Smooth DNA Transport through a Narrowed Pore Geometry
Smooth DNA Transport through a Narrowed Pore Geometry
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DOI：
10.1016/j.bpj.2014.10.017
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发表时间：
2014-11-18
影响因子：
3.4
通讯作者：
Wanunu, Meni
中科院分区：
文献类型：
--
作者：
Carson, Spencer;Wilson, James;Wanunu, Meni
电压驱动的双链DNA通过纳米级孔的运输在定量分子生物学和生物技术中具有很大的应用潜力，但易位的微观细节已被证明是具有挑战性的破译。早期的实验表明，传输动力学对孔径的强烈依赖性：在大孔（> 5 nm直径）中快速的规则传输，以及在亚5 nm孔中较慢但不均匀的传输时间分布，这意味着DNA在孔中作为易位时间的函数的较大位置不确定性。在这项工作中，我们表明，这种异常的运输是DNA自相互作用的结果，是严格的孔径依赖的现象。我们确定了一个制度，其中DNA运输是定期的，产生狭窄和良好的停留时间分布，适合一个简单的漂移扩散理论。此外，对停留时间对DNA长度的依赖性的系统研究揭示了在35- 20，000 bp范围内1.37的单一幂律标度。我们通过以>98%的准确度经由单脉冲区分混合物中的100和500 bp片段来突出我们的纳米孔装置的分辨率。当结合适当的序列标记方法时，我们对平滑DNA易位的观察可以为基因组学中的高分辨率DNA作图和尺寸应用铺平道路。
Voltage-driven transport of double-stranded DNA through nanoscale pores holds much potential for applications in quantitative molecular biology and biotechnology, yet the microscopic details of translocation have proven to be challenging to decipher. Earlier experiments showed strong dependence of transport kinetics on pore size: fast regular transport in large pores (> 5 nm diameter), and slower yet heterogeneous transport time distributions in sub-5 nm pores, which imply a large positional uncertainty of the DNA in the pore as a function of the translocation time. In this work, we show that this anomalous transport is a result of DNA self-interaction, a phenomenon that is strictly pore-diameter dependent. We identify a regime in which DNA transport is regular, producing narrow and well-behaved dwell-time distributions that fit a simple drift-diffusion theory. Furthermore, a systematic study of the dependence of dwell time on DNA length reveals a single power-law scaling of 1.37 in the range of 35-20,000 bp. We highlight the resolution of our nanopore device by discriminating via single pulses 100 and 500 bp fragments in a mixture with >98% accuracy. When coupled to an appropriate sequence labeling method, our observation of smooth DNA translocation can pave the way for high-resolution DNA mapping and sizing applications in genomics.