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RNA structure

Adding a second dimension

Nature Chemistry volume 3, pages 913–915 (2011)Cite this article

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Mutating RNA one nucleotide at a time and measuring the impact of this on its chemical reactivity provides a strategy for determining its three-dimensional structure, and from there, hopefully, its function.

In-depth biophysical studies of how RNA molecules fold and function often begin with the determination of the RNA secondary structure — a two-dimensional map that specifies which residues are base paired and which form loops, bulges and higher-order junctions. RNA chemical probing — in which those nucleotides not involved in secondary and tertiary interactions are selectively modified — can be used to experimentally map out residues that are base paired. These base-pairing patterns can then be fed into prediction algorithms that compute the energetic stabilities of RNA secondary structure based on well-known sequence-dependent stacking and hydrogen-bonding interactions. Such approaches have enabled the accurate determination of secondary structure for RNAs made from thousands of nucleotides1 — providing a powerful tool for exploring the expanding role of non-coding RNAs.

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Figure 1: From chemical mapping to 3D structure.

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Authors and Affiliations

  1. Katja Petzold and Hashim M. Al-Hashimi are in the Department of Chemistry and Biophysics at the University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA,

    Katja Petzold & Hashim M. Al-Hashimi

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  1. Katja Petzold
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  2. Hashim M. Al-Hashimi
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Correspondence to Hashim M. Al-Hashimi.

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Competing interests

H.M.A.-H. is an advisor to and holds an ownership interest in Nymirum, an RNA-based drug-discovery company.

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Petzold, K., Al-Hashimi, H. Adding a second dimension. Nature Chem 3, 913–915 (2011). https://doi.org/10.1038/nchem.1209

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