High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System.
High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System.
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DOI：
10.1021/acsnano.0c06191
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发表时间：
2020-11-24
期刊：
影响因子：
17.1
通讯作者：
Aksimentiev A
中科院分区：
文献类型：
--
作者：
Choudhary A;Joshi H;Chou HY;Sarthak K;Wilson J;Maffeo C;Aksimentiev A
核酸的纳米孔测序具有辉煌的创新历史，最终使商业纳米孔测序成为可能。然而，目前的纳米孔测序技术留下了很大的改进空间，特别是在原始读数的准确性和核苷酸修饰的检测方面。双纳米孔测序-一种通过两个纳米孔的拔河来回拉动DNA分子的方法-可以通过提供相同DNA片段的多个读取来潜在地提高单分子读取准确性和修饰检测。实现这种技术的一个主要困难是将单链DNA穿过两个纳米孔。在这里，我们描述并通过模拟演示了一个纳米流体系统，该系统用于以近100%的保真度通过双纳米孔设置加载和穿线DNA链。通过使用沙漏形侧通道来实现高效装载，所述沙漏形侧通道不仅将分子递送到纳米孔，而且还保留在第一次通过时错过纳米孔的分子以再次尝试纳米孔捕获。通过正交微流体流促进第二纳米孔捕获，所述正交微流体流解开由第一纳米孔捕获的分子并将其递送到第二纳米孔的捕获体积。我们通过模拟DNA链通过双纳米孔系统的重复来回运动-牙线，证明了我们的双纳米孔系统用于DNA测序的潜在效用。我们表明，重复暴露相同的DNA片段的纳米孔感测体积大大增加了核苷酸序列测定的准确性，并通过两个纳米孔的ssDNA的相关位移可能有助于识别均聚物片段。
Nanopore sequencing of nucleic acids has an illustrious history of innovations that eventually made commercial nanopore sequencing possible. Nevertheless, the present nanopore sequencing technology leaves much room for improvement, especially with respect to accuracy of raw reads and detection of nucleotide modifications. Double-nanopore sequencing—an approach where a DNA molecule is pulled back and forth by a tug-of-war of two nanopores—could potentially improve single molecule read accuracy and modification detection by offering multiple reads of the same DNA fragment. One principle difficulty in realizing such a technology is threading single-stranded DNA through both nanopores. Here, we describe and demonstrate through simulations a nanofluidic system for loading and threading DNA strands through a double-nanopore setup with nearly 100% fidelity. The high-efficiency loading is realized by using hourglass-shaped side channels that not only deliver the molecules to the nanopore but also retain molecules that missed the nanopore at the first passage to attempt the nanopore capture again. The second nanopore capture is facilitated by an orthogonal microfluidic flow that unravels the molecule captured by the first nanopore and delivers it to the capture volume of the second nanopore. We demonstrate potential utility of our double nanopore system for DNA sequencing by simulating repeat back-and- forth motion—flossing—of a DNA strand through the double nanopore system. We show that repeat exposure of the same DNA fragments to the nanopore sensing volume considerably increases accuracy of the nucleotide sequence determination, and that correlated displacement of ssDNA through the two nanopores may facilitate recognition of homopolymer fragments.
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影响因子：
10.8
作者：
Briggs K;Madejski G;Magill M;Kastritis K;de Haan HW;McGrath JL;Tabard-Cossa V
通讯作者：
Tabard-Cossa V
影响因子：
10.8
作者：
Cadinu P;Paulose Nadappuram B;Lee DJ;Sze JYY;Campolo G;Zhang Y;Shevchuk A;Ladame S;Albrecht T;Korchev Y;Ivanov AP;Edel JB
通讯作者：
Edel JB
影响因子：
16.6
作者：
Freedman KJ;Otto LM;Ivanov AP;Barik A;Oh SH;Edel JB
通讯作者：
Edel JB
影响因子：
1.6
作者：
DEBLOIS, RW;BEAN, CP
通讯作者：
BEAN, CP
影响因子：
5.5
作者：
Hart, Katarina;Foloppe, Nicolas;Baker, Christopher M.;Denning, Elizabeth J.;Nilsson, Lennart;MacKerell, Alexander D., Jr.
通讯作者：
MacKerell, Alexander D., Jr.