Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy |
| |
Authors: | Wu Zhengrong Delaglio Frank Tjandra Nico Zhurkin Victor B Bax Ad |
| |
Institution: | (1) Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, USA;(2) Laboratory of Biophysical Chemistry, National Heart, Lung and Blood Institute, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, U.S.A;(3) Laboratory of Experimental and Computational Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, U.S.A |
| |
Abstract: | 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 3Jsub
H3
P
sub 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![prime](/content/k16093752u108158/xxlarge8242.gif) 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. |
| |
Keywords: | chemical shift anisotropy Dickerson dodecamer dipolar coupling liquid crystal NMR sugar pucker |
本文献已被 PubMed SpringerLink 等数据库收录! |
|