Clivias aptamer

Jun 9, 2024 • Bo Fu, Jiali Wang

Timeline

Description

In a work published in 2023, Aiming Ren, Linyong Zhu and Yi Yang et al. isolated a series of RNA aptamers, named Clivias, which binds NBSI and transform its optical properties. Later, in a work published in 2024, the structure of the Clivia-NBSI derivates complex is analyzed by crystallization, diffraction data collection^[1,2].

SELEX

Aiming Ren, Linyong Zhu and Yi Yang et al. performed SELEX with a library containing ~4⁵² random library members and selected RNA sequences 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

Clivias aptamers were the aptamer sequences mainly studied in SELEX article. The predicted secondary structure of Clivia contains two stems, that are connected by one big internal loop. Here we used Ribodraw to complete the figure, through the 3D structure information^[1,2].

5'-GAAGAUUGUAAACAUGCCGAAAGGCAGACACUUCC-3'

3D visualisation

Aiming Ren, Linyong Zhu and Yi Yang et al. present the solution structure, as determined by crystallization and diffraction data collection of Clivia-NBSI complex. The overall structure of the complex adopts a coaxial long helix fold and is stabilized by continuous stacking interactions from the bottom stem P1 to the apical stem P2 with the ligand NBSI intercalated in the zipped junction region at the interface of stems P1 and P2. The PDB ID of these structures are 8HZE (1.59 Å)^[2].

Additional available structures that have been solved and detailed information are accessible on Structures page.

Binding pocket

Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 8HZE by NMR and X-ray crystallography. DFHBI (shown in sticks) is labeled in magenta. Right: The hydrogen bonds of binding sites of the aptamer bound with DFHBI or other nucleotides surround small molecules.

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 Nature methods, 20(10), 1563–1572.

PubChem CID: a unique identifier for substances in the PubChem database.

CAS number: a global registry number for chemical substances.

MedChemExpress: an entry number for the classification of chemicals by the well-known chemical manufacturing company MedChemExpress.

Name	PubChem CID	Molecular Formula	Molecular Weight	CAS	Solubility	MedChemExpress
NBSI581	163781292	C22H22FN3O2	379.4 g/mol	NA	NA	NA

Similar compound(s)

We screened the compounds with great similarity to NBSI581 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
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)