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RNA22 aptamer
Description
Gary Zhai and Maya Iskandar et al. reported aptamers with affinity for Wilms tumor protein in their article published in 2001[1].SELEX
In their work published in 2001, Gary Zhai and Maya Iskandar et al. used SELEX to isolate RNA aptamer sequences with affinity for wilms tumor protein from a nucleic acid library[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'-GGGGCCACCAACGACAUUGAUAUGGUGACCACCCCGGCGUUGAUAUAAAAUAGUGCCCAUGGAUCCGCGGGUGUCGGG-3'
Ligand information
SELEX ligand
WT1 is a type of transcription factor that plays an important role in cellular development and cell survival. Recognizes and binds to the DNA sequence 5'-GCG(T/G)GGGCG-3'. Regulates the expression of numerous target genes, including EPO. Plays an essential role for development of the urogenital system. It has a tumor suppressor as well as an oncogenic role in tumor formation. Function may be isoform-specific: isoforms lacking the KTS motif may act as transcription factors.-----From Uniprot
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| WT1 | P19544 | PF02165 | 49.188 kDa | MGSDVRDLNALLPAVPSLGGGGGCALPVSGAAQWAPVLDFAPPGASAYGSLGGPAPPPAPPPPPPPPPHSFIKQEPSWGGAEPHEEQCLSAFTVHFSGQFTGTAGACRYGPFGPPPPSQASSGQARMFPNAPYLPSCLESQPAIRNQGYSTVTFDGTPSYGHTPSHHAAQFPNHSFKHEDPMGQQGSLGEQQYSVPPPVYGCHTPTDSCTGSQALLLRTPYSSDNLYQMTSQLECMTWNQMNLGATLKGVAAGSSSSVKWTEGQSNHSTGYESDNHTTPILCGAQYRIHTHGVFRGIQDVRRVPGVAPTLVRSASETSEKRPFMCAYPGCNKRYFKLSHLQMHSRKHTGEKPYQCDFKDCERRFSRSDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTHTGKTSEKPFSCRWPSCQKKFARSDELVRHHNMHQRNMTKLQLAL | 2PRT | U06486.1 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| RNA20 aptamer | 5'-GGGGCCACCAACGACAUUGACGAAUGCGUAAAUUGCUAGGUUGAUAUUAAAUAGUGCCCAUGGAUCCGCGGGUGUCGGG-3' | WT1-ZFP | 87.4 ± 10.4 nM |
| RNA22 aptamer | 5'-GGGGCCACCAACGACAUUGAUAUGGUGACCACCCCGGCGUUGAUAUAAAAUAGUGCCCAUGGAUCCGCGGGUGUCGGG-3' | WT1-ZFP | 13.8 ± 1.1 nM |
| RNA38 aptamer | 5'-GGGGCCACCAACGACAUUAUCACCCACCCCGAGCUGGCGUUGAUAUAAAAUAGUGCCCAUGGAUCCGCGGGUGUCGGG-3' | WT1-ZFP | 17.8 ± 1.4 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 |
|---|---|---|---|
| 7W1M-H | 9.9 | 5.2 | Structural maintenance of chromosomes protein 1A |
| 6JNM-A | 9.4 | 2.5 | Lysine-specific demethylase Ref6 |
| 7Y3M-C | 7.6 | 2.4 | DNA (16-mer) |
| 4GZN-C | 7.5 | 2.0 | DNA (5'-d(*tp*ap*tp*tp*gp*cp*(5cm)p*gp*cp*ap*g)-3 |
| 8FFZ-A | 7.4 | 5.0 | Transcription factor IIIA |
| 1LLM-C | 7.0 | 6.7 | 5'-D(*tp*cp*cp*cp*ap*cp*gp*cp*gp*tp*gp*gp*g)-3' |
| 8GN3-B | 7.0 | 2.9 | Zinc finger and btb domain-containing protein 10 |
| 2LT7-A | 6.7 | 3.2 | Transcriptional regulator kaiso |
| 2DRP-D | 4.5 | 2.4 | DNA (5'- |
| 2EN2-A | 2.6 | 3.5 | B-cell lymphoma 6 protein |
References
[1] Characterization of RNA aptamer binding by the Wilms' tumor suppressor protein WT1.Zhai, G., Iskandar, M., Barilla, K., & Romaniuk, P. J.
Biochemistry, 40(7), 2032–2040. (2001)