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Clivias aptamer
Description
In a work published in 2023, Li Jiang and Xin Xie et al. isolated an RNA aptamer, named Clivias, which binds NBSI and transform its optical properties. Later, in a work published in 2024 by Kaiyi Huang and others, the structure of the Clivias-NBSI derivates complex is analyzed by crystallization, diffraction data collection[1,2].SELEX
SELEX was performed with a library and selected RNAs for their ability to bind NBSI derivates. The selection process went through 8 rounds. After SELEX, researchers selected a number of sequences, including Clivias, to characterize their affinity for the dye and its spectral properties[1].
Detailed information are accessible on SELEX page.
Structure
2D representation
Here we used Ribodraw to complete the figure, through the 3D structure information. Spinach aptamer was the aptamer sequence mainly studied in SELEX article[1].
5'-AGAUUGUAAACACGCCGAAGGCGGACACU-3'
3D visualisation
Kaiyi Huang and Qianqian Song et al. present the solution structure, as determined by crystallization and diffraction data collection of Clivias-NBSI complex. The PDB ID of these structures are 8HZE[2].The corresponding structures are being held for release.Additional available structures that have been solved and detailed information are accessible on Structures page.
(Clicking the "Settings/Controls info" to turn Spin off)
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Binding pocket
Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 4TS0 by NMR and X-ray crystallography. DFHBI(shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with DFHBI or other nucleotides surround small molecules.
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Ligand information
SELEX ligand
To determine the dissociation constants of Clivia with different fluorophores, 20 nM Clivia RNA was incubated with increasing concentrations of the fluorophore (0–5 μM) and the fluorescence intensity at the corresponding spectra was measured using a Neo2 multi-mode microplate reader(BioTek). The resulting data were fitted to a curve based on the Hill equation: Y = Bmax · Xh/(Kd + Xh), where Bmax represents the maximum specific binding parameter in the same units as Y, h represents the Hill slope and Kd represents the concentration needed to achieve a half-maximum binding at equilibrium[1].
Structure ligand
NBSI is a typical chromophore structure consisting of an electron donor and an electron acceptor linked by π conjugation. NBSI exhibit a large Stokes shift of 80 nm when it was constrained in glycerol.-----From 2023_nature methods_Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells.
| PubChem CID | Molecular Formula | MW | CAS | Solubility | MedChemExpress |
|---|---|---|---|---|---|
| 163781292 | C22H22FN3O2 | 379.4 g/mol | NA | NA | NA |
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Similar compound
We screened the compounds with great similarity to AMP 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 |
|---|---|---|---|---|
| ZINC2383302907 | (5Z)-2-[(E)-2-(4-fluorophenyl)ethenyl]-5-[[4-[2-hydroxyethyl(methyl)amino]phenyl]methylidene]-3-methylimidazol-4-one | NA | 163781292 |  |
| ZINC145364711 | (5Z)-5-[[4-(dimethylamino)phenyl]methylidene]-3-methyl-2-phenylimidazol-4-one | NA | 70809009 |  |
| NA | (5Z)-2-[(E)-2-(4-fluorophenyl)ethenyl]-3-methyl-5-[[4-[methyl(2-prop-2-ynoxyethyl)amino]phenyl]methylidene]imidazol-4-one | NA | 168141028 |  |
| NA | (5Z)-5-[[4-[2-(dimethylamino)ethyl-methylamino]phenyl]methylidene]-2-[(E)-2-(3-fluorophenyl)ethenyl]-3-methylimidazol-4-one | NA | 168727611 |  |
| ZINC2383303014 | (5Z)-2-[(E)-2-(3-fluorophenyl)ethenyl]-5-[[4-[2-hydroxyethyl(methyl)amino]phenyl]methylidene]-3-methylimidazol-4-one | NA | 168727620 |  |
| NA | (5Z)-2-[(E)-2-(3-fluorophenyl)ethenyl]-5-[[4-[2-isocyanoethyl(methyl)amino]phenyl]methylidene]-3-methylimidazol-4-one | NA | 168727621 |  |
| NA | 2-[4-[(Z)-[2-[(E)-2-(3-fluorophenyl)ethenyl]-1-methyl-5-oxoimidazol-4-ylidene]methyl]-N-methylanilino]ethoxy thiohypoiodite | NA | 169613093 |  |
| ZINC169512732 | (5Z)-5-[[3-(dimethylamino)phenyl]methylidene]-3-(2-hydroxyethyl)-2-methylimidazol-4-one | NA | 102456280 |  |
| NA | (5Z)-2-[(E)-2-(4-fluorophenyl)ethenyl]-3-methyl-5-[[4-[methyl(2-prop-2-enoxyethyl)amino]phenyl]methylidene]imidazol-4-one | NA | 169612817 |  |
| NA | (5Z)-2-[(E)-2-(4-fluorophenyl)ethenyl]-3-methyl-5-[[4-[methyl-[2-(2-methylprop-2-enoxy)ethyl]amino]phenyl]methylidene]imidazol-4-one | NA | 169612902 |  |
References
[1] Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells.Jiang, L., Xie, X., Su, N., Zhang, D., Chen, X., Xu, X., Zhang, B., Huang, K., Yu, J., Fang, M., Bao, B., Zuo, F., Yang, L., Zhang, R., Li, H., Huang, X., Chen, Z., Zeng, Q., Liu, R., Lin, Q., … Yang, Y.
Nature methods, 20(10), 1563–1572. (2023)
[2] Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift.
Huang, K., Song, Q., Fang, M., Yao, D., Shen, X., Xu, X., Chen, X., Zhu, L., Yang, Y., & Ren, A.
Nature chemical biology, 10.1038/s41589-024-01633-1. (2024)