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pUC19-aptamer
Description
In 2006, Lee, H. K., & Jeong, S. selected a high-affinity RNA aptamer that associated with beta-catenin in vivo. Nuclear localized aptamer inhibited beta-catenin-dependent transcription of cyclin D1 and c-myc in colon cancer cells; thus, cells stably expressing the aptamer exhibited cell cycle arrest and reduced tumor forming potential. Most significantly, the aptamer prevented the alternative splicing induced by stabilized beta-catenin[1].SELEX
In 2006, Lee, H. K., & Jeong, S. used an RNA library of random 50-nucleotide sequences (1 × 1014 different molecules, IDT) as starting material for the SELEX procedure . In each cycle, RNA was preincubated with glutathione S-transferase (GST) protein in binding buffer [25 mmol/L HEPES (pH 7.5), 150 mmol/L NaCl, 1 mmol/L MgCl2, 2 mmol/L DTT, and 40 units RNase inhibitor]. GST-bound RNA was discarded, and RNA bound to GST-Arm 1-12 was selected with glutathione-Sepharose beads. After four and eight cycles of selection, the selected sequences were cloned into pUC19 (pUC19-Aptamer) and sequenced[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'-GGACGCGUGGUACCAGGCCGAUCUAUGGACGCUAUAGGCACACCGGAUACUUUAACGAUUGGCUAAGCUUCCGCGGGGAUC-3'
Ligand information
SELEX ligand
Three different forms of catenin (designated alpha, beta and gamma) comprise the cytoplasmic domain of the cadherin cell-cell adhesion complex. Beta-catenin forms a cadherin/beta-catenin/alphaE-catenin complex that can tether the tripartite adhesion complex and regulate actin dynamics.-----from InterPro
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| β-catenin | F1QGH7 | IPR013284 | 57.64 kDa | AVVNLINYQDDAELATRAIPELTKLLNDEDQVVVNKAAVMVHQLSKKEASRHAIMRSPQMVSAIVRTMQNTNDVETARCTAGTLHNLSHHREGLLAIFKSGGIPALVKMLGSPVDSVLFYAITTLHNLLLHQEGAKMAVRLAGGLQKMVALLNKTNVKFLAITTDCLQILAYGNQESKLIILASGGPQALVNIMRTYTYEKLLWTTSRVLKVLSVCSSNKPAIVEAGGMQALGLHLTDPSQRLVQNCLWTLRNLSDAATKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKNKMMVCQVGGIEALVRTVLRAGDREDITEPAICALRHLTSRHQEAEMAQNAVRLHYGLPVVVKLLHPPSHWPLIKATVGLIRNLALCPANHAPLREQGAIPRLVQLLVRAHQDTQRRTSMGGTQQQFVEGVRMEEIVEGCTGALHILARDVHNRIVIRGLNTIPLFVQLLYSPIENIQRVAAGVLCELAQDKEAAEAIEAEGATAPLTELLHSRNEGVATYAAAVLFRMS | 1JDH | 30265 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| pUC19-aptamer | 5'-GGACGCGUGGUACCAGGCCGAUCUAUGGACGCUAUAGGCACACCGGAUACUUUAACGAUUGGCUAAGCUUCCGCGGGGAUC-3' | β-catenin | 5 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 |
|---|---|---|---|
| 4R0Z-A | 37.5 | 4.5 | Protein humpback-2 |
| 6KBN-C | 32.6 | 5.9 | Vacuolar protein 8 |
| 7VPT-A | 32.4 | 5.2 | C. glabrata importin alpha arm domain - upc2 nls |
| 3L6X-A | 30.7 | 3.9 | Catenin delta-1 |
| 7JTK-X | 28.8 | 6.4 | Flagellar radial spoke protein 1 |
| 6SA8-A | 27.9 | 20.2 | Ring-like darpin-armadillo fusion h83_d01 |
| 3NMZ-A | 26.0 | 7.2 | Apc variant protein |
| 5XGC-A | 24.9 | 12.3 | Rap1 gtpase-gdp dissociation stimulator 1 |
| 6HB3-B | 21.1 | 3.7 | Protein hgh1 |
| 7Y8R-L | 21.0 | 10.6 | Histone h3 |
References
[1] Modulation of oncogenic transcription and alternative splicing by beta-catenin and an RNA aptamer in colon cancer cells.Lee, H. K., & Jeong, S.
Cancer research, 66(21), 10560–10566. (2006)