ArticleJournal of biomolecular NMR2005
Iron responsive element RNA flexibility described by NMR and isotropic reorientational eigenmode dynamics.
Article in Journal of biomolecular NMR, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Review
- RNA Dynamics by NMR Spectroscopy.Chembiochem : a European journal of chemical biology · 2019Review
- NMR studies of nucleic acid dynamics.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2013Article
- Synergistic applications of MD and NMR for the study of biological systems.Journal of biomedicine & biotechnology · 2012Review
- Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy.Nature methods · 2011Review
- MD simulations of the dsRBP DGCR8 reveal correlated motions that may aid pri-miRNA binding.Biophysical journal · 2010Article
- Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA.The journal of physical chemistry. B · 2010Article
- Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs.Methods (San Diego, Calif.) · 2009Article
- RNA phosphodiester backbone dynamics of a perdeuterated cUUCGg tetraloop RNA from phosphorus-31 NMR relaxation analysis.Journal of biomolecular NMR · 2009Article
- Preparation, resonance assignment, and preliminary dynamics characterization of residue specific 13C/15N-labeled elongated DNA for the study of sequence-directed dynamics by NMR.Journal of biomolecular NMR · 2009Article
- Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition.Nucleic acids research · 2009Article
- Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling.Journal of the American Chemical Society · 2008Article
- RNA in motion.Current opinion in chemical biology · 2008Review
- Assessing the performance of implicit solvation models at a nucleic acid surface.Physical chemistry chemical physics : PCCP · 2008Article
- NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops.Nucleic acids research · 2008Article
- iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge.Biophysical journal · 2007Article
- Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings.Journal of biomolecular NMR · 2006Article
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4 authors.
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Abstract
The first example of the application of reorientational eigenmode dynamics (RED) to RNA is shown here for the small and floppy Iron Responsive Element (IRE) RNA hairpin. Order parameters calculated for bases and riboses from a 12 ns molecular dynamics trajectory are compared to experimentally determined order parameters from 13C-1H NMR relaxation experiments, and shown to be in qualitative agreement. Given the small size of the IRE hairpin and its very flexible loop, isotropic RED (iRED) was also used to analyze the trajectory in order to describe its dynamic motions. iRED analysis shows that the global and internal dynamics of the IRE are not rigorously separable, which will result in inaccurate experimental order parameters. In addition, the iRED analysis described the many correlated motions that comprise the dynamics of the IRE RNA. The combined use of NMR relaxation, RED, and iRED provide a uniquely detailed description of IRE RNA dynamics.
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