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Solution structure of the tobramycin–RNA aptamer complex

Nature Structural Biology volume 5, pages 769–774 (1998)Cite this article

Abstract

We have solved the solution structure of the aminoglycoside antibiotic tobramycin complexed with a stem-loop RNA aptamer. The 14 base loop of the RNA aptamer 'zippers up' alongside the attached stem through alignment of four mismatches and one Watson-Crick pair on complex formation. The tobramycin inserts into the deep groove centered about the mismatch pairs and is partially encapsulated between its floor and a looped out guanine base that flaps over the bound antibiotic. Several potential intermolecular hydrogen bonds between the charged NH 3 groups of tobramycin and acceptor atoms on base pair edges and backbone phosphates anchor the aminoglycoside antibiotic within its sequence/structure specific RNA binding pocket.

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Figure 1: a, Chemical formula and numbering system of the aminoglycoside antibiotic tobramycin.
Figure 2: Solution structure(s) of the tobramycin–RNA aptamer II (A4–U23) complex.
Figure 3: a, A view of the tobramycin binding site in a representative refined structure of the tobramycin–RNA aptamer II (A4–U23) complex.
Figure 4: A comparative view of a, a representative solution structure of the tobramycin–RNA aptamer I (U10–A17) complex11 and b, the tobramycin–RNA aptamer II (U10–A17) complex (this study).

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Acknowledgements

The research was supported by NIH. We thankC. Lin, Z. Cai, W. Hu, A. Majumdar and J. Hubbard for helpful discussions and W. Xu and S. Menzies for RNA sample preparations.

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  1. Cellular Biochemistry & Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, 10021, New York, USA

    Licong Jiang & Dinshaw J. Patel

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Jiang, L., Patel, D. Solution structure of the tobramycin–RNA aptamer complex . Nat Struct Mol Biol 5, 769–774 (1998). https://doi.org/10.1038/1804

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