Adenine aptamer

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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 SELEX technology to screen for RNA aptamers capable of binding to adenine. They started with a pool of RNA containing a random sequence of 50 nucleotides. After 12 rounds of selection using an adenine-agarose affinity chromatography column, the RNA sequences that bound to adenine were eluted, and 18 different high-affinity RNA aptamers were identified through cloning and sequencing[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. RNA 12 E4 aptamer binding to Adenine. RNA 12 E4 aptamer was named by Maurel, M. C[1].

5'-GGGAGAGGAUACUACACGUGAUAGGACGAUUAUCGAAAAUCACCAGAUUGGACCCUGGUUAACGAUCCAUUGCAUGUAGCAGAAGCUUCCG-3'

drawing

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

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
Adenine C5H5N5 135.13 g/mol 73-24-5 1030mg/L (at 25 °C) 190 DB00173
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
ZINC882 Adenine 73-24-5 190 drawing
ZINC13544284 2-Azaadenine 2308-56-7 5480214 drawing
ZINC18188160 1H-imidazo[4,5-c]pyridin-4-amine 6811-77-4 418745 drawing
ZINC669370153 7-methyl-1H-imidazo[4,5-b]pyridin-6-amine NA 118094694 drawing
ZINC255987181 CID 76852915 NA 76852915 drawing
ZINC12503143 1-methyl-9H-purin-6-amine NA 444453 drawing
ZINC13518237 4-Amino-7H-pyrrolo[2,3-d]pyrimidine 1500-85-2 5359620 drawing


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)