Open AccessStructure and functional reselection of the Mango-III fluorogenic RNA aptamer
Author(s) -
Robert J. Trachman,
Alexis Autour,
Sunny Jeng,
Amir Abdolahzadeh,
Alessio Andreoni,
Razvan Cojocaru,
Ramil Garipov,
Elena Dolgosheina,
Jay R. Knutson,
Michaël Ryckelynck,
Peter J. Unrau,
A.R. Ferré-D′Amaré
Publication year - 2019
Publication title -
nature chemical biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 6.412
H-Index - 216
eISSN - 1552-4469
pISSN - 1552-4450
DOI - 10.1038/s41589-019-0267-9
Subject(s) - rna , aptamer , chemistry , crystallography , fluorescence , mutant , biophysics , pyrimidine , pseudoknot , stereochemistry , biology , biochemistry , microbiology and biotechnology , physics , quantum mechanics , gene
Several turn-on RNA aptamers that activate small-molecule fluorophores have been selected in vitro. Among these, the ~30 nucleotide Mango-III is notable because it binds the thiazole orange derivative TO1-Biotin with high affinity and fluoresces brightly (quantum yield 0.55). Uniquely among related aptamers, Mango-III exhibits biphasic thermal melting, characteristic of molecules with tertiary structure. We report crystal structures of TO1-Biotin complexes of Mango-III, a structure-guided mutant Mango-III(A10U), and a functionally reselected mutant iMango-III. The structures reveal a globular architecture arising from an unprecedented pseudoknot-like connectivity between a G-quadruplex and an embedded non-canonical duplex. The fluorophore is restrained into a planar conformation by the G-quadruplex, a lone, long-range trans Watson-Crick pair (whose A10U mutation increases quantum yield to 0.66), and a pyrimidine perpendicular to the nucleobase planes of those motifs. The improved iMango-III and Mango-III(A10U) fluoresce ~50% brighter than enhanced green fluorescent protein, making them suitable tags for live cell RNA visualization.