ArticleMethods in enzymology2015
Characterizing RNA Excited States Using NMR Relaxation Dispersion.
Article in Methods in enzymology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Special Issue "Application of NMR Spectroscopy in Biomolecules".International journal of molecular sciences · 2026Article
- Application of NMR to Large RNAs.Journal of molecular biology · 2025Review
- DynaRNA: accurate dynamic RNA conformation ensemble generation with diffusion model.Communications biology · 2025Article
- Relaxation Optimized Heteronuclear Experiments for Extending the Size Limit of RNA Nuclear Magnetic Resonance.Journal of the American Chemical Society · 2025Article
- Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics.International journal of molecular sciences · 2024Review
- Visualizing a two-state conformational ensemble in stem-loop 3 of the transcriptional regulator 7SK RNA.Nucleic acids research · 2024Article
- Dynamically regulated two-site interaction of viral RNA to capture host translation initiation factor.Nature communications · 2023Article
- Pressure pushes tRNAProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs.Chemical reviews · 2022Review
- Rational design of hairpin RNA excited states reveals multi-step transitions.Nature communications · 2022Article
- Hidden intermediates in Mango III RNA aptamer folding revealed by pressure perturbation.Biophysical journal · 2022Article
- Mutate-and-chemical-shift-fingerprint (MCSF) to characterize excited states in RNA using NMR spectroscopy.Nature protocols · 2021Review
- Chemical shift prediction of RNA imino groups: application toward characterizing RNA excited states.Nature communications · 2021Article
- Slow motions in A·T rich DNA sequence.Scientific reports · 2020Article
- Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA.Biophysical journal · 2020Article
- Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon RJournal of biomolecular NMR · 2020Article
- Article
- NMR Relaxation Dispersion Reveals Macrocycle Breathing Dynamics in a Cyclodextrin-based Rotaxane.Journal of the American Chemical Society · 2020Article
- Article
- Exposing Hidden High-Affinity RNA Conformational States.Journal of the American Chemical Society · 2020Article
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Authors and funding
7 authors.
Funding
Abstract
Changes in RNA secondary structure play fundamental roles in the cellular functions of a growing number of noncoding RNAs. This chapter describes NMR-based approaches for characterizing microsecond-to-millisecond changes in RNA secondary structure that are directed toward short-lived and low-populated species often referred to as "excited states." Compared to larger scale changes in RNA secondary structure, transitions toward excited states do not require assistance from chaperones, are often orders of magnitude faster, and are localized to a small number of nearby base pairs in and around noncanonical motifs. Here, we describe a procedure for characterizing RNA excited states using off-resonance R1ρ NMR relaxation dispersion utilizing low-to-high spin-lock fields (25-3000 Hz). R1ρ NMR relaxation dispersion experiments are used to measure carbon and nitrogen chemical shifts in base and sugar moieties of the excited state. The chemical shift data are then interpreted with the aid of secondary structure prediction to infer potential excited states that feature alternative secondary structures. Candidate structures are then tested by using mutations, single-atom substitutions, or by changing physiochemical conditions, such as pH and temperature, to either stabilize or destabilize the candidate excited state. The resulting chemical shifts of the mutants or under different physiochemical conditions are then compared to those of the ground and excited states. Application is illustrated with a focus on the transactivation response element from the human immune deficiency virus type 1, which exists in dynamic equilibrium with at least two distinct excited states.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.