Merlitz H, Rippe K, Klenin K V, Langowski J
Division Biophysics of Macromolecules, German Cancer Research Center (DKFZ), Heidelberg.
Biophys J. 1998 Feb;74(2 Pt 1):773-9. doi: 10.1016/S0006-3495(98)74002-0.
A Brownian dynamics (BD) model described in the accompanying paper (Klenin, K., H. Merlitz, and J. Langowski. 1998. A Brownian dynamics program for the simulation of linear and circular DNA, and other wormlike chain polyelectrolytes. Biophys. J. 74:000-000) has been used for computing the end-to-end distance distribution function, the cyclization probability, and the cyclization kinetics of linear DNA fragments between 120 and 470 basepairs with optional insertion of DNA bends. Protein-mediated DNA loop formation was modeled by varying the reaction distance for cyclization between 0 and 10 nm. The low cyclization probability of DNA fragments shorter than the Kuhn length (300 bp) is enhanced by several orders of magnitude when the cyclization is mediated by a protein bridge of 10 nm diameter, and/or when the DNA is bent. From the BD trajectories, end-to-end collision frequencies were computed. Typical rates for loop formation of linear DNAs are 1.3 x 10(3) s(-1) (235 bp) and 4.8 x 10(2) s(-1) (470 bp), while the insertion of a 120 degree bend in the center increases this rate to 3.0 x 10(4) s(-1) (235 bp) and 5.5 x 10(3) s(-1) (470 bp), respectively. The duration of each encounter is between 0.05 and 0.5 micros for these DNAs. The results are discussed in the context of the interaction of transcription activator proteins.
随附论文（Klenin, K., H. Merlitz, and J. Langowski. 1998. A Brownian dynamics program for the simulation of linear and circular DNA, and other wormlike chain polyelectrolytes. Biophys. J. 74:000 - 000）中描述的布朗动力学（BD）模型已用于计算120至470个碱基对之间线性DNA片段的端到端距离分布函数、环化概率和环化动力学，这些片段可选择插入DNA弯曲。通过将环化反应距离在0至10纳米之间变化来模拟蛋白质介导的DNA环形成。当环化由直径为10纳米的蛋白质桥介导和/或DNA弯曲时，短于库恩长度（300 bp）的DNA片段的低环化概率会提高几个数量级。从BD轨迹计算端到端碰撞频率。线性DNA环形成的典型速率为1.3×10³ s⁻¹（235 bp）和4.8×10² s⁻¹（470 bp），而在中心插入120度弯曲会使该速率分别提高到3.0×10⁴ s⁻¹（235 bp）和5.5×10³ s⁻¹（470 bp）。这些DNA每次相遇的持续时间在0.05至0.5微秒之间。结果在转录激活蛋白相互作用的背景下进行了讨论。
