Corn aptamer

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Timeline

2017

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

2017

Corn-DFHO co-crystal structure was reported[2]

2019

Co-crystal of homodimeric RNA Corn and ThT binding to G quadruplexes was determined[3]

2019

A strategy for converting Corn dimer into a biosensor that detects S-adenosylmethionine in vitro and in living cells[4]

2021

Utilization of Corn as a split aptamer system for monitoring RNA self-assembly and sensing microRNA[5]

2022

An approach for inducing RNA self-assembly using dimeric Corn and Beetroot aptamers, enable multiplexing of distinct RNA assemblies in cells[6]

2023

A fluorescent light-up biosensor for detection of lncRNAs by coupling target recycling amplification with transcription-driven synthesis of Corns[7]

2023

The Beetroot-DFAME co-crystal structure was determined, from whose guide a variant toward DFHO was generated[8]

Description

 In 2017, Wenjiao Song et al. developed Corn aptamer, which enables monitoring of Pol III transcript levels by forming a light-stable RNA-fluorophore complex with fluorophores. In the same year, Katherine Deigan Warner et al, in collaboration with Wenjiao Song, analyzed the structure of the Corn-DFHO complex through crystallization and diffraction data collection[1,2].

SELEX

By exponential enrichment (SELEX) approach, aptamer bound to DFHO was evolved from approximately 1014 random RNA libraries that served as ligand systems. DFHO with aminohexyl linkers was synthesized for attachment to solid support. Boc-protected DFHO linker was synthesized followed by the removal of the Boc protecting group to generate DFHO linker. DFHO-binding aptamers were recovered on DFHO-derivatized agarose beads. After 8 rounds of SELEX, we identified a single 119 nt-long aptamer (Aptamer 6-1) that induced the fluorescence of DFHO, with an excitation maximum (ExMax) of 505 nm and an emission maximum (EmMax) of 545 nm. This aptamer was truncated to a 76 nt-long aptamer (T1) that retained the ability to induce DFHO fluorescence[1].
Detailed information are accessible on SELEX page.



Structure

2D representation

Then T1 performed further truncation analysis, resulting in the generation of T2, a 28-nt long aptamer that retained the ability to induce DFHO fluorescence. Because of the yellow fluorescence of this RNA-fluorophore complex, this aptamer was designated Corn. Here we use ribodraw to complete the figure, through the 3D structure information[2].

5'-GGCGCGAGGAAGGAGGUCUGAGGAGGUCACUGCGCC-3'

 drawing

3D visualisation

In 2007, Warner, K. D. et al. determined the crystal structure of the Corn-DFHO complex at 2.35 Å resolution, discovering that the functional species is a quasisymmetric homodimer. The homodimer encapsulates one DFHO at its inter-protomer interface, sandwiching it with a G-quadruplex from each protomer. The PDB ID of this structure is 5BJP[2].
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: 5BJP by X-ray crystallography. DFHO (shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with DFHO or other nucleotides surround small molecules.
drawing drawing


Ligand information

SELEX ligand

The Kd was determined 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].

drawing

Structure ligand

DFHO is a fluorogenic ligand of Corn fluorogenic aptamer. The RNA aptamer, Corn binds DFHO with a Kd value of 70 nM and converts it to a fluorescent form, enabling RNA imaging in cells. -----From MedChemExpress
Name PubChem CID Molecular Formula MW CAS Solubility Medchemexpress ID
DFHO 71492924 C12H9F2N3O3 281.21 g/mol 1420815-34-4 28120 mg/L (in DMSO) DFHO
drawing drawing

Similar compound

We used the PubChem database to screen compounds that were more similar to DFHO, and selected the most similar compounds for display. For those without CAS numbers, we will supplement them with Pubchem CID.
Named CAS Pubchem CID Structure
(5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-[(E)-hydroxyiminomethyl]-3-methylimidazolidin-4-one NA 168266216 drawing
(5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-[(Z)-hydroxyiminomethyl]-3-methylimidazolidin-4-one NA 168010756 drawing
(5Z)-2-(aminomethyl)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-3-methylimidazolidin-4-one NA 162396648 drawing
(5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-methyl-3-(2,2,2-trifluoroethyl)imidazolidin-4-one NA 155920151 drawing
(z)-4-(3,5-Difluoro-4-hydroxybenzylidene)-1-methyl-5-oxo-1h-imidazole-2-carbaldehyde oxime NA 140649354 drawing
(5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2,3-dimethylimidazolidin-4-one NA 134814233 drawing
(E)-1-(6-aminohexyl)-4-((Z)-3,5-difluoro-4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazole-2-carbaldehyde oxime NA 129627026 drawing
(5Z)-5-[(2-difluoroboranyl-5-fluoro-4-hydroxyphenyl)methylidene]-3-methyl-2-methylideneimidazolidin-4-one NA 123805052 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] A homodimer interface without base pairs in an RNA mimic of red fluorescent protein.
Warner, K. D., Sjekloća, L., Song, W., Filonov, G. S., Jaffrey, S. R., & Ferré-D'Amaré, A. R.
Nature chemical biology, 13(11), 1195–1201. (2017)
[3] 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)
[4] A fluorogenic RNA-based sensor activated by metabolite-induced RNA dimerization.
Kim, H., & Jaffrey, S. R.
Cell chemical biology, 26(12), 1725–1731.e6. (2019)
[5] Living-cell microRNA imaging with self-assembling fragments of fluorescent protein-mimic RNA aptamer.
Gu, Y., Huang, L. J., Zhao, W., Zhang, T. T., Cui, M. R., Yang, X. J., Zhao, X. L., Chen, H. Y., & Xu, J. J.
ACS sensors, 6(6), 2339–2347. (2021)
[6] Self-assembly of intracellular multivalent RNA complexes using dimeric Corn and beetroot aptamers.
Wu, J., Svensen, N., Song, W., Kim, H., Zhang, S., Li, X., & Jaffrey, S. R. 
Journal of the American Chemical Society, 144(12), 5471–5477. (2022)
[7] Corn-based fluorescent light-up biosensors with improved signal-to-background ratio for label-free detection of long noncoding RNAs.
Zhang, Q., Su, C., Tian, X., & Zhang, C. Y.
Analytical chemistry, 95(20), 8097–8104. (2023)
[8] 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)