Investigation of the solution structure of a DNA octamer [d(GGAATTCC)]2 using two-dimensional nuclear Overhauser enhancement spectroscopy.
Investigation of the solution structure of a DNA octamer [d(GGAATTCC)]2 using two-dimensional nuclear Overhauser enhancement spectroscopy.
复制标题
使用二维核 Overhauser 增强光谱研究 DNA 八聚体 [d(GGAATTCC)]2 的溶液结构。
DOI：
10.1111/j.1432-1033.1985.tb08996.x
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发表时间：
1985
期刊：
影响因子：
--
通讯作者：
Keepers,JW
中科院分区：
文献类型：
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作者：
Broido,MS;James,TL;Zon,G;Keepers,JW
在一系列混合时间下，在500 MHz下获得了水溶液中[d（GGAATTCC）] 2的纯吸收相中的质子二维核奥弗豪泽增强（2D NOE）光谱。通过与使用包括所有质子偶极-偶极相互作用和自旋扩散的完整70 × 70弛豫矩阵计算的理论光谱进行比较来分析实验数据[Keepers，J. W. & James，T. L.（1984）J. Magn. Reson. 57，404-426]。使用两种结构计算每个混合时间的理论光谱：标准B-型DNA结构和基于标题八聚体的六个内部残基与十二聚体[d（CGCGAATTCGCG）]2的六个内部残基的相似性的能量最小化结构，已确定其晶体结构。标准B-形式和能量最小化结构都不会产生精确再现实验光谱中所有峰强度的理论2D NOE光谱。然而，实验光谱的许多特征可以用B-形式和能量最小化结构来表示。序列依赖性结构特征在2D NOE光谱中表现出来，特别是在嘌呤-嘧啶连接处，如先前在晶体结构中所述。总的来说，能量最小化结构似乎产生了理论上的2D NOE光谱，其模拟了实验光谱的许多方面（如果不是全部的话）。所有2D NOE数据与质子自旋晶格弛豫时间测量所暗示的纳秒校正时间一致。但是，使用有效各向同性相关时间的小变化的一些2D NOE数据的更好拟合表明，溶液中的八聚体双链体结构内的迁移率可能存在一些局部变化。
Proton two‐dimensional nuclear Overhauser enhancement (2D NOE) spectra in the pure absorption phase were obtained at 500 MHz for [d(GGAATTCC)]2in aqueous solution at a series of mixing times. The experimental data were analyzed by comparison with theoretical spectra calculated using the complete 70 × 70 relaxation matrix including all proton dipole‐dipole interactions and spin diffusion [Keepers, J. W. & James, T. L. (1984)J. Magn. Reson. 57, 404–426]. The theoretical spectra at each mixing time were calculated using two structures: a standard B‐form DNA structure and an energy‐minimized structure based on the similarity of the six internal residues of the title octamer with those of the dodecamer [d(CGCGAATTCGCG)]2, for which the crystal structure has been determined. Neither the standard B‐form nor the energy‐minimized structure will yield theoretical 2D NOE spectra which accurately reproduce all peak intensities in the experimental spectra. However, many features of the experimental spectra can be represented by both the B‐form and the energy‐minimized structure. Sequence‐dependent structural characteristics are manifest in the 2D NOE spectra, in particular at the purine‐pyrimidine junction as noted previously in the crystal structure. On the whole, the energy‐minimized structure appears to yield theoretical 2D NOE spectra which mimic many, if not all, aspects of the experimental spectra. All 2D NOE data were consistent with nanosecond correction times as implied by proton spin‐lattice relaxation time measurements. But better fits of some of the 2D NOE data using small variations in an effective isotropic correlation time suggest that there may be some local variations in mobility within the octamer duplex structure in solution.