Structure and dynamics of M13mp19 circular single-strand DNA: effects of ionic strength.
Structure and dynamics of M13mp19 circular single-strand DNA: effects of ionic strength.
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M13mp19 环状单链 DNA 的结构和动力学：离子强度的影响。
DOI：
10.1002/bip.360290208
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发表时间：
1990
期刊：
影响因子：
2.9
通讯作者：
Benight,AS
中科院分区：
文献类型：
--
作者：
Wilson,DH;Price,HL;Henderson,J;Hanlon,S;Benight,AS
对 M13mp19 病毒环状单链 DNA 进行了动态和静态光散射、CD 和光学熔解实验，作为 NaCl 浓度的函数。在从 100 μM 到 1.0MNaCl 的 10,000 倍浓度范围内，熔解曲线和圆二色光谱表明，随着盐浓度的增加，碱基堆积和堆积区域的稳定性增加。对单链 DNA 溶液的动态光散射测量值与 K2（从 1.56 到 20 × 1010cm−2）的函数进行分析表明，收集到的自相关函数是双指数的，从而揭示了两个衰减动态分量的存在。这些分量被认为对应于（1）分子质心的全局平移运动和（2）内部分子亚基的运动。根据评估的这些成分的弛豫率，确定扩散系数D0和Dplat。质心平移扩散系数 D0 在 100 μM 至 1.0M 的 NaCl 浓度范围内以非单调方式变化，变化幅度为 10%，从 3.75 × 10−8 到 3.39 × 10−8cm2/s。同样，从静态光散射实验获得的回转半径RG，在相同的 NaCl 范围内从 699 到 830 Å 变化了 15%。内部亚基的扩散系数 Dplat 显示出对 NaCl 浓度的不同依赖性，并以可滴定的方式降低了近 22%，从 12.46 × 10−8 到 10.26 × 当盐从 100 μM 增加到 1.0M 时，速度为 10−8cm2/s。通过根据圆形劳斯-齐姆链分析光散射数据，可以对这些结果进行半定量解释。 Rouse-Zimm 模型参数是根据实验结果估计的，假设圆链由固定数量的高斯段组成，N+ 1 = 15。内部段的均方根位移 b 估计在 100 mMNaCl 中最小（442 Å）。观察到 b 在 100 μM 中增加到 467 Å，在 1.0 M NaCl 中增加到 524 Å。同时，内部亚基的假设摩擦系数 f 随着 NaCl 浓度的升高而逐渐增加。从评估的 Rouse-Zimm 模型参数推断，随着 NaCl 浓度从 100 mM 增加到 1.0 M，环链的静态柔韧性和内部亚基的扩散位移均减小。这些降低直接收缩了双链 DNA 的盐依赖性行为，当 Na + 浓度增加时，可以观察到更大的灵活性。解链和圆二色测量表明灵活性和内部运动的降低是由于在较高的 NaCl 环境中形成核苷酸堆积所致。在 100 μM NaCl 中，堆叠非常不利，静电对持久长度的贡献可能会使分子变硬。 M13mp19 单链 DNA 内部动力学的可观察变化似乎与从 100 μM 到 1.0M NaCl 的碱基堆积增加有关，这显然对 DNA 的整体三级构象产生相对较小的扰动。
Dynamic and static light scattering, CD, and optical melting experiments have been conducted on M13mp19 viral circular single‐strand DNA as a function of NaCl concentration. Over the 10,000‐fold range in concentration from 100 μMto 1.0MNaCl, the melting curves and CD spectra indicate an increase in base stacking and stability of stacked regions with increased salt concentration. Analysis of dynamic light scattering measurements of the single‐strand DNA solutions as a function ofK2from 1.56 to 20 × 1010cm−2indicates the collected autocorrelation functions are biexponential, thus revealing the presence of two decaying dynamic components. These components are taken to correspond to (1) global translational motions of the molecular center of mass and (2) motions of the internal molecular subunits. From the evaluated relaxation rates of these components, diffusion coefficientsD0andDplatare determined. The center of mass translational diffusion coefficientD0, varies in a nonmonotonic manner, by 10%, from 3.75 × 10−8to 3.39 × 10−8cm2/s over the NaCl concentration range from 100 μMto 1.0M. Likewise, the radius of gyrationRG, obtained from static light scattering experiments, varies by 15% from 699 to 830 Å over the same NaCl range.Dplat, the diffusion coefficient of the internal subunits, displays a different dependence on the NaCl concentration and decreases, by nearly 22% in a titratable fashion, from 12.46 × 10−8to 10.26 × 10−8cm2/s, when the salt is increased from 100 μMto 1.0M. A semiquantitative interpretation of these results is provided by analysis of the light scattering data in terms of the circular Rouse–Zimm chain. Rouse–Zimm model parameters are estimated from the experimental results, assuming the circular chains are composed of a fixed number of Gaussian segments,N+ 1 = 15. The rms displacement of the internal segments,b, is estimated to be the smallest (442 Å) in 100 mMNaCl. Increases ofbto 467 Å in 100 μMand 524 Å in 1.0MNaCl are observed. Meanwhile, the hypothetical friction factor of the internal subunits,f, progressively increases as the NaCl concentration is raised. It is inferred from the evaluated Rouse–Zimm model parameters that both the static flexibility of the circular chain and diffusive displacements of the internal subunits decrease with increases in NaCl concentration from 100 mMto 1.0M. These decreases directly contract the salt‐dependent behavior of double‐stranded DNA, where greater flexibility is observed when the Na+concentration is increased. The melting and CD measurements indicate the decrease in flexibility and internal motions is due to the formation of nucleotide stacking in the higher NaCl environments. In 100 μMNaCl, where stacking is highly unfavored, a significant electrostatic contribution to the persistence length likely acts to stiffen the molecule. It appears the observable changes in the internal dynamics of M13mp19 single‐strand DNA are associated with increases in base stacking that occur from 100 μMto 1.0MNaCl, which apparently induce relatively small perturbations in the overall global tertiary conformation of the DNA.