DNA Origami Gatekeepers for Solid-State Nanopores
DNA Origami Gatekeepers for Solid-State Nanopores
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DOI：
10.1002/anie.201200688
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发表时间：
2012-01-01
影响因子：
16.6
通讯作者：
Dietz, Hendrik
中科院分区：
文献类型：
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作者：
Wei, Ruoshan;Martin, Thomas G.;Dietz, Hendrik
分子与DNA的自组装可以构建具有纳米到微米级绝对尺寸和定制化学特征的可溶物体[1]，包括晶体、[2]图案、[3]砖、[4]盒、[5]和弯曲形状[6]，这可以开辟科学发现的新途径。[7]在此，我们报告了基于纳米孔的传感方法的DNA纳米板。生物膜或固态膜中的纳米孔为无标签的单分子传感应用提供了巨大的潜力。[8]生物纳米孔，如α-溶血素，可以在蛋白质工程的范围内定制。[9]固态膜中的人造纳米孔可以用用户定义的尺寸制造，但化学修饰需要大量的努力。该领域的一个挑战是获得对纳米孔的几何和化学规格的控制。我们假设，使用基于DNA的纳米板作为固态纳米孔的覆盖物，可以为迎接这一挑战提供一条途径。我们的装置(图1a)由两个电解液池组成，由厚度为L=50 nm的硅支撑的独立绝缘氮化硅(SiN)膜隔开。该膜包含一个直径D=18-25 nm的圆锥形纳米孔(图1b)，它是通过电子束光刻和反应离子刻蚀制备的。[11]当通过两个电极施加电压时，离子电流流过纳米孔，并由电流放大器记录。纳米孔的尺寸和形状决定了装置的阻力。纳米孔的顺侧面覆盖着一个宽a、长b、厚L的矩形纳米板。该板包括一个宽x、长y的中心孔(图1a)。纳米板由分子与支架DNA折纸(见支持信息，注S1)自组装而成，由46个紧密相连的双螺旋DNA结构域组成的双层，在蜂窝型堆积晶格中。我们制作了宽度和长度为50 nm、厚度为6 nm的纳米板版本(支持信息，图S1-S5)。用透射电子显微镜的负极扫描证实了纳米板的正确形成(图1b；另见支持信息，注释S6-S9)。通过注入顺式电解液隔间，纳米板被电组装到纳米孔上。施加偏置电压(辅助信息，注S2和S3)后，电流噪声通常在几秒钟内突然下降和加剧(图1c)。电流封锁持续了几个小时，除非施加反向电压或对薄膜进行深度清洗。在这两种情况下，纳米孔的初始电导水平都得到了恢复。在使用直径超过纳米板尺寸的纳米孔的实验中，我们观察到瞬时堵塞(支持信息，注S4)，表明在这些情况下，纳米板滑过较大的纳米孔。在用含有纳米孔阵列的膜进行的实验中，我们观察到电导率呈阶梯状下降(支持信息，图S12)，表明阵列中的单个纳米孔逐渐捕获了纳米板。我们发现，对于有孔的纳米板，纳米板-纳米孔杂化材料的电导随着孔径的减小而减小(图1d)。这一发现可以用一个模型来解释，在这个模型中，纳米板以平坦的方向覆盖纳米孔。垂直或随机取向应产生不依赖于孔大小的相对电导。纳米孔的电导下降了大约…
Molecular self-assembly with DNA enables the construction of soluble objects with nanometer to micrometer scale absolute dimensions and custom chemical features,[1] including crystals,[2] patterns,[3] bricks,[4] boxes,[5] and curved shapes,[6] that can open novel paths to scientific discovery.[7] Herein, we report on DNA nanoplates for nanopore-based sensing approaches. Nanopores in biological or solid-state membranes offer great potential for label-free single-molecule sensing applications.[8] Biological nanopores, such as alpha-hemolysin, can be customized within the limits of protein engineering.[9] Artificial nanopores in solid-state membranes can be made with user-defined dimensions, but chemical modifications require substantial effort.[10] A challenge in the field is to gain control over both the geometrical and chemical specifications of nanopores. We hypothesized that using DNA-based nanoplates as covers for solid-state nanopores could provide a route for meeting this challenge. Our setup (Figure 1a) consists of two electrolyte reservoirs separated by a silicon-supported free-standing insulating silicon nitride (SiN) membrane of thickness L= 50 nm. The membrane contains a single conical nanopore of diameter D= 18–25 nm (Figure 1b), which is fabricated by electron beam lithography and reactive ion etching.[11] When a voltage is applied through the two electrodes, an ionic current flows through the nanopore and is recorded with a current amplifier. The dimensions and shape of the nanopore dominate the resistance of the setup. The cis side of the nanopore is covered with a rectangular nanoplate of width a, length b, and thickness l. The plate includes a central aperture of width x and length y (Figure 1a). The nanoplates are produced by molecular self-assembly with scaffolded DNA origami (see the Supporting Information, note S1) and consist of a double layer of 46 tightly interlinked double-helical DNA domains in a honeycomb-type packing lattice. We made nanoplate versions (Supporting Information, Figures S1–S5) with a width and length of 50 nm, and a thickness of 6 nm. Correct formation of the nanoplates was confirmed using negativestain transmission electron microscopy (Figure 1b; see also the Supporting Information, notes S6–S9). The nanoplates were electrically assembled onto the nanopores by injection into the cis electrolyte compartment. A sudden current drop and intensification in the current noise was typically observed within a few seconds (Figure 1c) after the bias voltage was applied (Supporting Information, notes S2 and S3). The current blockades lasted for hours, unless reverse voltages were applied or the membrane was intensely rinsed. In both cases, the initial conductance level of the nanopore was restored. In experiments using nanopores with diameters exceeding the dimensions of the nanoplates, we observed transient blockades (Supporting Information, note S4), indicating that in those cases the nanoplates slipped through the larger nanopores. In experiments with membranes containing arrays of nanopores, we observed staircaselike decreases in conductivity (Supporting Information, Figure S12), indicating the progressive capture of nanoplates by individual nanopores in the array. We find that, for nanoplates with apertures the conductance of nanoplate-on-nanopore hybrids decreases with decreasing aperture size (Figure1d). This finding can be explained by a model in which the nanoplates cover the nanopore in a flat orientation. Orthogonal or random orientations should yield relative conductances that do not depend on the size of the apertures. The nanopore conductance drops by approximately …