buffer containing HEPES-NaOH (20 mM, pH 7.4), NaCl (150 mM), CaCl2 (1.5 mM), MgCl2 (0.5 mM), and 10% yeast tRNA (Sigma). To retain correct configurations, the RNA library was denatured at 90 °C for 1 min and snap-cooled on ice. Cell SELEX TUBO cells were dislodged from the flask after a short period of incubation with trypsin and then counted. The cells’ viability was assessed by Trypan blue assay. 5-10 million cells were centrifuged, washed 3 times with washing buffer (20 mM HEPES-NaOH, pH 7.4, 150 mM NaCl, 1.5 mM CaCl2, 0.5 mM MgCl2) and resuspended in the binding buffer washing buffer plus 10% yeast tRNA (Sigma)[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figures are based on the article by ribodraw tool to draw[1].TSA14 aptamer: 5'-GCUGGAGCAUUUAUGGAUGAACCUUGGACGGAA-3'
TSA12 aptamer: 5'-GAAAGUGAGAGUCGAUUUAGCAACAGAGAGUGAGG-3'
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Ligand information
SELEX ligand
Receptor tyrosine-protein kinase erbB-2 is a protein that normally resides in the membranes of cells and is encoded by the ERBB2 gene. ERBB is abbreviated from erythroblastic oncogene B, a gene originally isolated from the avian genome. The human protein is also frequently referred to as HER2 (human epidermal growth factor receptor 2) or CD340 (cluster of differentiation 340).-----From Wiki
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| HER2 protein | P04626 | CD05109 | 137.910 KDa | MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRENTSPKANKEILDEAYVMAGVGSPYVSRLLGICLTSTVQLVTQLMPYGCLLDHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPLDSTFYRSLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHRHRSSSTRSGGGDLTLGLEPSEEEAPRSPLAPSEGAGSDVFDGDLGMGAAKGLQSLPTHDPSPLQRYSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPSPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPEYLTPQGGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPEYLGLDVPV | 7MN5 | 2064 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| TSA14 aptamer | 5'-GGGCCAGGCAGCGAGGGUGUAUAGGUAUUGAAUCAAUUGUUUUAGCGUUGUCUUACCGACCACACGCGUCCGAGA-3' | HER2 protein (TUBO cell) | 133.9±12.78 nM |
| TSA12 aptamer | 5'-GGGCCAGGCAGCGAGGGAACGCGAGCUUAGAUUUCGGAGAACAGUUUGUAAUUGUUCCGACCACACGCGUCCGAGA-3' | HER2 protein (TUBO cell) | 191.9±21.77 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 |
|---|---|---|---|
| 3NJP-B | 34.9 | 1.6 | Epidermal growth factor receptor |
| 2AHX-B | 33.5 | 6.5 | Receptor tyrosine-protein kinase erbb-4 |
| 8PWH-E | 31.3 | 5.6 | Trastuzumab fab light chain |
| 5CUS-D | 29.3 | 21.6 | Receptor tyrosine-protein kinase erbb-3 |
| 3I2T-A | 27.8 | 3.9 | Epidermal growth factor receptor, isoform |
| 7S8V-B | 21.8 | 26.6 | Insulin-like growth factor 1 receptor |
| 8U4C-B | 21.6 | 23.0 | Insulin receptor |
| 7TYK-B | 21.5 | 18.8 | Insulin receptor-related protein |
| 6VWH-B | 21.1 | 21.7 | Leucine-zippered human type 1 insulin-lik |
| 7XGD-A | 20.8 | 18.6 | Insulin-like growth factor 1 receptor |
References
[1] Development of RNA aptamers as molecular probes for HER2(+) breast cancer study using cell-SELEX.Moosavian, S. A., Jaafari, M. R., Taghdisi, S. M., Mosaffa, F., Badiee, A., & Abnous, K.
Iranian journal of basic medical sciences, 18(6), 576–586. (2015)