TMR aptamer

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Timeline

2010

Aptamers bind a larger fluorescent dye, tetramethylrhodamine was selected[1]

2017

The NMR resonance assignment of an RNA aptamer binding to the fluorescent ligand tetramethylrhodamine TMR was present[2]

2020

The atomic resolution structure of an RNA-aptamer binding to the fluorescent xanthene dye tetramethylrhodamine was present[3]

Description

 In 2010, James M. Carothers et al. employed in vitro selection techniques to isolate aptamers with high-affinity binding sites for TMR. Subsequently, Elke Duchardt-Ferner et al. elucidated the structure of the TMR3 aptamer/TMR complex by NMR-spectroscopy in their work published in 2020[1,3].

SELEX

This work generated aptamers that bind TMR using SELEX. An RNA library containing ~1014 random library members was used and 5-carboxy TMR was conjugated to NovaBiochem Amino PEGA resin as positive target. After 10 rounds of SELEX, four of the TMR aptamers (TMR1, TMR2, TMR3 and TMR4) that exhibited substantial activity in the column-binding assays. The crystal structure of the TMR3-TMR complex was reported in subsequent work[1,3].
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'-GACUCAUUUCCGUUUUCUAUGGGUCUUGGCCUGCUUCGGCAGGAGGUAACAUACACCUGUCCACACCUGCGC-3'

 drawing

3D visualisation

Elke Duchardt-Ferner et al. solved the structure of the TMR3 aptamer/TMR complex by NMR-spectroscopy in their work published in 2020. The PDB ID of the structures are 6GZK and 6GZR[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: 6GZK by NMR. 5'-TAMRA (shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with 5'-TAMRA or other nucleotides surround small molecules.

drawing drawing


Ligand information

SELEX ligand

Apparent Kds were determined with the spin-filter method using at least three independent measurements taken across the linear range[1].

drawing

Structure ligand

Tetramethylrhodamine is a rhodamine in which four hydrogens have been replaced by methyl groups. Forms such as tetramethylrhodamine dextran are often used as fluorescent tracer dyes in cell research.-----From Wiktionary
PubChem CID Molecular Formula MW CAS Solubility Drugbank ID
9952143 C24H22N2O3 386.4 g/mol 120718-52-7 NA 52282
drawing drawing

Similar compound

We screened the compounds with great similarity to TMR 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
ZINC4521864 Rhodamine II 115532-49-5 5009757 drawing
ZINC4521863 Rhodamine I 115532-52-0 2762683 drawing
ZINC3873937 [9-(4-Amino-2-carboxyphenyl)-6-(dimethylamino)xanthen-3-ylidene]-dimethylazanium 167095-10-5 5421 drawing
ZINC71789489 [9-(5-Amino-2-carboxyphenyl)-6-(dimethylamino)xanthen-3-ylidene]-dimethylazanium 80724-18-1 10895427 drawing
ZINC35952357 [6-(Dimethylamino)-9-(2-methoxycarbonylphenyl)thioxanthen-3-ylidene]-dimethylazanium NA 11621055 drawing
ZINC34630916 [9-(2-Carboxyphenyl)-6-(dimethylamino)thioxanthen-3-ylidene]-dimethylazanium NA 11512296 drawing
ZINC139098115 NA NA NA drawing
ZINC38346243 N-(6-(dimethylamino)-9-phenyl-3H-thioxanthen-3-ylidene)-N-methylmethanaminium bromide NA 11188604 drawing
ZINC504537834 6-[3,6-bis(dimethylamino)xanthen-9-ylidene]-3-iminocyclohexa-1,4-diene-1-carboxylic acid NA 92043312 drawing


References

[1] Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity.
Carothers, J. M., Goler, J. A., Kapoor, Y., Lara, L., & Keasling, J. D.
Nucleic acids research, 38(8), 2736–2747. (2010)
[2] NMR resonance assignments for the tetramethylrhodamine binding RNA aptamer 3 in complex with the ligand 5-carboxy-tetramethylrhodamine.
Duchardt-Ferner, E., Juen, M., Kreutz, C., & Wöhnert, J.
Biomolecular NMR assignments, 11(1), 29–34. (2017)
[3] Structure of an RNA aptamer in complex with the fluorophore tetramethylrhodamine.
Duchardt-Ferner, E., Juen, M., Bourgeois, B., Madl, T., Kreutz, C., Ohlenschläger, O., & Wöhnert, J.
Nucleic acids research, 48(2), 949–961. (2020)