Nitrogen doping of carbon nanoelectrodes for enhanced control of DNA translocation dynamics

Abstract

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.

arXiv comment11 pages, 4 figures

References in corpus (16)

• The SIESTA method for ab initio order-N materials simulation
• Efficient index handling of multidimensional periodic boundary conditions
• Visualizing Individual Nitrogen Dopants in Monolayer Graphene
• Physical approaches to DNA sequencing and detection
• Fast DNA Sequencing via Transverse Electronic Transport
• DNA nucleotide-specific modulation of μA transverse edge currents through a metallic graphene nanoribbon with a nanopore
• Transverse conductance of DNA nucleotides in a graphene nanogap from first principles
• Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport
• Enhanced DNA sequencing performance through edge-hydrogenation of graphene electrodes
• Functionalized nanopore-embedded electrodes for rapid DNA sequencing
• Recent progress in atomistic simulation of electrical current DNA sequencing
• Atomistic Mechanisms of Codoping-Induced p- to n-Type Conversion in Nitrogen-Doped Graphene
• First-principles study of high conductance DNA sequencing with carbon nanotube electrodes
• Origin and Control of Polyacrylonitrile Alignments on Carbon Nanotube and Graphene Nanoribbon
• Distinct mechanisms of DNA sensing based on N-doped carbon nanotubes with enhanced conductance and chemical selectivity
• Carbon nanobuds based on carbon nanotube caps: A first-principles study

Cited by in corpus (2)

• ssDNA sequencing by rectification
• Convolutional network learning of self-consistent electron density via grid-projected atomic fingerprints