Chili aptamer

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Timeline

2011

In this work, researchers isolated Spinach RNA aptamer and obtained another 13-2 aptamer series which has affinity with DMHBI and can activate its fluorescence[1]

2019

An RNA aptamer named Chili mimics Large Stokes shift fluorescent proteins appeared[2]

2019

The interactions between the Chili RNA and a family of conditionally fluorescent ligands was analyzed using a variety of spectroscopic, calorimetric and biochemical techniques[3]

2021

Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands were revealed[4]

2023

Chili labeled snRNA is used for intracellular imaging in the presence of specific concentrations of DMHBI[5]

Description

 In 2011, Jeremy S. Paige et al. isolated Spinach RNA aptamer and obtained a 13-2 aptamer series that has affinity with DMHBI and can activate its fluorescence. In 2018, Christian Steinmetzger et al. obtained an RNA aptamer with stronger affinity to DMHBI through rational design of 13-2-min, and named it Chili. In 2021, Mateusz Mieczkowski et al. analyzed the structure of the Chili-DMHBI's derivatives complexs through crystallization, diffraction data collection and NMR spectroscopy[1,2,3].

SELEX

This work generated aptamers that bind DMHBI using SELEX. A DNA library containing ~5×1013 random library members was used and DMHBI was conjugated to agarose beads as positive target. After 10 rounds of SELEX, an RNA aptamer that binds DFAME and activates its fluorescence was identified[1].
Detailed information are accessible on SELEX page.



Structure

2D representation

Here we used ribodraw to complete the figure, through the 3D structure information[2].

5'-GGCUAGCUGGAGGGGCGCCAGUUCGCUGGUGGUUGGGUGCGGUCGGCUAGCC-3'

 drawing

3D visualisation

In 2021, Mateusz Mieczkowski et al. analyzed the structure of the Chili-DMHBI's derivatives complexs through crystallization, diffraction data collection and NMR spectroscopy. Structural data obtained by X-ray crystallography were deposited in the Protein Data Bank and are available with the following accession codes: 7OAW, 7OAX, 7OA3, 7OAV[3].
Additional available structures that have been solved and detailed information are accessible on Structures page.

(Clicking the "Settings/Controls info" to turn Spin off)      
drawing PDBe Molstar




Binding pocket

Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 7OAW by NMR and X-ray crystallography. DMHBI+ (shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with DMHBI+ or other nucleotides surround small molecules.
drawing drawing


Ligand information

SELEX ligand

The Kd was determined by and measuring the increase in fluorescence as a function of increasing dye concentration in the presence of a fixed concentration of RNA aptamer[2].

drawing

Structure ligand

DMHBI (4-[(4-hydroxy-3,5-dimethoxyphenyl)methylidene]-1,2-dimethyl-4,5-dihydro-1H-imidazol-5-one) is predominantly found in the phenolic form, the brighter DMFBI mimics EGFP and is anionic under standard conditions. The DMFBI-RNA complex has been called Spinach, it is the first fluorescent RNA tag that is both selective and non-toxic. It only fluoresces when bound to RNA, is resistant to photobleaching and has been used to follow RNA tagged molecules as they move through cells.-----From Green Fluorescent Protein
PubChem CID Molecular Formula MW CAS Solubility Drugbank ID
68787434 C14H16N2O4 276.29 g/mol 1241390-25-9 NA NA
drawing drawing

Similar compound

We screened the compounds with great similarity to DMHBI 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
ZINC2051913110 DFHBI NA 70808995 drawing
ZINC1857790839 DFHBI 1T NA 101889712 drawing
ZINC2048528770 DFHBI 2T NA 129080921 drawing
ZINC145340396 (5E)-5-[(4-hydroxy-3,5-dimethoxyphenyl)methylidene]-2,3-dimethylimidazol-4-one NA 46898418 drawing
ZINC4918310 NA NA NA drawing
ZINC34107441 (5E)-3-methyl-2-sulfanylidene-5-[(3,4,5-trimethoxyphenyl)methylidene]imidazolidin-4-one NA 6527199 drawing
ZINC8091545 (5E)-5-[(4-hydroxy-3,5-dimethoxyphenyl)methylidene]-3-methylimidazolidine-2,4-dione NA 19374977 drawing
ZINC409030759 (5Z)-5-[(4-hydroxy-3,5-dimethoxyphenyl)methylidene]-1,3-dimethyl-2-sulfanylideneimidazolidin-4-one NA 126037191 drawing
ZINC408815341 (5Z)-5-[(4-hydroxy-3,5-dimethoxyphenyl)methylidene]-3-methyl-1,3-thiazolidine-2,4-dione NA 125823074 drawing


References

[1] RNA mimics of green fluorescent protein.
Paige, J. S., Wu, K. Y., & Jaffrey, S. R.
Science (New York, N.Y.), 333(6042), 642–646. (2011)
[2] A multicolor large stokes shift fluorogen-activating RNA aptamer with cationic chromophores.
Steinmetzger, C., Palanisamy, N., Gore, K. R., & Höbartner, C.
Chemistry (Weinheim an der Bergstrasse, Germany), 25(8), 1931–1935. (2019)
[3] Structure-fluorescence activation relationships of a large Stokes shift fluorogenic RNA aptamer.
Steinmetzger, C., Bessi, I., Lenz, A. K., & Höbartner, C.
Nucleic acids research, 47(22), 11538–11550. (2019)
[4] Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine.
Mieczkowski, M., Steinmetzger, C., Bessi, I., Lenz, A. K., Schmiedel, A., Holzapfel, M., Lambert, C., Pena, V., & Höbartner, C.
Nature communications, 12(1), 3549. (2021)
[5] Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells.
Trachman, R. J., 3rd, Autour, A., Jeng, S. C. Y., Abdolahzadeh, A., Andreoni, A., Cojocaru, R., Garipov, R., Dolgosheina, E. V., Knutson, 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)