Quantitative analysis of DNA-looping kinetics from tethered particle motion experiments.
Quantitative analysis of DNA-looping kinetics from tethered particle motion experiments.
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DOI：
10.1016/s0076-6879(10)75009-6
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发表时间：
2010
影响因子：
--
通讯作者：
Finzi, Laura
中科院分区：
文献类型：
--
作者：
Manzo, Carlo;Finzi, Laura
在这一章中，我们展示了一种基于最大似然法的方法在从拴系粒子运动实验中重建DNA环单分子时间轨迹的应用。该方法不需要对数据进行时间滤波，并且相对于阈值交叉方法将时间分辨率提高了一个数量级。此外，它不是基于假定的动力学模型，克服了以前提出的其他方法的局限性，并允许将其应用于具有复杂动力学方案的机构。数值模拟已经被用来测试这种分析在广泛的时间范围内的性能。然后，我们应用这种方法来确定一种著名的DNA环蛋白，λ抑制物CI的环化动力学。
In this chapter we show the application of a maximum likelihood-based method to the reconstruction of DNA looping single-molecule time traces from tethered particle motion experiments. The method does not require time filtering of the data and improves the time resolution by an order of magnitude with respect to the threshold-crossing approach. Moreover, it is not based on presumed kinetic models, overcoming the limitations of other approaches proposed previously, and allowing its applications to mechanisms with complex kinetic schemes. Numerical simulations have been used to test the performances of this analysis over a wide range of time scales. We have then applied this method to determine the looping kinetics of a well-known DNA-looping protein, the λ-repressor CI.