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RANK aptamer
Description
In 2004, Mori Tadashi and Oguro Akihiro had used the SELEX methodology to select RNA aptamers with high affinity for RANK by in vitro RNA selection-amplification[1].SELEX
In 2004, Mori Tadashi and colleagues used existing research to design the method required for the in vitro genetic-selection. Starting from a RNA pool that had a sequence of 40 random nucleotide positions, aptamers that bind specifically to RANK were selected after 10 rounds of selection and amplification. The aptamer, apt1, can bind specifically to RANK were selected with high affinity[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'-GGGACACAAUGGACGGAUUCGUAUGGGUGGGAUCGGGAAGGGCUACGAACACCGUAACGGCCGACAUGAGAG-3'
Ligand information
SELEX ligand
Receptor for TNFSF11/RANKL/TRANCE/OPGL; essential for RANKL-mediated osteoclastogenesis. Its interaction with EEIG1 promotes osteoclastogenesis via facilitating the transcription of NFATC1 and activation of PLCG2. Involved in the regulation of interactions between T-cells and dendritic cells.-----From Pfam
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| RANK(TNFRSF11A ) | Q9Y6Q6 | PF18278 | 66.034 kDa | MAPRARRRRPLFALLLLCALLARLQVALQIAPPCTSEKHYEHLGRCCNKCEPGKYMSSKCTTTSDSVCLPCGPDEYLDSWNEEDKCLLHKVCDTGKALVAVVAGNSTTPRRCACTAGYHWSQDCECCRRNTECAPGLGAQHPLQLNKDTVCKPCLAGYFSDAFSSTDKCRPWTNCTFLGKRVEHHGTEKSDAVCSSSLPARKPPNEPHVYLPGLIILLLFASVALVAAIIFGVCYRKKGKALTANLWHWINEACGRLSGDKESSGDSCVSTHTANFGQQGACEGVLLLTLEEKTFPEDMCYPDQGGVCQGTCVGGGPYAQGEDARMLSLVSKTEIEEDSFRQMPTEDEYMDRPSQPTDQLLFLTEPGSKSTPPFSEPLEVGENDSLSQCFTGTQSTVGSESCNCTEPLCRTDWTPMSSENYLQKEVDSGHCPHWAASPSPNWADVCTGCRNPPGEDCEPLVGSPKRGPLPQCAYGMGLPPEEEASRTEARDQPEDGADGRLPSSARAGAGSGSSPGGQSPASGNVTGNSNSTFISSGQVMNFKGDIIVVYVSQTSQEGAAAAAEPMGRPVQEETLARRDSFAGNGPRFPDPCGGPEGLREPEKASRPVQEQGGAKA | 1LB5 | 8792 |
The aptamer bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| apt1 | 5'-GGGACACAAUGGACGGAUUCGUAUGGGUGGGAUCGGGAAGGGCUACGAACACCGUAACGGCCGACAUGAGAG-3' | RANK(TNFRSF11A ) | 0.33 uM |
| apt2 | 5'-GGGACACAAUGGACGAUAUGGUAUUGAGGUGGGAAGGGGAUUGGGAUAAUUGCCAUAACGGCCGACAUGAGAG-3' | RANK(TNFRSF11A ) | 1.8 uM |
| apt3 | 5'-GGGACACAAUGGACGAUAGUGGUUGGGAUUGGGUGGGCGCACAAGUUGUUCCGUUAACGGCCGACAUGAGAG-3' | RANK(TNFRSF11A ) | 5.8 uM |
References
[1] RNA aptamers selected against the receptor activator of NF-kappaB acquire general affinity to proteins of the tumor necrosis factor receptor family.Mori T, Oguro A, Ohtsu T, Nakamura Y.
Nucleic Acids Res. 32(20):6120-8. (2004)