FB-1 aptamer

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Description

In 1998, Wilson, C. 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. In vitro tests showed that FB-1 can efficiently sequester fluorescein from solution and concentrate it, with minimal cross-binding to sulforhodamine[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. It was isolated through mutagenesis of a sulforhodamine aptamer followed by re-selection. From this collection, FB-1 was identified as a clone that exhibited high-efficiency binding to fluorescein and minimal cross-binding to sulforhodamine[1].

Detailed information are accessible on SELEX page.



Structure

The 2D structure of the figure is based on the article by online secondary structure prediction tool to draw. The figure shows the secondary structure prediction of the original aptamer sequence. The acquisition of this aptamer underwent a second round of screening. It consists of three stem loops of different lengths connected through junction. All three stem loops contain U-G non-classical pairings. The FB-1 aptamer was named by Wilson, C. et al. in the article[1].

5'-GGACGGCACCACGGUCGGAUCCGUGAGUUGUGACAAUUUAGCGGGUGGUAUUAGAGCCUACUGCCACAGCAAUAGGAUCGAUACAGAUCU-3'

drawing


Ligand information

SELEX ligand

Fluorescein sodium is used extensively as a diagnostic tool in the field of ophthalmology. Fluorescein is a fluorescent compound or fluorophore having a maximum absorbance of 494 m and an emission maximum of 521 nm. The yellowish-green fluorescence of the compound can be used to demarcate the vascular area under observation, distinguishing it from adjacent areas. It is applied topically in the form of a drop or it can be injected intravenously to produce a fluorescein angiogram.-----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
FB-1 RNA aptamer C20H12O5 332.3 g/mol 2321-07-5 83.33 mg/mL in DMSO 16850 DB00693
drawing drawing

Similar compound(s)

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: 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
ZINC3872582 Fluorescein 518-47-8,
2321-07-5,
72088-94-9		 16850 drawing
ZINC5847030 Fluorescin 518-44-5 68205 drawing
ZINC4261850 Dichlorofluorescein 76-54-0,
263400-88-0		 64944 drawing
ZINC3831317 Phenolphthalein 77-09-8,
62625-16-5		 4764 drawing
ZINC15020070 ((3R)-3'-hydroxy-6'-methoxyspiro[2-benzofuran-3,9'-xanthene]-1-one) 65144-30-1 26369045 drawing
ZINC5863605 NA NA NA drawing
ZINC6756692 5-Aminofluorescein 3326-34-9,
27599-63-9		 76845 drawing
ZINC43199397 ((3S)-3'-amino-6'-hydroxyspiro[2-benzofuran-3,9'-xanthene]-1-one) NA 93948834 drawing
ZINC4506036 6-Aminofluorescein 51649-83-3 103924 drawing


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)