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ERα-aptamer
Description
In 2012, Xu et al. identified three high affinity aptamers and characterized one of the AptER-1 in detail. This aptamer interacted with ERα in a way not affected by the presence or absence of either the steroidal ligands or the estrogen response DNA elements, and effectively inhibited ER-mediated transcriptional activation in a breast cancer cell line[1].SELEX
In 2012, Xu et al. identified isolated 3 specific sequences for targeting ERα in a 50nt sequence poolthrough 7 rounds of selection[1].
Detailed information are accessible on SELEX page.
Structure
AptER-1 was the aptamer sequence mainly studied in the article, which had a high affinity with ERα. The 2D structure of the figure is based on the article by ribodraw tool to draw[1].5'-CCACAGUUCAGAGGCACCGCGAACAAAACGCAAGACAGAGUGCCGACAAGAGC-3'
Ligand information
SELEX ligand
The oestrogen receptors (ERs) are steroid or nuclear hormone receptors that act as transcription regulators involved in diverse physiological functions. Oestrogen receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner.-----from Pfam
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Estrogen receptor α (ERα) | P03372 | IPR001292 | 28.86 kDa | SKKNSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAPT | 1ere | AAD52984.1 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| AptER-1 | 5'-CCACAGUUCAGAGGCACCGCGAACAAAACGCAAGACAGAGUGCCGACAAGAGC-3' | Estrogen receptor α (ERα) | 16 nM |
| AptER-2 | 5'-ACACGCGAGAUAGAGCGAGGCCUCCAAAAAUGGCCACGCCAGGAAGCAAGU-3' | Estrogen receptor α (ERα) | 21 nM |
| AptER-1 | 5'-GACCCAGGGCCGGGACGCAAAGCAGCCAAAACAGACGGCCCCAGUCAGGGAGUU-3' | Estrogen receptor α (ERα) | 30 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 |
|---|---|---|---|
| 8JF7-J | 20.6 | 1.9 | Glutamate receptor ionotropic, nmda 1 |
| 4HJJ-H | 20.4 | 1.9 | interleukin-18 |
| 8IQS-H | 20.2 | 5.4 | M11 Vl-sarah |
| 7CEA-A | 19.8 | 5.1 | Huts-4 VH(s112c)-sarah |
| 6OPA-S | 19.7 | 1.3 | Envelope glycoprotein GP160 |
| 7KHF-A | 19.4 | 10.0 | Mdb1 fab heavy chain |
| 6RUL-A | 19.0 | 1.5 | Gfp-lama-f98 a gfp enhancer nanobody with cpdhfr |
| 6XUX-A | 18.3 | 1.8 | Nanobody,glucosidase ygjk,glucosidase ygjk,nanobo |
| 7RGA-E | 17.7 | 1.8 | Nano clostridial antibody mimetic protein 3 VHH |
| 1ETZ-A | 17.7 | 4.0 | Fab nc10.14 - light chain |
References
[1] In search of novel drug target sites on estrogen receptors using RNA aptamers.Xu, D., Chatakonda, VK., Kourtidis, A., Conklin, DS., & Shi, H.
Nucleic Acid Therapeutics,24(3):226-38. (2014)