ArticleJournal of biomolecular NMR2006
Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings.
Article in Journal of biomolecular NMR, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 58 citations in OpenAlex.
- Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction.Nature communications · 2020Article
- Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.RNA (New York, N.Y.) · 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
- Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA.Journal of molecular biology · 2016Article
- Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.Journal of the American Chemical Society · 2015Article
- Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs.The journal of physical chemistry. B · 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
- Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges.The journal of physical chemistry. B · 2014Article
- Structure and sequence elements of the CR4/5 domain of medaka telomerase RNA important for telomerase function.Nucleic acids research · 2014Article
- Advances in the determination of nucleic acid conformational ensembles.Annual review of physical chemistry · 2014Review
- Molecular mechanism of GTPase activation at the signal recognition particle (SRP) RNA distal end.The Journal of biological chemistry · 2013Article
- Nucleic acid helix structure determination from NMR proton chemical shifts.Journal of biomolecular NMR · 2013Article
- Binding of the 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs to tRNA(phe.).PloS one · 2013Article
- Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch.Nucleic acids research · 2012Article
- Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy.Nature methods · 2011Review
- 3D maps of RNA interhelical junctions.Nature protocols · 2011Article
- Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.Current opinion in structural biology · 2011Review
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
We examined how static and dynamic deviations from the idealized A-form helix propagate into errors in the principal order tensor parameters determined using residual dipolar couplings (rdcs). A 20-ns molecular dynamics (MD) simulation of the HIV-1 transactivation response element (TAR) RNA together with a survey of spin relaxation studies of RNA dynamics reveals that pico-to-nanosecond local motions in non-terminal Watson-Crick base-pairs will uniformly attenuate base and sugar one bond rdcs by approximately 7%. Gaussian distributions were generated for base and sugar torsion angles through statistical comparison of 40 RNA X-ray structures solved to <3.0 A resolution. For a typical number (>or=11) of one bond C-H base and sugar rdcs, these structural deviations together with rdc uncertainty (1.5 Hz) lead to average errors in the magnitude and orientation of the principal axis of order that are <9% and <4 degrees, respectively. The errors decrease to <5% and <4 degrees for >or=17 rdcs. A protocol that allows for estimation of error in A-form order tensors due to both angular deviations and rdc uncertainty (Aform-RDC) is validated using theoretical simulations and used to analyze rdcs measured previously in TAR in the free state and bound to four distinct ligands. Results confirm earlier findings that the two TAR helices undergo large changes in both their mean relative orientation and dynamics upon binding to different targets.
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