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cAMP aptamer
Description
In 2000, Koizumi and Breaker isolated RNA binding to some cAMPs through in vitro selection experiment. Two classes of aptamers were isolated, class I and class II. Class II aptamers, which dominate the final selected RNA population, require divalent cations for complex formation and display a dissociation constant (K(D)) for cAMP of approximately 10 microM. The aptamer recognizes 8,5'-O-cycloadenosine but not N 3’, 5'-cycloadenosine, indicating that this RNA might selectively recognize the anti conformation of the N-glycosidic bond of cAMP[1].SELEX
Koizumi, M., & Breaker, R. R.isolated two classes of RNA aptamers that bind the second messenger adenosine 3′,5′-cyclic by vitro selection， Class II aptamers, which dominate the final selected RNA population, require divalent cations for complex formation and display a dissociation constant (KD) for cAMP of ∼10 µM.The class II aptamer exhibits substantial discrimination against 5′- and 3′-phosphorylated nucleosides such as ATP, 5′-AMP, and 3′-AMP[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 prediction results of the RNA fold website by ribodraw tool to draw.5'-GGAAGAGAUGGCGACUAAAACGACUUGUCGC-3'
Ligand information
SELEX ligand
Cyclic AMP (Cyclic adenosine monophosphate) is a derivative of adenosine triphosphate, an intracellular signalling molecule responsible for directing cellular responses to extracellular signals.-----From MedChemExpress
| Name | Molecular Formula | MW | CAS | Solubility | PubChem | Drug ID |
|---|---|---|---|---|---|---|
| cAMP | C10H12N5O6P | 329.21 g/mol | 60-92-4 | 4 mg/mL | 6076 | DB02527 |
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 |
|---|---|---|---|---|
| ZINC3873977 | Camp | 60-92-4 | 6076 |  |
| ZINC12502230 | (4aR,6R,7S,7aR)-6-(6-aminopurin-9-yl)-2-hydroxy-2-oxo-4a,6,7,7a-tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol | NA | 25322946 |  |
| ZINC4245698 | Adenosin-3',5'-monophosphat | NA | 12071879 |  |
| ZINC3581269 | Cyclic ara-AMP | 32465-18-2 | 6603718 |  |
| ZINC3869451 | (4aS,6R,7S,7aR)-6-(6-aminopurin-9-yl)-2-hydroxy-2-oxo-4a,6,7,7a-tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol | NA | 6604194 |  |
| ZINC3869449 | (4aS,6R,7R,7aR)-6-(6-aminopurin-9-yl)-2-hydroxy-2-oxo-4a,6,7,7a-tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol | NA | 12866365 |  |
| ZINC12502232 | (4aR,6S,7S,7aR)-6-(6-aminopurin-9-yl)-2-hydroxy-2-oxo-4a,6,7,7a-tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol | NA | 25322948 |  |
References
[1] Molecular recognition of cAMP by an RNA aptamer.Koizumi, M., & Breaker, R. R.
Biochemistry, 39(30), 8983–8992. (2000)