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FB-1 aptamer
Description
In 1998, Leslie A Holeman et al. employed in vitro selection techniques to isolate aptamers with high-affinity binding sites for Fluorescein. The aptamer binds the fluorophore with high affinity, recognizing both the planar aromatic ring system and a negatively charged sulfonate, a rare example of anion recognition by RNA[1].SELEX
SELEX was performed with a library containing ~5×1014 random RNA molecules and selected RNAs for their ability to bind Fluorescein. After SELEX, researchers selected a number of sequences, including FB-1, to characterize their affinity for the dye and its spectral properties[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figure is based on the article by ribodraw tool to draw[1].5'-GGACGGCACCACGGUCGGAUCCGUGAGUUGUGACAAUUUAGCGGGUGGUAUUAGAGCCUACUGCCACAGCAAUAGGAUCGAUACAGAUCU-3'
Ligand information
SELEX ligand
The Kd for sulforhodamine was determined both in solution and following immobilization on a solid support. The increase in fluorophore anisotropy, presumed to result from the change in rotational diffusion accompanying complex formation, may be accurately modeled using a simple hyperbolic function. The amount of aptamer bound as a function of ligand concentration (accessible packed bead concentration corrected for dilution) was fit by a non-linear least squares method using Kaliedagraph (Abelbeck Software) to a function of the form: % bound = f × [SR] / (KD + [SR]), where f is the fraction of RNA properly folded, [SR] is the accessible immobilized fluorophore concentration, and Kd is the dissociation constant for binding immobilized ligand.| Name | Molecular Formula | MW | CAS | Solubility | PubChem | Drug ID |
|---|---|---|---|---|---|---|
| FB-1 RNA aptamer | C20H12O5 | 332.3 g/mol | 2321-07-5 | 83.33 mg/mL in DMSO | 16850 | DB00693 |
Similar compound
We screened the compounds with great similarity 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.
| Zinc_id | Named | CAS | Pubchem CID | Structure |
|---|---|---|---|---|
| ZINC3872582 | Fluorescein | 518-47-8, 2321-07-5, 72088-94-9 | 16850.0 |  |
| ZINC5847030 | Fluorescin | 518-44-5 | 68205.0 |  |
| ZINC4261850 | Dichlorofluorescein | 76-54-0, 263400-88-0 | 64944.0 |  |
| ZINC3831317 | Phenolphthalein | 77-09-8, 62625-16-5 | 4764.0 |  |
| ZINC15020070 | ((3R)-3'-hydroxy-6'-methoxyspiro[2-benzofuran-3,9'-xanthene]-1-one) | 65144-30-1 | 26369045.0 |  |
| ZINC5863605 | NA | NA | NA |  |
| ZINC6756692 | 5-Aminofluorescein | 3326-34-9, 27599-63-9 | 76845.0 |  |
| ZINC43199397 | ((3S)-3'-amino-6'-hydroxyspiro[2-benzofuran-3,9'-xanthene]-1-one) | nan | 93948834.0 |  |
| ZINC4506036 | 6-Aminofluorescein | 51649-83-3 | 103924.0 |  |
References
[1] Isolation and characterization of fluorophore-binding RNA aptamers.Holeman, L. A., Robinson, S. L., Szostak, J. W., & Wilson, C.
Folding & design, 3(6), 423–431. (1998)