ArticleNature protocols2007
Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings.
Article in Nature protocols, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- The RNA structural code: orchestrating gene expression and enabling precision therapies.Acta pharmacologica Sinica · 2026Review
- Decoding RNA Structural Ensembles: Energy Landscape Exploration of the TAR Stemloop.Journal of chemical theory and computation · 2026Article
- Application of NMR to Large RNAs.Journal of molecular biology · 2025Review
- Relaxation Optimized Heteronuclear Experiments for Extending the Size Limit of RNA Nuclear Magnetic Resonance.Journal of the American Chemical Society · 2025Article
- Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble.Journal of the American Chemical Society · 2023Article
- RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems.Biophysical journal · 2022Article
- Article
- RNA Dynamics by NMR Spectroscopy.Chembiochem : a European journal of chemical biology · 2019Review
- Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy.Wiley interdisciplinary reviews. RNA · 2019Review
- Maximizing accuracy of RNA structure in refinement against residual dipolar couplings.Journal of biomolecular NMR · 2019Article
- Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.RNA (New York, N.Y.) · 2018Article
- Accurate Measurement of Residual Dipolar Couplings in Large RNAs by Variable Flip Angle NMR.Journal of the American Chemical Society · 2018Article
- Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales.Biochemistry · 2016Article
- Measuring Residual Dipolar Couplings in Excited Conformational States of Nucleic Acids by CEST NMR Spectroscopy.Journal of the American Chemical Society · 2015Article
- New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.Nucleic acids research · 2015Review
- Dynamic motions of the HIV-1 frameshift site RNA.Biophysical journal · 2015Article
- Structural dynamics of a single-stranded RNA-helix junction using NMR.RNA (New York, N.Y.) · 2014Article
- From a structural average to the conformational ensemble of a DNA bulge.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges.The journal of physical chemistry. B · 2014Article
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Authors and funding
6 authors.
Funding
Abstract
We present a protocol for determining the relative orientation and dynamics of A-form helices in 13C/15N isotopically enriched RNA samples using NMR residual dipolar couplings (RDCs). Non-terminal Watson-Crick base pairs in helical stems are experimentally identified using NOE and trans-hydrogen bond connectivity and modeled using the idealized A-form helix geometry. RDCs measured in the partially aligned RNA are used to compute order tensors describing average alignment of each helix relative to the applied magnetic field. The order tensors are translated into Euler angles defining the average relative orientation of helices and order parameters describing the amplitude and asymmetry of interhelix motions. The protocol does not require complete resonance assignments and therefore can be implemented rapidly to RNAs much larger than those for which complete high-resolution NMR structure determination is feasible. The protocol is particularly valuable for exploring adaptive changes in RNA conformation that occur in response to biologically relevant signals. Following resonance assignments, the procedure is expected to take no more than 2 weeks of acquisition and data analysis time.
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