用于增强DNA易位动力学控制的碳纳米电极的氮掺杂
Nitrogen doping of carbon nanoelectrodes for enhanced control of DNA translocation dynamics
摘要：
控制DNA易位的动力学是新兴的基于纳米孔的DNA测序中的中心问题。为了解决碳纳米结构的杂原子掺杂的潜力，以实现这一目标，在这里，我们进行原子分子动力学模拟的单链DNA之间的两个原始或掺杂的碳纳米管（CNT）电极易位。具体来说，我们考虑了取代氮掺杂的帽碳纳米管（capCNT）电极和进行两种类型的分子动力学模拟的截留和易位的单链DNA。我们发现，取代氮掺杂的capCNTs稳定的边缘上的核碱基的配置，而不是原来的面对面的，并通过建立N掺杂剂原子和核碱基之间的氢键减慢DNA易位的速度。由于DNA和N掺杂的capCNT之间增强的相互作用，纳米间隙内的核碱基的持续时间延长了高达~ 290%，并且核碱基的波动降低了高达~ 70%。考虑到与非本征光或栅电压调制方法相结合的可能性，目前的工作表明，取代氮掺杂是通过基于碳纳米材料的纳米孔或纳米间隙控制DNA易位动力学的一个有前途的方向。
英文摘要：
Controlling the dynamics of DNA translocation is a central issue in the emerging nanopore-based DNA sequencing. To address the potential of heteroatom doping of carbon nanostructures to achieve this goal, herein we carry out atomistic molecular dynamics simulations for single-stranded DNAs translocating between two pristine or doped carbon nanotube (CNT) electrodes. Specifically, we consider the substitutional nitrogen doping of capped CNT (capCNT) electrodes and perform two types of molecular dynamics simulations for the entrapped and translocating single-stranded DNAs. We find that the substitutional nitrogen doping of capCNTs stabilizes the edge-on nucleobase configurations rather than the original face-on ones and slows down the DNA translocation speed by establishing hydrogen bonds between the N dopant atoms and nucleobases. Due to the enhanced interactions between DNAs and N-doped capCNTs, the duration time of nucleobases within the nanogap was extended by up to ~ 290 % and the fluctuation of the nucleobases was reduced by up to ~ 70 %. Given the possibility to be combined with extrinsic light or gate voltage modulation methods, the current work demonstrates that the substitutional nitrogen doping is a promising direction for the control of DNA translocation dynamics through a nanopore or nanogap based of carbon nanomaterials.
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