Home
Database
Research
About us
Search
TMR aptamer
Timeline
The NMR resonance assignment of an RNA aptamer binding to the fluorescent ligand tetramethylrhodamine TMR was present[2]
The atomic resolution structure of an RNA-aptamer binding to the fluorescent xanthene dye tetramethylrhodamine was present[4]
RhoBAST bound to tetramethylrhodamine-dinitroaniline was isolated from random RNA nucleic acid libraries by in vitro selection[5]
A fluorogenic self-quenched dimer based on rhodamine whose cognate aptamer is o-Coral was rationally designed[6]
By embedding biRhoBAST and biSiRA into RNA scaffolds, Fluorescent light-up aptamers with higher fluorogenicity and more remarkable photostability were obtained[7]
The co-crystal structure of RhoBAST in complex with tetramethylrhodamine-dinitroaniline was determined to elucidate the molecular basis for ligand binding and fluorescence activation[8]
Description
In 2010, Jay D. Keasling et al. employed in vitro selection techniques to isolate aptamers with high-affinity binding sites for TMR. Subsequently, Jens Wohnert et al. elucidated the structure of the TMR3 aptamer/TMR complex by NMR-spectroscopy in their work published in 2020. The high-resolution structure, solved by NMR spectroscopy in solution, revealed binding features that were both common and distinct from the binding modes of other aptamers with affinity for ligands carrying planar aromatic ring systems[1,4].
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 were identified. The crystal structure of the TMR3-TMR complex was reported in subsequent work[1,4].
Detailed information are accessible on SELEX page.
Structure
2D representation
The TMR3 aptamer folds into an open three-way junction, consisting of a closing stem (P1) and two short hairpins (P2 and P3), which are connected by stretches of 5–8 formally single-stranded residues. Here we used ribodraw to complete the figure, through the 3D structure information[4].
5'-GGACGACUGAACCGAAAGGUUCUUGGCUGCUUCGGCAGAGGUACGUCC-3'
3D visualisation
Jens Wohnert et al. solved the structure of the TMR3 aptamer/TMR complex by NMR-spectroscopy in their work published in 2020. The ligand-binding pocket of TMR3 was lined by the C7:G41 Watson–Crick base pair, which closed stem P1, the trans Watson–Crick/Watson–Crick G25:G40 base pair of P3, and the unpaired U24 that closed stem P2. The 5-TAMRA fluorophore intercalated its planar xanthene ring system between the C7:G41 base pair of P1 and the G25:G40 base pair of P3. The PDB ID of the structures are 6GZK and 6GZR[4].
Additional available structures that have been solved and detailed information are accessible on Structures page.
(Clicking the "Settings/Controls info" to turn Spin off)
|
|
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 magenta. Right: The hydrogen bonds of binding sites of the aptamer bound with 5'-TAMRA or other nucleotides surround small molecules.
|
|
Ligand information
SELEX ligand
Apparent Kd was determined with the spin-filter method using at least three independent measurements taken across the linear range[1].
Structure ligand
TMR (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: a unique identifier for substances in the PubChem database.
CAS number: a global registry number for chemical substances.
ChEBI ID: a unique identifier assigned to each molecular entity in the Chemical Entities of Biological Interest database.
| Name | PubChem CID | Molecular Formula | Molecular Weight | CAS | Solubility | CHEBI ID |
|---|---|---|---|---|---|---|
| TMR | 9952143 | C24H22N2O3 | 386.4 g/mol | 120718-52-7 | NA | 52282 |
 |
 |
Similar compound(s)
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: a compound identifier used by the ZINC database, one of the largest repositories for virtual screening of drug-like molecules.
PubChem CID: a unique identifier for substances in the PubChem database.
CAS number: a global registry number for chemical substances.
| ZINC ID | Name | CAS | Pubchem CID | Structure |
|---|---|---|---|---|
| ZINC4521864 | Rhodamine II | 115532-49-5 | 5009757 |  |
| ZINC4521863 | Rhodamine I | 115532-52-0 | 2762683 |  |
| ZINC3873937 | NA | 167095-10-5 | 5421 |  |
| ZINC71789489 | NA | 80724-18-1 | 10895427 |  |
| ZINC35952357 | NA | NA | 11621055 |  |
| ZINC34630916 | NA | NA | 11512296 |  |
| ZINC139098115 | NA | NA | NA |  |
| ZINC38346243 | NA | NA | 11188604 |  |
| ZINC504537834 | NA | NA | 92043312 |  |
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] SiRA: A Silicon Rhodamine-Binding Aptamer for Live-Cell Super-Resolution RNA Imaging.
Wirth, R., Gao, P., Nienhaus, G. U., Sunbul, M., & Jäschke, A.
Journal of the American Chemical Society, 141(18), 7562–7571. (2019)
[4] 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)
[5] Super-resolution RNA imaging using a rhodamine-binding aptamer with fast exchange kinetics.
Sunbul, M., Lackner, J., Martin, A., Englert, D., Hacene, B., Grün, F., Nienhaus, K., Nienhaus, G. U., & Jäschke, A.
Nature biotechnology, 39(6), 686–690. (2021)
[6] Rational Design of Self-Quenched Rhodamine Dimers as Fluorogenic Aptamer Probes for Live-Cell RNA Imaging.
Fam, K. T., Pelletier, R., Bouhedda, F., Ryckelynck, M., Collot, M., & Klymchenko, A. S.
Analytical chemistry, 94(18), 6657–6664. (2022)
[7] Avidity-based bright and photostable light-up aptamers for single-molecule mRNA imaging.
Bühler, B., Schokolowski, J., Benderoth, A., Englert, D., Grün, F., Jäschke, A., & Sunbul, M.
Nature chemical biology, 19(4), 478–487. (2023)
[8] Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST.
Zhang, Y., Xu, Z., Xiao, Y., Jiang, H., Zuo, X., Li, X., & Fang, X.
Nature communications, 15(1), 4206. (2024)
[9] Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer.
Siwik, S. H., Wierzba, A. J., Lennon, S. R., Olenginski, L. T., Palmer, A. E., & Batey, R. T.
bioRxiv : the preprint server for biology, 2024.12.30.630784. (2024)