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Okra aptamer
Description
In 2024, Fangting Zuo and Li Jiang et al. employed in vitro selection techniques to isolate aptamers with high-affinity binding sites for ACE. The aptamer binds the fluorophore with high affinity. Favorable features of ACE together contribute to the high photostability of Okra-ACE complex[1].SELEX
SELEX was performed with a library containing ~1014 random RNA molecules and selected RNAs for their ability to bind bind and activate the fuorophore ligand ACE to emit bright green fuorescence. After SELEX, researchers selected a number of sequences, including Okra, 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.5'-CGGGGACCAUCCAGCGAUGGAUACUGCUGCUUCGGCAGAGCAAGGAUAAUAUCUAGAACGACCAUCCG-3'
Ligand information
SELEX ligand
3-(2,3,6,7-tetrahydro-1H,5H-pyrido(3,2,1-ij)quinolin-9-yl)acrylamide- 2-cyano-N-(2-(2-aminoethoxy) ethyl) (ACE) was a non-GFP-like fluorophore, a hydrophilic derivative of 9-(2-carboxy-2-cyanovinyl) julolidine molecule rotor that has low fluorescence in solution.-----From PMID: 38783134| Name | Molecular Formula | MW | CAS | Solubility | PubChem | Drug ID |
|---|---|---|---|---|---|---|
| ACE | C20H26N4O2 | 354.4 g/mol | NA | NA | 170898143 | NA |
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. For another compound, we used a similar compound query method from the PubChem database.
| Zinc_id | Named | CAS | Pubchem CID | Structure |
|---|---|---|---|---|
| NA | N-(2-(2-Aminoethoxy)ethyl)-2-cyano-3-(1,2,3,5,6,7-hexahydropyrido[3,2,1-ij]quinolin-9-yl)acrylamide | NA | 170898143 |  |
| NA | (E)-3-(1-azatricyclo[7.3.1.05,13]trideca-5,7,9(13)-trien-7-yl)-2-cyano-N-[2-[(2,2,2-trifluoroacetyl)amino]oxyethyl]prop-2-enamide | NA | 156684979 |  |
| ZINC14879905 | N-[(1-methyl-1,2,3,4-tetrahydro-6-quinolinyl)methyl]-6-(4-morpholinylmethyl)-2-oxo-1,2-dihydro-3-pyridinecarboxamide | NA | 26275887 |  |
| ZINC209173648 | (E)-3-(1-azatricyclo[7.3.1.05,13]trideca-5,7,9(13)-trien-7-yl)-2-cyano-N-methylprop-2-enamide | NA | 59401066 |  |
| ZINC202676737 | 6-Methyl-1-(2-morpholin-4-ylethyl)-2-oxo-4-piperazin-1-ylquinoline-3-carbonitrile | NA | 59740520 |  |
| NA | 3-acetamidopropyl (E)-3-(1-azatricyclo[7.3.1.05,13]trideca-5,7,9(13)-trien-7-yl)-2-cyanoprop-2-enoate | NA | 121464698 |  |
| NA | (E)-3-(1-azatricyclo[7.3.1.05,13]trideca-5,7,9(13)-trien-7-yl)-2-cyano-N-pentylprop-2-enamide | NA | 121464699 |  |
| NA | (E)-3-(1-azatricyclo[7.3.1.05,13]trideca-5,7,9(13)-trien-7-yl)-N-[2-[2-(6-chlorohexoxy)ethoxy]ethyl]-2-cyanoprop-2-enamide | NA | 154615008 |  |
| NA | tert-butyl N-[2-[[(E)-3-(1-azatricyclo[7.3.1.05,13]trideca-5,7,9(13)-trien-7-yl)-2-cyanoprop-2-enoyl]amino]ethoxy]carbamate | NA | 156376202 |  |
References
[1] Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA.Zuo, F., Jiang, L., Su, N., Zhang, Y., Bao, B., Wang, L., Shi, Y., Yang, H., Huang, X., Li, R., Zeng, Q., Chen, Z., Lin, Q., Zhuang, Y., Zhao, Y., Chen, X., Zhu, L., & Yang, Y.
Nature chemical biology, 10.1038/s41589-024-01629-x. (2024)