Mango aptamer

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Timeline

2014

A high affinity RNA aptamer called RNA Mango was selected[1]

2017

1.7-Å-resolution co-crystal structure of Mango-TO1-Biotin was determined[2]

2018

A microfluidics-based selection of three new high-affinity RNA Mango fluorogenic aptamers[3]

2018

The crystal structures of Mango-II in complex with two fluorophores, TO1-Biotin and TO3-Biotin were determined[4]

2019

Crystal structures of TO1-Biotin complexes of Mango-III and its mutants were reported[5]

2020

A novel array of Mango II aptamers for RNA imaging in live and fixed cells with high contrast and single-molecule sensitivity[6]

2020

Crystal structure of TO1-Biotin complexed with Mango-IV was determined[7]

2021

The utility RNA Peach and Mango provides a possible route to in vivo two-color RNA imaging[8]

2022

Pressure was used as a variable to probe the suboptimal states of the Mango III aptamer[9]

2022

Computational study on the binding of Mango-II RNA aptamer and fluorogen using the polarizable force field AMOEBA[10]

2023

A new Mango-based imaging platform whose advantages are the tunability of spectral properties and applicability for visualization of small RNA molecules[11]

Description

In 2014, Peter J. Unrau et al. isolated RNA aptamer Mango that binds a series of thiazole orange (fluorophore) using in vitro screening techniques. In 2017, Adrian R Ferré-D’Amaré et al. determined the Mango-TO1-biotin co-crystal structure of 1.7-Å-resolution RNA. A method to improve the tool for RNA visualization in vivo is also proposed. Adrian R Ferré-D’Amaré et al. also found that minimizing the angle between the two heterocycles formed by TO increased quantum yields, thereby improving the tool's utility for in vivo RNA visualization[1,2].



SELEX

An RNA pool containing ∼3×1013 distinct sequences was obtained by in vitro transcription of the corresponding random sequence DNA pool and was subjected to multiple rounds of high affinity selection. Streptavidin magnetic beads were derivatized with TO1-biotin to facilitate the enrichment of sequences with affinity. 12 rounds of selection were performed and twenty-four isolates from the final round of selection were sequenced and fell into a total of 7 distinct RNA families which exhibited both tight binding and a high fluorescent enhancement[1].

Detailed information are accessible on SELEX page.



Structure

2D representation

Adrian R Ferré-D'Amaré and Robert J Trachman III et al. analyzed the RNA Mango-TO1-Biotin 1.7-Å-resolution co-crystal structure. RNA Mango adopts a mixed parallel/antiparallel G-quadruplex architecture, stabilised by six loops that interconnect the 12 guanine residues of its three G-quartets. A22, located within a propeller loop bridging T3 and T1, contributes to the formation of a pentad by engaging the sugar edge of G18 via its Hoogsteen face. U15, A20, and A25-each forming one of three directional reversal loops positioned above T3-collectively establish the TO1–Biotin-binding site through direct structural coordination. The PDB ID of this structure is 1AM0[2].

5'-GUGCGAAGGGACGGUGCGGAGAGGAGAGCACA-3'

drawing

3D visualisation

Robert J Trachman III and Natalia A Demeshkina et al. analyzed the RNA Mango-TO1-Biotin 1.7-Å-resolution co-crystal structure. The PDB ID of this structure is 1AM0[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: 5V3F by X-ray crystallography. Thiazole orange-biotin (shown in sticks) is labeled in magenta. Right: The hydrogen bonds of binding sites of the aptamer bound with TO1-biotin or other nucleotides surround small molecules.

drawing drawing


Ligand information

SELEX ligand

Binding affinity was determined by fluorescence titration in the buffer and calculated by the concentration correlation function of ligand fluorescence molecules[1].

drawing

Structure ligand

TO1 (Thiazole Orange) is an asymmetric anthocyanin dye that can be coupled with oligonucleotides to prepare fluorescent hybridization probes.-----From MedChemExpress

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
TO1-biotin 6438345 C26H24N2O3S2 476.6 g/mol 107091-89-4 NA HY-D0150
drawing drawing

Similar compound(s)

