Beetroot aptamer(ThT)

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Timeline

2017

Corn aptamer competent for RNA polymerase III transcription imaging was developed[1]

2019

Co-crystal of homodimeric RNA Corn and ThT binding to G quadruplexes was determined[2]

2023

The structure of the complexes of Beetroot with Thioflavin-T is determined[3]

Description

 In 2022, Jiahui Wu, et al. developed Beetroot aptamer, which enables to bind DFAME and forms an RNA-fluorophore complex. In 2023, Luiz F. M. Passalacqua et al. analyzed the structure of the Beetroot-ThT complex through crystallization, diffraction data collection and NMR spectroscopy[1,2].

SELEX

About ~1014 random RNA sequences was used in the systematic evolution of ligands by exponential enrichment approach to generated aptamers that bind DFHO. DFHO with an aminohexyl linker was synthesized so that this fluorophore could be attached to solid support. After eight rounds of SELEX, a single 119 nucleotides-long aptamer (aptamer 6-1) that induced the fluorescence of DFHO 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[1].

5'-GUUAGGCAGAGGUGGGUGGUGUGGAGGAGUAUCUGUC-3'

 drawing

3D visualisation

In 2023, Luiz F. M. Passalacqua et al. analyzed the structure of the Beetroot-DFAME complex through crystallization, diffraction data collection, structure determination and refinement. The atomic coordinates and structure factor amplitudes have been deposited with Protein Data bank under accession codes 8EYU (Beetroot-DFAME), 8EYV (Beetroot-DFHO), 8EYW (Beetroot-ThT), and 8F0N (Beetroot A16U, U38G-DFHO)[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: 8EYW by X-ray crystallography. Thioflavin T(ThT)(shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with ThT or other nucleotides surround small molecules.
drawing drawing


Ligand information

SELEX ligand

Kd is calculated by both ITC and measuring the increase in fluorescence as a function of increasing fluorophore concentration in the presence of a fixed concentration (50 nM) of RNA aptamer[1,2].

drawing

Structure ligand

ThT (Thioflavin T) are fluorescent dyes used for histology staining and biophysical studies of protein aggregation and investigate amyloid formation. They are also used in biophysical studies of the electrophysiology of bacteria.-----From Wikipedia
PubChem CID Molecular Formula MW CAS Solubility Drugbank ID
16953 C17H19ClN2S 318.9 g/mol 2390-54-7 16.67 mg/mL in DMSO; 5 mg/mL in H2O HY-D0218
drawing drawing

Similar compound

We screened the compounds with great similarity to ThT 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
ZINC38539054 2-[4-(Dimethylamino)phenyl]-6-Hydroxy-3-Methyl-1,3-Benzothiazol-3-Ium NA 24832019 drawing
ZINC56936 N,N-dimethyl-4-(6-methyl-1,3-benzothiazol-2-yl)aniline 10205-62-6 82450 drawing
ZINC584593350 N,N-dimethyl-4-(5-methyl-1,3-benzothiazol-2-yl)aniline NA 125465487 drawing
ZINC167917029 4-(1,5-dimethylbenzimidazol-2-yl)-N,N-dimethylaniline NA 20625541 drawing
ZINC553312 N,N-dimethyl-4-(6-methyl-1H-benzimidazol-2-yl)aniline 69570-95-2 950737 drawing
ZINC4127888 N,N-dimethyl-4-(6-methyl-1,3-benzoxazol-2-yl)aniline NA 6486758 drawing
ZINC1659652 N,N-dimethyl-4-(5-methyl-1,3-benzoxazol-2-yl)aniline 127753-24-6 401586 drawing
ZINC751217940 NA NA NA drawing
ZINC1857599770 2-[4-(dimethylamino)phenyl]-1,3-benzothiazol-5-ol NA 155555168 drawing


References

[1] Imaging RNA polymerase III transcription using a photostable RNA-fluorophore complex.
Song, W., Filonov, G. S., Kim, H., Hirsch, M., Li, X., Moon, J. D., & Jaffrey, S. R.
Nature chemical biology, 13(11), 1187–1194. (2017)
[2] Binding between G quadruplexes at the homodimer interface of the corn RNA aptamer strongly activates thioflavin T fluorescence.
Sjekloća, L., & Ferré-D'Amaré, A. R.
Cell chemical biology, 26(8), 1159–1168.e4. (2019)
[3] Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture.
Passalacqua, L. F. M., Starich, M. R., Link, K. A., Wu, J., Knutson, J. R., Tjandra, N., Jaffrey, S. R., & Ferré-D'Amaré, A. R.
Nature communications, 14(1), 2969. (2023)