Solution structure and dynamics of DNA topoisomers: Dynamic light scattering studies and Monte Carlo simulations
Solution structure and dynamics of DNA topoisomers: Dynamic light scattering studies and Monte Carlo simulations
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DNA 拓扑异构体的溶液结构和动力学：动态光散射研究和蒙特卡罗模拟
DOI：
10.1002/bip.360340506
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发表时间：
1994
期刊：
影响因子：
2.9
通讯作者：
A. Vologodskii
中科院分区：
文献类型：
--
作者：
J. Langowski;U. Kapp;K. Klenin;A. Vologodskii
用动态光散射(DLS)测量了pUCl8 DNA(2687个碱基对)窄分布拓扑异构体的扩散系数和内运动随连接数的变化。用C-18反相高效液相色谱分离拓扑异构酶I/乙锭生成的拓扑异构体家族，得到拓扑异构体的分布。测量的扩散系数与蒙特卡罗模型预测的扩散系数吻合得很好，该模型用于产生具有指定连接数的DNA拓扑异构体的平衡系综。模型中使用的唯一参数是DNA的弯曲持续长度、扭转刚度和流体力学半径，这些参数是独立于其他技术的。采用α=4.10−12和8.8·10−12dyn cm两种不同的扭转刚度值。通过使用“有效DNA半径”来考虑DNA中的链内相互作用，该半径在rDNA=1-8 nm之间变化。当α=4·10−12dyn cm，rDNA=4 nm时，计算值与实测值吻合最好。用DLS自相关函数的快速松弛幅度来表征DNA拓扑异构体的内部运动。我们先前的结果证实了超螺旋会导致内部运动幅度的降低。此外，在超螺旋密度为σ=−0.03时，我们还观察到了内部运动振幅的特征极大值。最大值出现在与之前由L.Song等人描述的pUC8二聚体的结构转变相同的范围内。(1990年J.Mol.比奥尔。214、307-326)。©1994 John Wiley&Sons，Inc.
Using dynamic light scattering (DLS), we have measured the diffusion coefficient and internal motions of narrow topoisomer distributions of pUCl8 DNA (2687 base pairs) as a function of linking number. The topoisomer distributions were prepared by C‐18 reversed phase high performance liquid chromatography separation of topoisomerase I/ethidium‐generated topoisomer families. The measured diffusion coefficients agree well with those predicted by a Monte Carlo model for the generation of equilibrium ensembles of DNA topoisomers of defined linking number. The only parameters used in the model were the bending persistence length, torsional rigidity, and hydrodynamic radius of DNA known independently from other techniques. Two different values for the torsional rigidity, α = 4 · 10−12 and 8.8 · 10−12 dyn cm, were used. Intrachain interactions in the DNA were taken into account by using an “effective DNA radius,” which was varied between rDNA = 1–8 nm. The best agreement between the measured and calculated values was obtained for α = 4 · 10−12 dyn cm, rDNA = 4 nm. The internal motions of the DNA topoisomers were characterized by the amplitude of the fast relaxation of the DLS autocorrelation function. Our earlier result that supercoiling leads to a decrease in the amplitude of internal motion was confirmed. In addition, we see a characteristic maximum of the internal motion amplitude at a superhelix density of σ = −0.03. The maximum occurs in the same range as a structural transition in pUC8 dimers previously described by L. Song et al. (1990 J. Mol. Biol. 214, 307–326). © 1994 John Wiley & Sons, Inc.
DNA 超螺旋的计算机模拟。
影响因子：
--
作者：
Olson,WK;Zhang,PS
通讯作者：
Zhang,PS
通过计算机模拟的超螺旋 DNA 能量学和动力学。
影响因子：
5.6
作者：
Schlick,T;Olson,WK
通讯作者：
Olson,WK