Journal of Biomolecular NMR

, Volume 30, Issue 3, pp 287–301 | Cite as

Resolution-optimized NMR measurement of 1DCH, 1DCC and 2DCH residual dipolar couplings in nucleic acid bases

  • Jérôme Boisbouvier
  • David L. Bryce
  • Erin O’Neil-Cabello
  • Edward P. Nikonowicz
  • Ad Bax


New methods are described for accurate measurement of multiple residual dipolar couplings in nucleic acid bases. The methods use TROSY-type pulse sequences for optimizing resolution and sensitivity, and rely on the E.COSY principle to measure the relatively small two-bond 2DCH couplings at high precision. Measurements are demonstrated for a 24-nt stem-loop RNA sequence, uniformly enriched in 13C, and aligned in Pf1. The recently described pseudo-3D method is used to provide homonuclear 1H-1H decoupling, which minimizes cross-correlation effects and optimizes resolution. Up to seven 1H-13C and 13C-13C couplings are measured for pyrimidines (U and C), including 1DC5H5, 1DC6H6, 2DC5H6, 2DC6H5, 1DC5C4, 1DC5C6, and 2DC4H5. For adenine, four base couplings (1DC2H2, 1DC8H8, 1DC4C5, and 1DC5C6) are readily measured whereas for guanine only three couplings are accessible at high relative accuracy (1DC8H8, 1DC4C5, and 1DC5C6). Only three dipolar couplings are linearly independent in planar structures such as nucleic acid bases, permitting cross validation of the data and evaluation of their accuracies. For the vast majority of dipolar couplings, the error is found to be less than ±3% of their possible range, indicating that the measurement accuracy is not limiting when using these couplings as restraints in structure calculations. Reported isotropic values of the one- and two-bond J couplings cluster very tightly for each type of nucleotide.

Key words

carbon-13 cross-validation DNA heteronuclear NMR residual dipolar coupling RNA resolution enhancement TROSY 


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Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Jérôme Boisbouvier
    • 1
    • 2
  • David L. Bryce
    • 1
  • Erin O’Neil-Cabello
    • 1
    • 3
  • Edward P. Nikonowicz
    • 3
  • Ad Bax
    • 1
  1. 1.National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthLaboratory of Chemical PhysicsBethesdaUSA
  2. 2.Laboratoire de RMNInstitut de Biologie Structurale, Jean-Pierre Ebel, UMR 5075 CNRS-CEA-UJFGrenoble, Cedex 1France
  3. 3.Department of Biochemistry and Cell BiologyRice UniversityHoustonUSA

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