Identification of DNA bases using nanopores created in finite-size nanoribbons from graphene, phosphorene, and silicene

Abstract

Graphene's success for nanopore DNA sequencing has shown that it is possible to explore other potential single-and few-atom thick layers of elemental 2D materials beyond graphene (e.g., phosphorene and silicene), and also that these materials can exhibit fascinating and technologically useful properties for DNA base detection that are superior to those of graphene. Using density functional theory (DFT), we studied the interaction of DNA bases with nanopores created in finite-size nanoribbons from graphene, phosphorene, and silicene. Due to the small size of DNA bases, the bases interact with only a small section of the nanoribbon, hence using a finite-size model is appropriate for capturing the interaction of bases and 2D membrane materials. Furthermore, by using a finite-size model, our system is approximated as a molecular system, which does not require a periodic DFT calculation. We observe that binding energies of DNA bases using nanopores from phosphorene and silicene are similar, and generally smaller compared to graphene. This shows that minimal sticking of DNA bases to pore is expected for phosphorene and silicene devices. Furthermore, nanopores from phosphorene and silicene show a characteristic change in the density of states for each base. The band gaps of phosphorene and silicene are significantly altered due to interaction with DNA bases compared to graphene. Our findings show that phosphorene and silicene are promising alternatives to graphene for DNA base detection using advanced detection principles such as transverse tunneling current measurement.

Copolymers of vinylferrocene and vinylimidazole for potential sensing applications

“…The geometry was then optimized at the B3LYP level of theory using the 6‐31G* + SBK mixed basis set that utilizes effective core potential on the Fe atom and the 6‐31G* double zeta Pople type basis set on all other atoms. All geometries were optimized using a force convergence criterion of 0.02 eV/Å 25 . The combination of the B3LYP hybrid‐GGA (generalized gradient approximation) functional with the 6‐31G* + SBK mixed basis set provides a reasonable basis set size for performing geometry optimizations especially for systems with large number of atoms like polymers.…”

“…All geometries were optimized using a force convergence criterion of 0.02 eV/Å. 25 The combination of the B3LYP hybrid-GGA (generalized gradient approximation) functional with the 6-31G* + SBK mixed basis set provides a reasonable basis set size for performing geometry optimizations especially for systems with large number of atoms like polymers. Excited state calculations were performed using time-dependent DFT (TDDFT).…”

Single-molecule DNA sequencing using two-dimensional Ti2C(OH)2 MXene nanopores: A first-principles investigation

“…Another important aspect is the residence time of the nucleotides inside the nanopore. In practical applications, the translocation time can be determined by both DNA lengths and their orientations [60,61] which contain information about chemical interactions correlated to the binding energies. The residence time (τ) for each DNA base type is proportional to ~ , where is the binding energy, is the Boltzmann constant, and is the temperature.…”

DNA sequencing: an overview of solid-state and biological nanopore-based methods

“…From sequencing point of view, MoS2 can perform better than graphene. For example, signal to noise ratio and non-stickiness of DNA to MoS2 surface make it suitable (Graf et al 2019a ) (Henry et al 2021 ). Instead, phosphorene nanopore and silicene (graphene like two-dimensional silicon) nanopore seem much more suitable (Henry et al 2021 ).…”

“…For example, signal to noise ratio and non-stickiness of DNA to MoS2 surface make it suitable (Graf et al 2019a ) (Henry et al 2021 ). Instead, phosphorene nanopore and silicene (graphene like two-dimensional silicon) nanopore seem much more suitable (Henry et al 2021 ). One of the main problems in detecting bases through solid-state nanopores is the fact that they have a low spatial resolution since dozens of bases can pass through them at any given moment (Yanagi et al 2015 ).…”