Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy

被引:0
作者
Zhengrong Wu
Frank Delaglio
Nico Tjandra
Victor B. Zhurkin
Ad Bax
机构
[1] National Institute of Diabetes and Digestive and Kidney Diseases,Laboratory of Chemical Physics
[2] National Heart,Laboratory of Biophysical Chemistry
[3] Lung and Blood Institute,Laboratory of Experimental and Computational Biology
[4] National Cancer Institute,undefined
[5] National Institutes of Health,undefined
[6] National Cancer Institute,undefined
[7] National Institutes of Health,undefined
来源
Journal of Biomolecular NMR | 2003年 / 26卷
关键词
chemical shift anisotropy; Dickerson dodecamer; dipolar coupling; liquid crystal; NMR; sugar pucker;
D O I
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中图分类号
学科分类号
摘要
The solution structure of d(CGCGAATTCGCG)2 has been determined on the basis of an exceptionally large set of residual dipolar couplings. In addition to the heteronuclear 13C-1H and 15N-1H and qualitative homonuclear 1H-1H dipolar couplings, previously measured in bicelle medium, more than 300 quantitative 1H-1H and 22 31P-1H dipolar restraints were obtained in liquid crystalline Pf1 medium, and 22 31P chemical shift anisotropy restraints. High quality DNA structures can be obtained solely on the basis of these new restraints, and these structures are in close agreement with those calculated previously on the basis of 13C-1H and 15N-1H dipolar couplings. In the newly calculated structures, 31P-1H dipolar and 3JsubH3′Psub couplings and 31P CSA data restrain the phosphodiester backbone torsion angles. The final structure represents a quite regular B-form helix with a modest bending of ∼10°, which is essentially independent of whether or not electrostatic terms are used in the calculation. Combined, the number of homo- and heteronuclear dipolar couplings significantly exceeds the number of degrees of freedom in the system. Results indicate that the dipolar coupling data cannot be fit by a single structure, but are compatible with the presence of rapid equilibria between C2′-endo and C3′-endo deoxyribose puckers (sugar switching). The C2′-H2′/H2′′ dipolar couplings in B-form DNA are particularly sensitive to sugar pucker and yield the largest discrepancies when fit to a single structure. To resolve these discrepancies, we suggest a simplified dipolar coupling analysis that yields N/S equilibria for the ribose sugar puckers, which are in good agreement with previous analyses of NMR JHH couplings, with a population of the minor C3′-endo form higher for pyrimidines than for purines.
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页码:297 / 315
页数:18
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