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Beetroot aptamer(DFAME)
Timeline
A second dimeric fluorogenic aptamer, Beetroot, which shows partial sequence similarity to Corn aptamers and bind DFAME was described[1]
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-DFAME complex through crystallization and diffraction data collection[1,2].SELEX
This work generated aptamers that bind DFAME using SELEX. A DNA library containing ∼1014 random library members was used and DFAME was conjugated to agarose beads using an aminohexyl linker as positive target. After 10 rounds of SELEX, an RNA aptamer that binds DFAME and activates its fluorescence by threefold 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'
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)[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)
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Binding pocket
Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 8EYU by X-ray crystallography. DFAME (shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with DFAME or other nucleotides surround small molecules.
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Ligand information
SELEX ligand
The Kd was determined by and measuring the increase in fluorescence as a function of increasing RNA aptamer concentration in the presence of a fixed concentration of fluorophore[1,2].
Structure ligand
DFAME is a red fluorophore(Ex=508 nm, Em=641 nm). Beetroot and Corn are dimeric fluorogenic RNA aptamers that can bind to DFAME to form Beetroot-DFAME (Kd=460 nM) and Corn-DFAME (Kd= 3600 nM). Beetroot-DFAME (Kd=460 nM) and Corn-DFAME can be used to form RNA assemblies in living cells. Creating RNA assemblies can be used for the study of RNA Nanostructures. DNA/RNA Nanostructures would be useful in cell and gene therapy (CGT) research.-----From MedChemExpress
| PubChem CID | Molecular Formula | MW | CAS | Solubility | Drugbank ID |
|---|---|---|---|---|---|
| 71240548 | C15H12F2N2O4 | 322.26 g/mol | 1420815-55-9 | NA | HY-W073524 |
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Similar compound
We screened the compounds with great similarity to DFAME 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 |
|---|---|---|---|---|
| ZINC218483872 | (5E)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-3-methyl-2-(nitrosomethylidene)imidazolidin-4-one | 1420815-34-4 | 71492924 |  |
| ZINC811701546 | (3E)-3-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-1H-indol-2-one | NA | NA |  |
| ZINC492568317 | NA | NA | NA |  |
References
[1] 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)
[2] 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)