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bG40min aptamer
Description
Donald H Burke et al. screened Boron-containing aptamers to ATP, suggesting that boronated nucleotides could be used to develop boronated RNA ligands for boron neutron capture therapy with potential therapeutic applications[1].SELEX
Burke DH et al. constructed an RNA library containing 70 random nucleotides by an in vitro transcription method and performed 7 to 10 rounds of screening using the SELEX technique for RNA aptamers capable of specifically binding ATP. During the screening process, some of the RNAs were synthesized with boron-containing nucleotide analogs, bG or bU, instead of normal GTP or UTP. Ultimately, the investigators identified aptamers containing the ζ-structure from the bU and control pools, while this structure was not found in the bG pool. In particular, the ATP-binding specificity of the bG40min aptamer was verified by affinity chromatography experiments, which involved the use of different concentrations of ATP and its analogs to assess its binding and elution properties[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. The 2D structure of the figure is based on the article by ribodraw tool to draw. bG40min aptamer binding to ATP.5'-GGGAAAAGCGAAUCAUACACAAGAUUCACUCUACACCCAUGUCCCUAGGACUACAGGUUAACUACAAACCUCGAUCCGGUGCUUAGGGUGUGCUGG-3'
Ligand information
SELEX ligand
ATP is an adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways. It has a role as a nutraceutical, a micronutrient, a fundamental metabolite and a cofactor. It is an adenosine 5'-phosphate and a purine ribonucleoside 5'-triphosphate. It is a conjugate acid of an ATP(3-).-----From ChEBI| Name | Molecular Formula | MW | CAS | Solubility | PubChem | Drug ID |
|---|---|---|---|---|---|---|
| ATP (Adenosine 5'-triphosphate) | C10H16N5O13P3 | 507.18 g/mol | 56-65-5 | 10000mg/L (at 20 °C) | 5957 | DB00131 |
Similar compound
We used the PubChem database to screen compounds that were more similar to ATP, and selected the most similar compounds for display. For those without CAS numbers, we will supplement them with Pubchem CID.
| Named | CAS | Pubchem CID | Structure |
|---|---|---|---|
| Vidarabine Phosphate | 29984-33-6 | 34768 |  |
| Alpha-Methylene Adenosine Monophosphate | NA | 46936495 |  |
| 6-Chloropurine Riboside, 5'-Monophosphate | NA | 70789235 |  |
| 6-Thioinosine-5'-Monophosphate | 53-83-8 | 3034391 |  |
| 6-Methylthiopurine 5'-Monophosphate Ribonucleotide | 7021-52-5 | 3037883 |  |
| Fludarabine | 21679-14-1 | 657237 |  |
References
[1] Boron-containing aptamers to ATP.Lato SM, Ozerova ND, He K, Sergueeva Z, Shaw BR, Burke DH
Nucleic acids research. 2002 Mar 15;30(6):1401-7. (2002)