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arXiv 0806.1551q-bio.BMq-bio.QM
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束缚粒子实验中DNA环的第一性原理计算

First-principles calculation of DNA looping in tethered particle experiments

Kevin B. Towles, John F. Beausang, Hernan G. Garcia, Rob Phillips, Philip C. Nelson

备注：
See the supplement at http://www.physics.upenn.edu/~pcn/Ms/TowlesEtalSuppl.pdf . This revised version accepted for publication at Physical Biology
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摘要：

我们使用DNA弹性的数学模型计算了由调节蛋白如Lac阻遏物（LacI）介导的DNA环形成的概率。我们的模型适用于计算在系留粒子运动（TPM）实验中直接观察到的量，它占在这样的实验中存在的所有熵力。我们的模型没有自由参数;它使用其他类型实验中获得的信息来表征DNA弹性。[...]我们展示了如何计算"循环J因子"（或等价地，循环自由能）的各种DNA结构的几何形状和LacI浓度，以及详细的概率密度函数的珠偏移。我们还展示了如何从最近的实验数据中提取相同的数量拴系粒子运动，然后比较我们的模型的预测。[...]我们的模型成功地再现了珠偏移的详细分布，包括其令人惊讶的三峰结构，没有任何拟合参数，也没有调用任何替代构象的LacI四聚体。事实上，该模型定性地再现了观察到的这些分布对系链长度的依赖性（例如，定相）和LacI浓度（滴定）。然而，对于短的DNA环（约95个碱基对），实验显示出比谐波弹性模型预测的更多的环，这与最近的其他实验结果相呼应。由于我们研究的实验是在体外进行的，这种异常高的成环不能被合理化为DNA弯曲蛋白或其他细胞机制的存在。我们还表明，这是不太可能的结果，一个假设的“开放”构象的LacI四聚体。

英文摘要：

We calculate the probability of DNA loop formation mediated by regulatory proteins such as Lac repressor (LacI), using a mathematical model of DNA elasticity. Our model is adapted to calculating quantities directly observable in Tethered Particle Motion (TPM) experiments, and it accounts for all the entropic forces present in such experiments. Our model has no free parameters; it characterizes DNA elasticity using information obtained in other kinds of experiments. [...] We show how to compute both the "looping J factor" (or equivalently, the looping free energy) for various DNA construct geometries and LacI concentrations, as well as the detailed probability density function of bead excursions. We also show how to extract the same quantities from recent experimental data on tethered particle motion, and then compare to our model's predictions. [...] Our model successfully reproduces the detailed distributions of bead excursion, including their surprising three-peak structure, without any fit parameters and without invoking any alternative conformation of the LacI tetramer. Indeed, the model qualitatively reproduces the observed dependence of these distributions on tether length (e.g., phasing) and on LacI concentration (titration). However, for short DNA loops (around 95 basepairs) the experiments show more looping than is predicted by the harmonic-elasticity model, echoing other recent experimental results. Because the experiments we study are done in vitro, this anomalously high looping cannot be rationalized as resulting from the presence of DNA-bending proteins or other cellular machinery. We also show that it is unlikely to be the result of a hypothetical "open" conformation of the LacI tetramer.

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