Zhao Xiongce, Payne Christina M, Cummings Peter T, Lee James W
Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
Nanotechnology. 2007 Oct 24;18(42):424018. doi: 10.1088/0957-4484/18/42/424018. Epub 2007 Sep 19.
Molecular dynamics simulations were performed to investigate the translocation of single-strand DNA through nanoscale electrode gaps under the action of a constant driving force. The application behind this theoretical study is a proposal to use nanoelectrodes as a screening gap as part of a rapid genomic sequencing device. Preliminary results from a series of simulations using various gap widths and driving forces suggest that the narrowest electrode gap that a single-strand DNA can pass is ∼1.5 nm. The minimum force required to initiate the translocation within nanoseconds is ∼0.3 nN. Simulations using DNA segments of various lengths indicate that the minimum initiation force is insensitive to the length of DNA. However, the average threading velocity of DNA varies appreciably from short to long DNA segments. We attribute such variation to the different nature of drag force experienced by the short and long DNA segments in the environment. It is found that DNA molecules deform significantly to fit in the shape of the nanogap during the translocation.
进行了分子动力学模拟，以研究在恒定驱动力作用下单链DNA通过纳米级电极间隙的转运情况。该理论研究背后的应用是一项提议，即使用纳米电极作为快速基因组测序设备一部分的筛选间隙。一系列使用各种间隙宽度和驱动力的模拟初步结果表明，单链DNA能够通过的最窄电极间隙约为1.5纳米。在纳秒内启动转运所需的最小力约为0.3纳牛。使用各种长度DNA片段的模拟表明，最小启动力对DNA长度不敏感。然而，DNA的平均穿入速度在短DNA片段和长DNA片段之间有明显变化。我们将这种变化归因于短DNA片段和长DNA片段在环境中所经历的不同阻力性质。研究发现，DNA分子在转运过程中会发生显著变形以适应纳米间隙的形状。