We screened the compounds with great similarity to TO1 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
ZINC1081175 NA 107091-89-4 1268073 drawing
ZINC253615069 NA NA 134093721 drawing
ZINC138776193 NA NA 11532835 drawing
ZINC202369662 NA NA 58436249 drawing
ZINC263621892 NA NA 122174062 drawing
ZINC2040469426 NA NA 3330972 drawing
ZINC1465938 NA NA 1537162 drawing
ZINC6441438 NA NA 124312875 drawing
ZINC1616176047 NA NA NA drawing


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] Structural basis for high-affinity fluorophore binding and activation by RNA Mango.
Trachman, R. J., 3rd, Demeshkina, N. A., Lau, M. W. L., Panchapakesan, S. S. S., Jeng, S. C. Y., Unrau, P. J., & Ferré-D'Amaré, A. R.
Nature chemical biology, 13(7), 807–813. (2017)
[3] Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells.
Autour, A., C Y Jeng, S., D Cawte, A., Abdolahzadeh, A., Galli, A., Panchapakesan, S. S. S., Rueda, D., Ryckelynck, M., & Unrau, P. J.
Nature communications, 9(1), 656. (2018)
[4] Crystal structures of the Mango-II RNA aptamer reveal heterogeneous fluorophore binding and guide engineering of variants with improved selectivity and brightness.
Trachman, R. J., 3rd, Abdolahzadeh, A., Andreoni, A., Cojocaru, R., Knutson, J. R., Ryckelynck, M., Unrau, P. J., & Ferré-D'Amaré, A. R.
Biochemistry, 57(26), 3544–3548. (2018)
[5] Structure and functional reselection of the Mango-III fluorogenic RNA aptamer.
Trachman, R. J., 3rd, Autour, A., Jeng, S. C. Y., Abdolahzadeh, A., Andreoni, A., Cojocaru, R., Garipov, R., Dolgosheina, E. V., Knutson, J. R., Ryckelynck, M., Unrau, P. J., & Ferré-D'Amaré, A. R.
Nature chemical biology, 15(5), 472–479. (2019)
[6] Live cell imaging of single RNA molecules with fluorogenic Mango II arrays.
Cawte, A. D., Unrau, P. J., & Rueda, D. S.
Nature communications, 11(1), 1283. (2020)
[7] Structure-guided engineering of the homodimeric Mango-IV fluorescence turn-on aptamer yields an RNA FRET pair.
Trachman, R. J., 3rd, Cojocaru, R., Wu, D., Piszczek, G., Ryckelynck, M., Unrau, P. J., & Ferré-D'Amaré, A. R.
Structure (London, England : 1993), 28(7), 776–785.e3. (2020)
[8] RNA Peach and Mango: Orthogonal two-color fluorogenic aptamers distinguish nearly identical ligands.
Kong, K. Y. S., Jeng, S. C. Y., Rayyan, B., & Unrau, P. J.
RNA (New York, N.Y.), 27(5), 604–615. (2021)
[9] Hidden intermediates in Mango III RNA aptamer folding revealed by pressure perturbation.
Harish, B., Wang, J., Hayden, E. J., Grabe, B., Hiller, W., Winter, R., & Royer, C. A.
Biophysical journal, 121(3), 421–429. (2022)
[10] Computational study on the binding of Mango-II RNA aptamer and fluorogen using the polarizable force field AMOEBA.
Yang, X., Liu, C., Kuo, Y. A., Yeh, H. C., & Ren, P.
Frontiers in molecular biosciences, 9, 946708. (2022)
[11] Red light-emitting short Mango-based system enables tracking a mycobacterial small noncoding RNA in infected macrophages.
Bychenko, O. S., Khrulev, A. A., Svetlova, J. I., Tsvetkov, V. B., Kamzeeva, P. N., Skvortsova, Y. V., Tupertsev, B. S., Ivanov, I. A., Aseev, L. V., Khodarovich, Y. M., Belyaev, E. S., Kozlovskaya, L. I., Zatsepin, T. S., Azhikina, T. L., Varizhuk, A. M., & Aralov, A. V.
Nucleic acids research, 51(6), 2586–2601. (2023)