Onset of channeling during DNA electrophoresis in a sparse ordered post array
Onset of channeling during DNA electrophoresis in a sparse ordered post array
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DOI：
10.1063/1.3283903
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发表时间：
2010-03-01
期刊：
影响因子：
3.2
通讯作者：
Dorfman, Kevin D.
中科院分区：
文献类型：
--
作者：
Ou, Jia;Carpenter, Samuel J.;Dorfman, Kevin D.
在稀疏、有序的柱阵列中进行 DNA 电泳的“通道假说”预测，如果 (i) 柱之间的间距大于 DNA 线圈并且 (ii) 电场线是直的，则 DNA 将相对不受阻碍地穿过阵列。我们通过研究小质粒 DNA（pUC19，2686 个碱基对）和大线性 DNA（lambda-DNA，48 500 个碱基对）在直径为 1 μm、节距为 7 μm 的六边形阵列中的电泳分离来测试这一假设。在低电场强度下，由于 lambda-DNA 与柱子的长寿命、绳索滑轮碰撞，这些 DNA 被分离。由于 lambda-DNA 通道效应的开始，电场增加，分辨率随之降低。使用扩散模型，我们表明由于阵列尺寸有限，在低电场下会出现沟道。这种通道不是系统固有的，并且会通过增加阵列的大小而减弱。较高的电场会导致固有沟道，这是由于绳索滑轮碰撞和碰撞之间的横向扩散的不同时间尺度造成的。窜流的发生是一个渐进的过程，与现有的布朗动力学模拟数据一致。即使在弱电场下，阵列中 lambda-DNA 的电泳迁移率也比 DNA 频繁与柱碰撞时的预期高得多。
The "channeling hypothesis" of DNA electrophoresis in sparse, ordered arrays of posts predicts that the DNA will move through the array relatively unhindered if (i) the spacing between the posts is larger than the DNA coil and (ii) the electric field lines are straight. We tested this hypothesis by studying the electrophoretic separation of a small plasmid DNA (pUC19, 2686 base pairs) and a large, linear DNA (lambda-DNA, 48 500 base pairs) in a hexagonal array of 1 mu m diameter posts with a pitch of 7 mu m. At low electric field strengths, these DNAs are separated due to the long-lived, rope-over-pulley collisions of lambda-DNA with the posts. The resolution is lost as the electric field increases due to the onset of channeling by the lambda-DNA. Using a diffusive model, we show that channeling arises at low electric fields due to the finite size of the array. This channeling is not intrinsic to the system and is attenuated by increasing the size of the array. Higher electric fields lead to intrinsic channeling, which is attributed to the disparate time scales for a rope-over-pulley collision and transverse diffusion between collisions. The onset of channeling is a gradual process, in agreement with extant Brownian dynamics simulation data. Even at weak electric fields, the electrophoretic mobility of lambda-DNA in the array is considerably higher than would be expected if the DNA frequently collided with the posts.