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Adenine aptamer
Description
In 2002, Meli and Décout discovered that the adenine binding site consists of two separate secondary structure elements forming a two-part binding site that interacts with adenine in a novel manner of purine recognition[1].SELEX
Meli and Décout used an in vitro screening technique, starting with a pool of RNA opened with a random sequence of 50 nucleotides, and after 12 rounds of screening, cloning resulted in 18 different sequences[1].
Detailed information are accessible on SELEX page.
Structure
The sequence and secondary prediction structure of the aptamer will be shown here, here we used ribodraw to complete the figure. In addition, an analytical affinity column was run under isocratic conditions to determine an approximate dissociation constant (Kd) for the RNA-ligand interaction. The 2D structure of the figure is based on the article by ribodraw tool to draw. We used the minimum free energy (MFE) structure. RNA 12 E4 aptamer binding to Adenine.5'-GGGAGAGGAUACUACACGUGAUAGGACGAUUAUCGAAAAUCACCAGAUUGGACCCUGGUUAACGAUCCAUUGCAUGUAGCAGAAGCUUCCG-3'
Ligand information
SELEX ligand
Adenine is a purine base which forms a component of DNA among other functions and is present in many multivitamins.-----From Drugbank
| Name | Molecular Formula | MW | CAS | Solubility | PubChem | Drug ID |
|---|---|---|---|---|---|---|
| Adenine | C5H5N5 | 135.13 g/mol | 73-24-5 | 1030mg/L (at 25 °C) | 190 | DB00173 |
Similar compound
We screened the compounds with great similarity to by using the ZINC database and showed some of the compounds' structure diagrams. For some CAS numbers not available, we will supplement them with Pubchem CID. For another compound, we used a similar compound query method from the PubChem database.
| Zinc_id | Named | CAS | Pubchem CID | Structure |
|---|---|---|---|---|
| ZINC882 | Adenine | 73-24-5 | 190 |  |
| ZINC13544284 | 2-Azaadenine | 2308-56-7 | 5480214 |  |
| ZINC18188160 | 1H-imidazo[4,5-c]pyridin-4-amine | 6811-77-4 | 418745 |  |
| ZINC669370153 | 7-methyl-1H-imidazo[4,5-b]pyridin-6-amine | NA | 118094694 |  |
| ZINC255987181 | CID 76852915 | NA | 76852915 |  |
| ZINC12503143 | 1-methyl-9H-purin-6-amine | NA | 444453 |  |
| ZINC13518237 | 4-Amino-7H-pyrrolo[2,3-d]pyrimidine | 1500-85-2 | 5359620 |  |
References
[1] Adenine-aptamer complexes: a bipartite RNA site that binds the adenine nucleic base.Meli, M., Vergne, J., Décout, J. L., & Maurel, M. C.
The Journal of biological chemistry, 277(3), 2104–2111. (2002)