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Investigating the Conformational Diversity of the TMR‑3 Aptamer

Maximilian Gauger,E. Duchardt-Ferner,Anna-Lena J Halbritter,Thilo Hetzke,S. T. Sigurdsson,J. Wöhnert,Thomas F. Prisner

Published 2025 in Journal of the American Chemical Society

ABSTRACT

Aptamers are a class of in vitro selected small RNA motifs that bind a small-molecule ligand with high affinity and specificity. They are promising candidates for the regulation of gene expression in vivo and can aid in further understanding the interaction of RNA with small molecules and conformational changes that may occur upon ligand binding. The TMR-3 aptamer was selected via systematic evolution of ligands by exponential enrichment (SELEX) and binds the fluorophores tetramethylrhodamine (TMR) and 5-carboxy-tetramethylrhodamine (5-TAMRA) with nanomolar affinity. The three-dimensional structure of the TMR-3 aptamer complex with 5-TAMRA was previously determined using liquid-state NMR. By combining the existing NMR restraints with long-range PELDOR distance and orientation information, a broad structural ensemble was generated. From this broad ensemble, a subset of structures was selected by globally fitting orientation-selective PELDOR data from multiple frequency bands. The subensemble represents the conformational variety resulting from the dynamics of the complex. The overall structure of the three-way junction, previously reported by NMR experiments, is retained in the ensemble of the bound state and we were additionally able to characterize the fluctuation of the different stems of the aptamer. Furthermore, in addition to the ligand-bound state we could access the unbound state of the TMR-3 aptamer which was previously uncharacterized. The unbound state of the aptamer is much more structurally diverse, compared to the ligand-bound state. A significant fraction of the ensemble of the unbound state strongly resembles the ligand-bound state, indicating that the ligand-bound state is preformed, which further suggests a conformational-capture ligand-binding mechanism. Apart from the conformations that resemble the ligand-bound state, distinct conformational states which are not present in the presence of the ligand, were successfully identified.

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