ArticleNucleic acids research2008
Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 26 citations in OpenAlex.
- Beyond structures: solution NMR as the quantitative engine of integrated structural biology.Frontiers in molecular biosciences · 2026Review
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- NMR Methods for Structural Characterization of Protein-Protein Complexes.Frontiers in molecular biosciences · 2020Article
- Conformational Ensemble of Disordered Proteins Probed by Solvent Paramagnetic Relaxation Enhancement (sPRE).Angewandte Chemie (International ed. in English) · 2018Article
- RNA structure refinement using NMR solvent accessibility data.Scientific reports · 2017Article
- Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering.Chemical reviews · 2016Review
- Revealing an outward-facing open conformational state in a CLC Cl(-)/H(+) exchange transporter.eLife · 2016Article
- Dynamic motions of the HIV-1 frameshift site RNA.Biophysical journal · 2015Article
- A decadentate Gd(III)-coordinating paramagnetic cosolvent for protein relaxation enhancement measurement.Journal of biomolecular NMR · 2014Article
- A novel paramagnetic relaxation enhancement tag for nucleic acids: a tool to study structure and dynamics of RNA.ACS chemical biology · 2013Article
- Studying the structure and dynamics of biomolecules by using soluble paramagnetic probes.Chemphyschem : a European journal of chemical physics and physical chemistry · 2013Review
- Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping.Journal of molecular biology · 2009Article
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
Abstract
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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