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CED-9 aptamer
Description
In 2006, Yang, C. et al. used a technique known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX), RNA molecules with high affinity and specificity for the Caenorhabditis elegans Bcl-2 family member CED-9 were successfully isolated. Subsequent studies were conducted to evaluate the impact of these RNA aptamers on the regulation of programmed cell death within the C. elegans model organism[1].SELEX
An RNA library was generated in vitro using an oligonucleotide library that contains a central region of 49 randomized nucleotides flanked at both ends by constant sequences and a bacterial T7 promoter for in vitro transcription. For the first round of SELEX ∼1015 unique sequences were represented. Each round of SELEX consisted of the following steps. CED-9/RNA complexes were recovered and reverse transcribed to cDNAs, which were then PCR-amplified to generate a new oligonucleotide library enriched in DNAs encoding RNAs with higher binding affinity for CED-9. After nine rounds of SELEX, obtained a pool of RNA molecules that bound CED-9 with high affinity. From the last two rounds of SELEX, identified a total of 12 different aptamers that bind CED-9[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figures is based on the prediction results of the RNA fold website by ribodraw tool to draw[1].R9-2 aptamer: 5'-AGGGAGGACGAUGCGGGGUGCUUCGAGCGUAGGAAGAAAGCCGGGGGCUGCAGAUAAUGUAUAGCCAGACGACGGA-3'
R9-7 aptamer: 5'-AGGGAGGACGAUGCGGGAUGGACGCUUAUCCGCAUAGAGGUUUACUACUUCGGAGACUGCCGAUACAGACGACGGA-3'
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Ligand information
SELEX ligand
Cell death abnormality gene 9 (CED-9), also known as apoptosis regulator CED-9, is a gene found in Caenorhabditis elegans that inhibits/represses programmed cell death (apoptosis). The gene was discovered while searching for mutations in the apoptotic pathway after the discovery of the apoptosis promoting genes CED-3 and CED-4. The gene gives rise to the apoptosis regulator CED-9 protein found as an Integral membrane protein in the mitochondrial membrane. The protein is homologous to the human apoptotic regulator Bcl-2 as well as all other proteins in the Bcl-2 protein family. CED-9 is involved in the inhibition of CED-4 which is the activator of the CED-3 caspase. Because of the pathway homology with humans as well as the specific protein homology, CED-9 has been used to represent the human cell apoptosis interactions of Bcl-2 in research.-----From WiKi
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| CED-9 | P41958 | IPR016854 | 31.82 KDa | MTRCTADNSLTNPAYRRRTMATGEMKEFLGIKGTEPTDFGINSDAQDLPSPSRQASTRRMSIGESIDGKINDWEEPRLDIEGFVVDYFTHRIRQNGMEWFGAPGLPCGVQPEHEMMRVMGTIFEKKHAENFETFCEQLLAVPRISFSLYQDVVRTVGNAQTDQCPMSYGRLIGLISFGGFVAAKMMESVELQGQVRNLFVYTSLFIKTRIRNNWKEHNRSWDDFMTLGKQMKEDYERAEAEKVGRRKQNRRWSMIGAGVTAGAIGIVGVVVCGRMMFSLK | 2A5Y | 3565776 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| R9-2 aptamer | 5'-AGGGAGGACGAUGCGGGGUGCUUCGAGCGUAGGAAGAAAGCCGGGGGCUGCAGAUAAUGUAUAGCCAGACGACGGA-3' | CED-9 | ~4 nM |
| R9-7 aptamer | 5'-AGGGAGGACGAUGCGGGAUGGACGCUUAUCCGCAUAGAGGUUUACUACUUCGGAGACUGCCGAUACAGACGACGGA-3' | CED-9 | ~16 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 |
|---|---|---|---|
| 2A5Y-A | 35.1 | 0.0 | Apoptosis regulator ced-9 |
| 6V4M-A | 15.7 | 2.8 | Bcl-2 |
| 6LHD-B | 15.5 | 2.3 | Fusion protein of Bcl-2-like protein1 and isofor |
| 1LXL-A | 13.3 | 3.3 | Bcl-xl |
| 7JMT-C | 12.9 | 2.7 | Bcl-2 protein |
| 2MHS-A | 12.7 | 2.7 | Anduced myeloid leukemia cell differentiation pro |
| 5UA5-A | 11.8 | 2.9 | 5-hl |
| 5W60-A | 11.0 | 3.1 | Apoptosis regulator bax |
| 6TQP-A | 10.5 | 3.0 | 16l protein |
| 5TWA-A | 10.4 | 3.2 | Bcl-x homologous protein, bhp2 |
References
[1] RNA aptamers targeting the cell death inhibitor CED-9 induce cell killing in Caenorhabditis elegans.Yang, C., Yan, N., Parish, J., Wang, X., Shi, Y., & Xue, D.
The Journal of biological chemistry, 281(14), 9137–9144. (2006)