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Journal of Biomolecular NMR

, Volume 30, Issue 1, pp 61–70 | Cite as

Enhanced spectral resolution in RNA HCP spectra for measurement of 3JC2′P and 3JC4′P couplings and 31P chemical shift changes upon weak alignment

  • Erin O'Neil-Cabello
  • Zhengrong Wu
  • David L. Bryce
  • Edward P. Nikonowicz
  • Ad Bax
Article

Abstract

The `out-and-back' 3D HCP experiment, using gradient- and sensitivity-enhanced detection, provides a convenient method for assignment of the 31P NMR spectra and accurate measurement of the 31P chemical shifts of ribonucleic acids. The 13C resolution in such spectra can be doubled, at the cost of a 50% reduction in sensitivity, by combining 13C evolution during the 13C-\31P\ de- and rephasing periods. The multiple connectivities observable for a given 31P, including correlations to the intranucleotide C5′H2 and C4′H groups, and the C2′H, C3′H and C4′H groups of the preceding nucleotide, permit independent measurements of the 31P shift. The 13C spectrum of these groups is typically crowded for an RNA molecule in isotropic solution and overlap becomes more problematic in media used to achieve partial alignment. However, many of these correlations are resolvable in the combined-evolution HCP spectrum. The difference in 31P chemical shift between isotropic solution and a medium containing liquid crystalline Pf1 provides information on the orientation of phosphate groups. The intensities measured in the 3D HCP spectrum, obtained for an isotropic sample, yield values for the 3JC2′P and 3JC4′P couplings, thereby providing important restraints for the backbone torsion angles ε and β. The experiments are illustrated for a uniformly 13C-enriched, 24-residue stem-loop RNA sequence, and results for the helical stem region show close agreement between observed Δδ(31P) values and those predicted for a model A-form RNA helix when using a uniform 31P CSA tensor. This confirms that Δδ(31P) values can be used directly as restraints in refining nucleic acid structures.

CSA Karplus equation liquid crystal Pf1 phosphodiester RNA torsion angle 

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Supplementary material

APp.5381097_1.pdf
Supplementary material

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Erin O'Neil-Cabello
    • 1
    • 2
  • Zhengrong Wu
    • 1
  • David L. Bryce
    • 1
  • Edward P. Nikonowicz
    • 2
  • Ad Bax
    • 1
  1. 1.Laboratory of Chemical Physics, NIDDKNational Institutes of HealthBethesdaU.S.A
  2. 2.Rice UniversityDepartment of Biochemistry and Cell BiologyHoustonU.S.A

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