The persistence length of double stranded DNA determined using dark field tethered particle motion
The persistence length of double stranded DNA determined using dark field tethered particle motion
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DOI：
10.1063/1.3142699
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发表时间：
2009-06-07
影响因子：
4.4
通讯作者：
Rieger, Bernd
中科院分区：
文献类型：
--
作者：
Brinkers, Sanneke;Dietrich, Heidelinde R. C.;Rieger, Bernd
虫链模型通过引入持续长度来描述半柔性聚合物的微观力学。我们提出了一种在可控的近原生环境中测量DNA持久长度的方法。利用暗场显微镜，捕捉到金纳米粒子在受约束布朗运动中的投影位置。利用单双链DNA （dsDNA）分子将纳米颗粒拴在底物上，并浸泡在缓冲液中。没有力施加在DNA上。我们对实验进行了蒙特卡罗模拟，从而深入了解DNA的微观力学，并可用于解释纳米颗粒的运动。我们的模拟和实验表明，与其他类似的实验不同，使用纳米而不是微米大小的颗粒会导致颗粒-基质和颗粒- dna相互作用对颗粒位置分布的影响可以忽略不计。我们还表明，通过将纳米粒子的投影位置分布的统计数据与蒙特卡罗模拟的统计数据进行比较，可以估计出捆绑DNA的持续长度，统计误差为2 nm。在相同的环境条件下，测定了4种不同长度的45个单分子dsDNA在高盐浓度下的持久长度。我们发现的持续长度的平均值为35纳米（标准误差为2.8纳米），这与以前使用类似盐浓度发现的值相比很好。我们的方法可以直接用于研究环境条件（如缓冲液和温度）对持续长度的影响。
The wormlike chain model describes the micromechanics of semiflexible polymers by introducing the persistence length. We propose a method of measuring the persistence length of DNA in a controllable near-native environment. Using a dark field microscope, the projected positions of a gold nanoparticle undergoing constrained Brownian motion are captured. The nanoparticle is tethered to a substrate using a single double stranded DNA (dsDNA) molecule and immersed in buffer. No force is exerted on the DNA. We carried out Monte Carlo simulations of the experiment, which give insight into the micromechanics of the DNA and can be used to interpret the motion of the nanoparticle. Our simulations and experiments demonstrate that, unlike other similar experiments, the use of nanometer instead of micrometer sized particles causes particle-substrate and particle-DNA interactions to be of negligible effect on the position distribution of the particle. We also show that the persistence length of the tethering DNA can be estimated with a statistical error of 2 nm, by comparing the statistics of the projected position distribution of the nanoparticle to the Monte Carlo simulations. The persistence lengths of 45 single molecules of four different lengths of dsDNA were measured under the same environmental conditions at high salt concentration. The persistence lengths we found had a mean value of 35 nm (standard error of 2.8 nm), which compares well to previously found values using similar salt concentrations. Our method can be used to directly study the effect of the environmental conditions (e.g., buffer and temperature) on the persistence length.