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Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL
Nucleic Acids Research (2008)
  • Vincenzo Venditti, University of Siena
  • Neri Niccolai, University of Siena
  • Samuel E. Butcher, University of Siena

The surface accessibility of macromolecules plays a key role in modulating molecular recognition events. RNA is a complex and dynamic molecule involved in many aspects of gene expression. However, there are few experimental methods available to measure the accessible surface of RNA. Here, we investigate the accessible surface of RNA using NMR and the small paramagnetic molecule TEMPOL. We investigated two RNAs with known structures, one that is extremely stable and one that is dynamic. For helical regions, the TEMPOL probing data correlate well with the predicted RNA surface, and the method is able to distinguish subtle variations in atom depths, such as the relative accessibility of pyrimidine versus purine aromatic carbon atoms. Dynamic motions are also detected by TEMPOL probing, and the method accurately reports a previously characterized pH-dependent conformational transition involving formation of a protonated C–A pair and base flipping. Some loop regions are observed to exhibit anomalously high accessibility, reflective of motions that are not evident within the ensemble of NMR structures. We conclude that TEMPOL probing can provide valuable insights into the surface accessibility and dynamics of RNA, and can also be used as an independent means of validating RNA structure and dynamics in solution.

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This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Citation Information
Vincenzo Venditti, Neri Niccolai and Samuel E. Butcher. "Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL" Nucleic Acids Research Vol. 36 Iss. 4 (2008)
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