Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
ACS Appl Mater Interfaces. 2017 Jan 11;9(1):92-100. doi: 10.1021/acsami.6b11001. Epub 2016 Dec 22.
DNA origami nanostructures can be used to functionalize solid-state nanopores for single molecule studies. In this study, we characterized a nanopore in a DNA origami-graphene heterostructure for DNA detection. The DNA origami nanopore is functionalized with a specific nucleotide type at the edge of the pore. Using extensive molecular dynamics (MD) simulations, we computed and analyzed the ionic conductivity of nanopores in heterostructures carpeted with one or two layers of DNA origami on graphene. We demonstrate that a nanopore in DNA origami-graphene gives rise to distinguishable dwell times for the four DNA base types, whereas for a nanopore in bare graphene, the dwell time is almost the same for all types of bases. The specific interactions (hydrogen bonds) between DNA origami and the translocating DNA strand yield different residence times and ionic currents. We also conclude that the speed of DNA translocation decreases due to the friction between the dangling bases at the pore mouth and the sequencing DNA strands.
DNA 折纸纳米结构可用于对固态纳米孔进行功能化，以进行单分子研究。在这项研究中，我们对 DNA 折纸-石墨烯杂化结构中的纳米孔进行了 DNA 检测特性分析。DNA 折纸纳米孔在孔边缘的特定核苷酸类型上进行了功能化。通过广泛的分子动力学（MD）模拟，我们计算和分析了在石墨烯上覆盖一层或两层 DNA 折纸的杂化结构中的纳米孔的离子电导率。我们证明，DNA 折纸-石墨烯中的纳米孔会导致四种 DNA 碱基类型的停留时间可区分，而在裸露的石墨烯中的纳米孔中，所有类型的碱基的停留时间几乎相同。DNA 折纸与迁移 DNA 链之间的特定相互作用（氢键）会产生不同的停留时间和离子电流。我们还得出结论，由于孔口处悬垂碱基与测序 DNA 链之间的摩擦，DNA 迁移的速度会降低。
