Measurement of 1H3′-31P dipolar couplings in a DNA oligonucleotide by constant-time NOESY difference spectroscopy

The ratios of cross peak intensities in a selective constant-time NOESY experiment, recorded with and without 31P decoupling, yield values for the sum of the H3′-P scalar and dipolar couplings. The selective refocusing of H3′ resonances in this experiment results in excellent resolution and sensitivity, even in the liquid crystalline phase where the 1H spectrum is broadened by unresolved homonuclear dipolar couplings. The vicinal H3′-P scalar and dipolar couplings in the DNA oligomer d(CGCGAATTCGCG)2 were measured in both isotropic solution, and in a liquid crystalline phase. Isotropic values are in good agreement with values reported previously. Dipolar couplings are in excellent agreement with the NMR structure for this dodecamer, and to a somewhat lesser extent with the X-ray structures.

[1]  H R Drew,et al.  Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. , 1981, Journal of molecular biology.

[2]  A. Bax,et al.  Measurement of proton phosphorus 31 nmr coupling constants in double stranded dna fragments , 1987 .

[3]  Ad Bax,et al.  The NMR Structure of a DNA Dodecamer in an Aqueous Dilute Liquid Crystalline Phase , 2000 .

[4]  K. Wüthrich,et al.  The 2D [31P] spin-echo-difference constant-time [13C, 1H]-HMQC experiment for simultaneous determination of 3J(H3'P) and 3J(C4'P) in 13C-labeled nucleic acids and their protein complexes. , 1999, Journal of magnetic resonance.

[5]  G. Varani,et al.  How accurately and precisely can RNA structure be determined by NMR? , 1997, Journal of molecular biology.

[6]  L. Mueller,et al.  Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions , 1998, Nature Structural Biology.

[7]  G G Hu,et al.  The B-DNA dodecamer at high resolution reveals a spine of water on sodium. , 1998, Biochemistry.

[8]  G. Varani,et al.  Refinement of the structure of protein–RNA complexes by residual dipolar coupling analysis , 1999, Journal of biomolecular NMR.

[9]  S. Grzesiek,et al.  Measurement of homo- and heteronuclear J couplings from quantitative J correlation. , 1994, Methods in enzymology.

[10]  S. Bouaziz,et al.  Determination of and Coupling Constants in 13C-Labeled Nucleic Acids Using Constant-Time HMQC , 1999 .

[11]  G. Marius Clore,et al.  Determination of Three-Bond1H3′–31P Couplings in Nucleic Acids and Protein–Nucleic Acid Complexes by QuantitativeJCorrelation Spectroscopy , 1998 .

[12]  A. Bax,et al.  Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. , 1997, Science.

[13]  C. Griesinger,et al.  Determination of the Angles α and ζ in RNA by cross correlated dipolar and CSA-relaxation. , 2000 .

[14]  A. Gronenborn,et al.  Measurement of Residual Dipolar Couplings of Macromolecules Aligned in the Nematic Phase of a Colloidal Suspension of Rod-Shaped Viruses , 1998 .

[15]  M Kainosho,et al.  H···N hydrogen bond lengths in double stranded DNA from internucleotide dipolar couplings , 2001, Journal of biomolecular NMR.

[16]  B. Reid,et al.  Three-dimensional structure of a DNA hairpin in solution: two-dimensional NMR studies and distance geometry calculations on d(CGCGTTTTCGCG). , 1986, Biochemistry.

[17]  T. James,et al.  How to generate accurate solution structures of double-helical nucleic acid fragments using nuclear magnetic resonance and restrained molecular dynamics. , 1995, Methods in enzymology.

[18]  S. Grzesiek,et al.  Direct Observation of Hydrogen Bonds in Nucleic Acid Base Pairs by Internucleotide 2JNN Couplings , 1998 .

[19]  Ray Freeman,et al.  Band-selective radiofrequency pulses , 1991 .