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Wilms tumor protein aptamer
Description
Romaniuk, P. J. et al. reported aptamers with affinity for Wilms tumor protein in their article published in 2001. The RNA22 aptamer was named by Romaniuk, P. J. et al. in the article[1].
SELEX
In their work published in 2001, Romaniuk, P. J. et al. used SELEX to isolate RNA aptamer sequences with affinity for wilms tumor protein from a nucleic acid library. Recombinant proteins were expressed by inducing log-phase E. coli[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figure is based on the article by online secondary structure prediction tool to draw. The figure shows the secondary structure prediction of the original aptamer sequence. This aptamer contains two stem loops of different lengths. It is speculated that the two paired regions closer to the two ends of the nucleic acid chain are coaxial[1].
5'-GGGGCCACCAACGACAUUGAUAUGGUGACCACCCCGGCGUUGAUAUAAAAUAGUGCCCAUGGAUCCGCGGGUGUCGGG-3'
Ligand information
SELEX ligand
Wilms tumor protein (WT1) is a type of transcription factor that plays an important role in cellular development and cell survival. WT1 recognizes and binds to the DNA sequence 5'-GCG(T/G)GGGCG-3' and regulates the expression of numerous target genes, including EPO. Wilms tumor protein plays an essential role for development of the urogenital system. It has a tumor suppressor as well as an oncogenic role in tumor formation. Its function may be isoform-specific: isoforms lacking the KTS motif may act as transcription factors.-----From Uniprot
UniProt ID: uniquely identifies protein sequences in the UniProt database, a resource for protein information.
Pfam: a widely recognised database of protein families and domains.
GenBank: maintained by NCBI(National Center for Biotechnology Information), is a database of nucleotide sequences from various organisms, vital for genetic and molecular biology research.
Mass: an intrinsic property of a body.
| Name | Uniprot ID | Pfam | Mass | Protein sequence | PDB ID | GenBank |
|---|---|---|---|---|---|---|
| WT1 | P19544 | PF02165 | 49.188 kDa |
......
MGSDVRDLNALLPAVPSLGGGGGCALPVSGAAQWAPVLDFAPPGASAYGSLGGPAPPPAPPPPPPPPPHSFIKQEPSWGGAEPHEEQCLSAFTVHFSGQFTGTAGACRYGPFGPPPPSQASSGQARMFPNAPYLPSCLESQPAIRNQGYSTVTFDGTPSYGHTPSHHAAQFPNHSFKHEDPMGQQGSLGEQQYSVPPPVYGCHTPTDSCTGSQALLLRTPYSSDNLYQMTSQLECMTWNQMNLGATLKGVAAGSSSSVKWTEGQSNHSTGYESDNHTTPILCGAQYRIHTHGVFRGIQDVRRVPGVAPTLVRSASETSEKRPFMCAYPGCNKRYFKLSHLQMHSRKHTGEKPYQCDFKDCERRFSRSDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTHTGKTSEKPFSCRWPSCQKKFARSDELVRHHNMHQRNMTKLQLAL
|
2PRT | U06486.1 |
Some isolated sequences bind to the affinity of the protein[1].
| 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(s)
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.
Dail server website: a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB).
Z-score: 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) is used to measure the degree to which atoms deviate from the alignment position.
PDB: PDB ID+ chain name.
| PDB | Z-socre | RMSD (Å) | Description |
|---|---|---|---|
| 2PRT-A | 15.5 | 0 | Original chain |
| 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)