CHARACTERIZATION OF THE OVERALL AND INTERNAL DYNAMICS OF SHORT OLIGONUCLEOTIDES BY DEPOLARIZED DYNAMIC LIGHT-SCATTERING AND NMR RELAXATION MEASUREMENTS
CHARACTERIZATION OF THE OVERALL AND INTERNAL DYNAMICS OF SHORT OLIGONUCLEOTIDES BY DEPOLARIZED DYNAMIC LIGHT-SCATTERING AND NMR RELAXATION MEASUREMENTS
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DOI：
10.1021/bi00455a030
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发表时间：
1990-01-23
期刊：
影响因子：
2.9
通讯作者：
PECORA, R
中科院分区：
文献类型：
--
作者：
EIMER, W;WILLIAMSON, JR;PECORA, R
用去偏振动态光散射(DDLS)和时间分辨核Overhaser效应交叉弛豫方法研究了不同长度和形状的d(CG)4、d(CG)5和d(CGCGTTGTTCGCG)在溶液中的动力学.对于柱对称分子，DDLS谱主要受圆柱主对称轴的旋转控制。实验关联时间描述了在流体动力棒边界条件下寡核苷酸的旋转。结果表明，Tirado和Garcia de la Torre的流体力学理论很好地预测了本文所研究的小轴比的轴对称分子的旋转扩散系数。这些关系被用来根据测量的关联时间计算DNA片段的溶液尺寸。八聚体和十二聚体的流体力学直径为20.5±-。1.0.ANG，假设每个基数上升3.4ANG。十三聚体d(CGTTGTTCGCG)采用发夹结构，尺寸接近球形，直径23.0.+-。2.0。ANG..DDLS弛豫测量为区分不同构象的寡核苷酸(例如，DNA双螺旋结构和发夹结构)提供了一种强有力的方法。此外，旋转相关时间是不同片段长度的一个非常敏感的探针。核磁共振结果反映了分子的各向异性运动以及存在的局部内部运动量。核磁共振的实验关联时间由寡核苷酸的短轴和长轴的旋转决定。如果假设振动运动的衰减比整体重定向运动快得多，则各种关联时间的贡献由核间矢量相对于主轴的相对取向和内部运动的关联函数给出。将我们的结果与其他长度高达20个碱基对的短寡核苷酸的核磁共振弛豫测量结果进行了比较。核间载体重定向的各种动力学模型被应用于它们的解释。局部内运动的程度明显与DNA片段的长度和碱基序列无关，并且对用交叉弛豫速率测量的有效关联时间有显著的贡献。
The dynamics of three synthetic oligonucleotides d(CG)4, d(CG)5, and d(CGCGTTGTTCGCG) of different length and shape were studied in solution by depolarized dynamic light scattering (DDLS) and time-resolved nuclear Overhauser effect cross-relaxation measurements. For cylindrically symmetric molecules the DDLS spectrum is dominated by the rotation of the main symmetry axis of the cylinder. The experimental correlation times describe the rotation of the oligonucleotides under hydrodynamic stick boundary conditions. It is shown that the hydrodynamic theory of Tirado and Garcia de la Torre gives good predictions of the rotational diffusion coefficients of cylindrically symmetric molecules of the small axial ratios studied here. These relations are used to calculate the solution dimensions of the DNA fragments from measured correlation times. The hydrodynamic diameter of the octamer and dodecamer is 20.5 .+-. 1.0 .ANG., assuming a rise per base of 3.4 .ANG.. The tridecamer, d(CGCGTTGTTCGCG), adopts a hairpin structure with nearly spherical dimensions and a diameter of 23.0 .+-. 2.0 .ANG.. The DDLS relaxation measurements provide a powerful method for distinguishing between different conformations of the oligonucleotides (e.g., DNA double-helix versus hairpin structure). Furthermore, the rotational correlation times are a very sensitive probe of the length of different fragments. The NMR results reflect the anisotropic motion of the molecules as well as the amount of local internal motion present. The experimental correlation time from NMR is determined by the rotation of both the short and long axes of the oligonucleotide. The contributions of the various correlation times are given by the relative orientation of the internuclear vector with respect to the main axis and the correlation function for internal motion, if it is assumed that the librational motions decay much faster than the overall reorientation motion. Our results are compared with those from NMR relaxation measurements on other short oligonucleotides with lengths of up to 20 base pairs. Various dynamic models for the reorientation of the internuclear vector are applied to their interpretation. The extent of local internal motion is apparently independent of the length and base sequence of the DNA fragments and gives a significant contribution to the effective correlation time measured by the cross-relaxation rate.