Non-equilibrium folding of individual DNA molecules recaptured up to 1000 times in a solid state nanopore.
Non-equilibrium folding of individual DNA molecules recaptured up to 1000 times in a solid state nanopore.
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DOI：
10.1088/0957-4484/24/47/475101
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发表时间：
2013-11-29
期刊：
影响因子：
3.5
通讯作者：
Dekker C
中科院分区：
文献类型：
--
作者：
Plesa C;Cornelissen L;Tuijtel MW;Dekker C
我们研究了线性和环状双链DNA分子通过固态纳米孔的易位，其中每个分子被重新捕获和重新易位多次。单个分子可以通过切换电压极性数百甚至数千次来重新捕获。大量的再捕获事件允许对单个分子的易位进行统计。令人惊讶的是，我们观察到重新捕获的DNA分子不以线性的头对尾的方式易位，而是作为折叠的斑点易位，其中DNA分子的多个部分同时平行地易位通过孔。通过在孔内同时存在来自同一分子的多达13条DNA双链以及在易位事件过程中发生的许多较小的折叠数来观察这种折叠。当分子在短时间尺度上被重新捕获时，即短于其特征时间以松弛到其平衡构型时，强折叠特别突出。在较长的再捕获时间，折叠的量和易位的平均持续时间接近在非再捕获实验中观察到的值。数据显示，分子的易位时间取决于易位过程开始时分子的构象，延伸的分子具有更长的易位时间。观察结果可以归因于高密度非平衡DNA构型，其在易位后立即在纳米孔附近出现，其在由Zimm弛豫时间给出的时间尺度上消散。
We investigate translocation of linear and circular double-stranded DNA molecules through solid state nanopores where each molecule is recaptured and re-translocated many times. Single molecules can be recaptured by switching voltage polarity for hundreds or even thousands of times. The large number of recapture events allows statistics on the translocation of individual molecules. Surprisingly, we observe that recaptured DNA molecules do not translocate in a linear head-to-tail fashion, but instead translocate as a folded blob where multiple parts of the DNA molecule simultaneously translocate through the pore in parallel. This folding is observed through the presence of up to 13 DNA double strands from the same molecule simultaneously inside the pore, as well as many smaller fold numbers occurring during the course of a translocation event. The strong folding is particularly prominent when the molecule is recaptured at short time scales, i.e. shorter than its characteristic time to relax to its equilibrium configuration. At longer recapture times, both the amount of folding and the mean duration of translocation approach the values observed in non-recapture experiments. The data shows that the translocation time of a molecule depends on the molecule’s conformation at the start of the translocation process, with extended molecules having a longer translocation time. The observations can be attributed to a high-density non-equilibrium DNA configuration that arises in the close vicinity of the nanopore immediately after translocation, which dissipates on a time scale given by the Zimm relaxation time.
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