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rafl7s aptamer
Description
In 2000, Ellington, A. D. et al. had therefore attempted to develop selection methods that couple the broad molecular recognition properties of aptamers with signal transduction. Anti-adenosine aptamers were selected from a pool that was skewed to contain very few fluoresceinated uridines. The primary family of aptamers showed a doubling of relative fluorescence intensity at saturating concentrations of a cognate analyte, ATP, and could sense ATP concentrations as low as 25 microM. A single uridine was present in the best signaling aptamer[1].
SELEX
Ellington, A. D. et al. used SELEX to select fluorescently labelled aptamers from a pool skewed to contain very few fluoresceinated uridines. After 11 rounds of selection and amplification, the primary family of aptamers exhibited a doubling of relative fluorescence intensity at saturating concentrations of ATP and could sense ATP concentrations as low as 25 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 article by ribodraw tool to draw. rafl7-U61C aptamer was named by Ellington, A. D[1].
5'-GGAAGGCACGACGAAGCAAGCAGGCAACGAACACAGAAGACCGGGGGAACUACCGCGCGCGCCAGACCCAACCAGCCAGAGACC-3'
Ligand information
SELEX ligand
An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.-----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 |
|---|---|---|---|---|---|---|
| ATP | C10H16N5O13P3 | 507.18 g/mol | 56-65-5 | 1000.0 mg/mL | 5957 | DB00171 |
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: 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 |
|---|---|---|---|---|
| ZINC000002126310 | Vidarabine Phosphate | 29984-33-6 | 34768 |  |
| ZINC000053684016 | Alpha-Methylene Adenosine Monophosphate | NA | 46936495 |  |
| ZINC000053684213 | 6-Chloropurine Riboside, 5'-Monophosphate | NA | 70789235 |  |
| ZINC000004096488 | 6-Thioinosine-5'-Monophosphate | 53-83-8 | 3034391 |  |
| ZINC000013543089 | 6-Methylthiopurine 5'-Monophosphate Ribonucleotide | 7021-52-5 | 3037883 |  |
| ZINC000003927870 | Fludarabine | 21679-14-1 | 657237 |  |
| ZINC000013543718 | Vidarabine Phosphoric Acid | NA | 22840996 |  |
| ZINC000001631259 | 3'-Adenylic acid | 84-21-9 | 41211 |  |
References
[1] In vitro selection of signaling aptamers.Jhaveri, S., Rajendran, M., & Ellington, A. D.
Nature biotechnology, 18(12), 1293–1297. (2000)