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

TL;DR

This study uses molecular dynamics simulations to show that nitrogen doping of carbon nanotube electrodes enhances control over DNA translocation by stabilizing nucleobase configurations and slowing translocation speed, improving sequencing precision.

Contribution

It introduces nitrogen doping of carbon nanotubes as a novel method to regulate DNA translocation dynamics in nanopore sequencing.

Findings

N-doped capCNTs stabilize edge-on nucleobase configurations.

Nitrogen doping extends nucleobase residence time by up to 290%.

Doping reduces nucleobase fluctuation by up to 70%.

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.