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Mango-III aptamer
Timeline
The Mango aptamer which can be used to simultaneously fluorescently label and purify biologically important RNAs was selected[1]
The cocrystal structures of YO3-biotin and Mango III were analyzed to measure the angular dependence of FRET[3]
Description
In 2014, Peter J. Unrau et al. employed in vitro selection techniques to isolate Mango aptamers with high-affinity binding sites for TO1-biotin. Subsequently, they used this motif to design ribozymes displaying polynucleotide kinase activity. In 2021, Peter J. Unrau et al. elucidated the structure of the Mango-III fluorescent aptamer bound to YO3-biotin by X-ray diffraction[1,3].
SELEX
This work generated aptamers that bind TO1-biotin using SELEX. An RNA library containing ∼3×1013 random library members was used and TO1-Biotin was conjugated to streptavidin magnetic as positive target. After 12 rounds of SELEX, one RNA family that exhibited both tight binding and a high fluorescent enhancement was identified from 7 distinct families. This work also proposed a novel fluorescence-based selection approach, which simplifies the generation of aptamers optimised for expression and performance in living cells[1].
Detailed information are accessible on SELEX page.
Structure
2D representation
The structures of Mango-I and Mango-IV suggest considerable flexibility at the junction between the fluorophore-binding pocket and the variable helix. The fluorophore-binding pocket of the Spinach-class aptamers resides between two coaxially stacked paired elements, characterised by variable sequence and length. Here we used ribodraw to complete the figure, through the 3D structure information[1].
5'-GCUACGAAGGAAGGAUUGGUAUGUGGUAUAUUCGUAGC-3'
3D visualisation
In 2021, Peter J. Unrau et al. analyzed the structure of the Mango-YO3-biotin complexs through crystallization and X-ray diffraction data collection. Mango-I connected its fluorophore-binding quadruplex module to an external helix via a partially crystallographically disordered GAAA tetraloop-like junction, whereas the corresponding helix–quadruplex junction in Mango-III formed a well-defined coaxially stacked triplex. In contrast, the fluorophore-binding pocket of Spinach-class aptamers was positioned between two coaxially stacked paired elements with variable sequences and lengths. Coordinates and structure factors have been deposited to the Protein Database under accession codes PDB: 6UP0 (2.80 Å)[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)
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Binding pocket
Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 6UP0 by X-ray crystallography. YO3-biotin (shown in sticks) is labeled in magenta. Right: The hydrogen bonds of binding sites of the aptamer bound with YO3-biotin or other nucleotides surround small molecules.
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Ligand information
SELEX ligand
The EC50 was determined by measuring the increase in fluorescence as a function of increasing RNA aptamer concentration in the presence of a fixed concentration of dye[2]. 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 dye[1].
Structure ligand
YO3 (Oxazole yellow 3) is a synthetic fluorescent small molecule whose spectral properties are very similar to Texas Red. YO3-biotin fluoresces with comparable intensities when bound in either the Mango or the Spinach construct, similarly to TO1-biotin. DFHBI-1T outcompetes YO3-biotin bound in Spinach, whereas YO3-biotin is unable to outcompete DFHBI-1T bound in Spinach.-----Ikeda, S., Kubota, T., Yuki, M., & Okamoto, A. (2009). Exciton‐controlled hybridization‐sensitive fluorescent probes: multicolor detection of nucleic acids. Angewandte Chemie, 121(35), 6602-6606.
PubChem CID: a unique identifier for substances in the PubChem database.
CAS number: a global registry number for chemical substances.
Drugbank: a comprehensive database with detailed information on drugs and drug targets.
| Name | PubChem CID | Molecular Formula | Molecular Weight | CAS | Solubility | Drugbank ID |
|---|---|---|---|---|---|---|
| YO3 | 59853378 | C21H19N2O+ | 315.4 g/mol | NA | NA | NA |
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Similar compound(s)
We screened the compounds with great similarity to YO3 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 |
|---|---|---|---|---|
| ZINC114784389 | NA | NA | 59274362 |  |
References
[1] RNA mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking.Dolgosheina, E. V., Jeng, S. C., Panchapakesan, S. S., Cojocaru, R., Chen, P. S., Wilson, P. D., Hawkins, N., Wiggins, P. A., & Unrau, P. J.
ACS chemical biology, 9(10), 2412–2420. (2014)
[2] Development of a genetically encodable FRET system using fluorescent RNA aptamers.
Jepsen, M. D. E., Sparvath, S. M., Nielsen, T. B., Langvad, A. H., Grossi, G., Gothelf, K. V., & Andersen, E. S.
Nature communications, 9(1), 18. (2018)
[3] Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET.
Jeng, S. C. Y., Trachman, R. J., 3rd, Weissenboeck, F., Truong, L., Link, K. A., Jepsen, M. D. E., Knutson, J. R., Andersen, E. S., Ferré-D'Amaré, A. R., & Unrau, P. J.
RNA (New York, N.Y.), 27(4), 433–444. (2021)
[4] Characterizing fluorescence properties of turn-on RNA aptamers.
Trachman, R. J., 3rd, Link, K. A., Knutson, J. R., & Ferré-D'Amaré, A. R.
Methods in molecular biology (Clifton, N.J.), 2568, 25–36. (2023)