cAMP aptamer

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Description

In 2000, Koizumi, M. and Breaker, R. R. isolated RNA aptamers binding to cAMPs through in vitro selection experiment. Two classes of RNA aptamers that bind the second messenger adenosine 3',5'-cyclic monophosphate (cAMP; 1) were isolated from a random-sequence pool using in vitro selection. Class I and class II aptamers are formed by 33- and 31-nucleotide RNAs, respectively, and each is comprised of similar stem-loop and single-stranded structural elements. 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[1].



SELEX

Koizumi, M. and Breaker, R. R. used SELEX to isolate two classes of RNA aptamers from a random-sequence pool containing 50 nucleotides of random sequence. After four rounds of selection, more than 20% of the RNA population bound to the cAMP-derivatized column matrix and was subsequently eluted with 4 mM cAMP. Further analysis revealed that the final selected RNA population was dominated by class II aptamers, which require divalent cations for complex formation and display a dissociation constant (KD) for cAMP of ∼10 µM[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 prediction results of the RNA fold website by ribodraw tool to draw. cAMP-b aptamer was named by Koizumi, M. and Breaker, R. R[1].

5'-GGAAGAGAUGGCGACUAAAACGACUUGUCGC-3'

drawing

Ligand information

SELEX ligand

Cyclic adenosine monophosphate (cAMP, cyclic AMP, or 3',5'-cyclic adenosine monophosphate) is a second messenger, or cellular signal occurring within cells, that is important in many biological processes. cAMP is a derivative of adenosine triphosphate (ATP) and used for intracellular signal transduction in many different organisms, conveying the cAMP-dependent pathway.-----From Wiki

PubChem CID: a unique identifier for substances in the PubChem database.

CAS number: a global registry number for chemical substances.

Drugbank: a comprehensive database with detailed information on drugs and drug targets.

Name Molecular Formula Molecular Weight CAS Solubility PubChem Drugbank ID
cAMP C10H12N5O6P 329.21 g/mol 60-92-4 4 mg/mL 6076 DB02527
drawing

Similar compound(s)

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: a compound identifier used by the ZINC database, one of the largest repositories for virtual screening of drug-like molecules.

PubChem CID: a unique identifier for substances in the PubChem database.

CAS number: a global registry number for chemical substances.

ZINC ID Name CAS Pubchem CID Structure
ZINC3873977 Camp 60-92-4 6076 drawing
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 drawing
ZINC4245698 Adenosin-3',5'-monophosphat NA 12071879 drawing
ZINC3581269 Cyclic ara-AMP 32465-18-2 6603718 drawing
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 drawing
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 drawing
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 drawing


References

[1] Molecular recognition of cAMP by an RNA aptamer.
Koizumi, M., & Breaker, R. R.
 Biochemistry, 39(30), 8983–8992. (2000)