ArticleJournal of biomolecular NMR2008
Comparison of alignment tensors generated for native tRNA(Val) using magnetic fields and liquid crystalline media.
Article in Journal of biomolecular NMR, 2008. 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, 29 citations in OpenAlex.
- Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA.Journal of molecular biology · 2016Article
- Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations.Physical chemistry chemical physics : PCCP · 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
- Information content of long-range NMR data for the characterization of conformational heterogeneity.Journal of biomolecular NMR · 2015Article
- Insights into domain-domain motions in proteins and RNA from solution NMR.Accounts of chemical research · 2014Review
- Advances in the determination of nucleic acid conformational ensembles.Annual review of physical chemistry · 2014Review
- NMR studies of nucleic acid dynamics.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2013Article
- Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA.Molecules (Basel, Switzerland) · 2013Article
- A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.Journal of the American Chemical Society · 2013Article
- Independent alignment of RNA for dynamic studies using residual dipolar couplings.Journal of biomolecular NMR · 2012Article
- Residual dipolar couplings: are multiple independent alignments always possible?Journal of biomolecular NMR · 2011Article
- Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography.Journal of molecular biology · 2010Article
- Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering.Methods (San Diego, Calif.) · 2010Review
- Major groove width variations in RNA structures determined by NMR and impact of 13C residual chemical shift anisotropy and 1H-13C residual dipolar coupling on refinement.Journal of biomolecular NMR · 2010Article
- Variable helix elongation as a tool to modulate RNA alignment and motional couplings.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2010Article
- A method for helical RNA global structure determination in solution using small-angle x-ray scattering and NMR measurements.Journal of molecular biology · 2009Article
- Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data.Journal of biomolecular NMR · 2008Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Residual dipolar couplings (RDCs) complement standard NOE distance and J-coupling torsion angle data to improve the local and global structure of biomolecules in solution. One powerful application of RDCs is for domain orientation studies, which are especially valuable for structural studies of nucleic acids, where the local structure of a double helix is readily modeled and the orientations of the helical domains can then be determined from RDC data. However, RDCs obtained from only one alignment media generally result in degenerate solutions for the orientation of multiple domains. In protein systems, different alignment media are typically used to eliminate this orientational degeneracy, where the combination of RDCs from two (or more) independent alignment tensors can be used to overcome this degeneracy. It is demonstrated here for native E. coli tRNA(Val) that many of the commonly used liquid crystalline alignment media result in very similar alignment tensors, which do not eliminate the 4-fold degeneracy for orienting the two helical domains in tRNA. The intrinsic magnetic susceptibility anisotropy (MSA) of the nucleobases in tRNA(Val) was also used to obtain RDCs for magnetic alignment at 800 and 900 MHz. While these RDCs yield a different alignment tensor, the specific orientation of this tensor combined with the high rhombicity for the tensors in the liquid crystalline media only eliminates two of the four degenerate orientations for tRNA(Val). Simulations are used to show that, in optimal cases, the combination of RDCs obtained from liquid crystalline medium and MSA-induced alignment can be used to obtain a unique orientation for the two helical domains in tRNA(Val).
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