Interaction of Nucleic Acid Bases (NABs) with Graphene (GR) and Boron Nitride Graphene (BNG)

In-depth electronic behavior of pentagraphene and pentagonal silicene sheets for DNA nucleobase detection: implications for genetic biomarker sensing

Silicon-based chemical sensors are optimal for detecting biological entities due to their fast response, biocompatibility, and non-invasive nature. In this work, we proposed pristine and metal [gold (Au) and tungsten (W)]-doped pentagonal silicene (p-Si) and pentagraphene (PG) as materials for single DNA nucleobase sensors. Using first-principles calculations, we presented a comparative study of DNA nucleobases-adenine (A), guanine (G), cytosine (C), and thymine (T)-adsorbed on pristine and metal-doped PG and p-Si to determine their potential as nucleobase detectors or for detecting other chemical species. The calculated binding affinities on the PG and p-Si surfaces using the M062X/6-31G* level of theory and adsorption energies from DFT predicted higher sensitivity of PG towards DNA nucleobases compared to p-Si, with evident changes in their work function and band structure properties. In the later section, we showed that doping with Au and W significantly enhanced the sensitivity of both PG and p-Si towards DNA nucleobases, as evidenced by their electronic band structures and PDOS calculations. The significant changes in the electronic properties of PG and p-Si upon adsorption of nucleobases make them promising candidates for rapid sensing, sequencing, and identification of DNA nucleobase elements. This study provides new insights into the physical and chemical interactions between biomolecules and PG/p-Si, highlighting their potential as templates for nanobiological devices. Both Au and W doping enhanced the adsorption properties, suggesting that PG and p-Si could be effectively used for biomolecule sensing applications.

First principles studies on the adsorption of rare base-pairs on the surface of B/N atom doped γ-graphyne

Rare base-pairs consists of guanine (G) paired with rare bases, such as 5-methylcytosine (5-meCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-carboxylcytosine (5-caCyt), and 5-formylcytosine (5-fCyt), have become the focus of epigenetic research because they can be used as markers to detect some chronic diseases and cancers. However, the correlation detection of these rare base-pairs is limited, which in turn limits the development of diagnostic tests and devices. Herein, the interaction of rare base-pairs adsorbed on pure and B/N-doped γ-graphyne (γ-GY) nanosheets was explored using the density functional theory. The calculated adsorption energy showed that the system of rare base-pairs on B-doped γ-GY is more stable than that on pure γ-GY or N-doped γ-GY. Translocation time values indicate that rare base-pairs can be successfully distinguished as the difference in their translocation times is very large for pure and B/N-doped γ-GY nanosheets. Meanwhile, sensing response values illustrated that pure and B-doped γ-GY are the best for G-5-hmCyt adsorption, while the N-doped γ-GY is the best for G-Cyt adsorption. The findings indicate that translocation times and sensing response can be used as detection indexes for pure and B/N doped γ-GY, which will provide a new way for experimental scientists to develop the biosensor components.

Quantum Simulation of the Silicene and Germanene for Sensing and Sequencing of DNA/RNA Nucleobases

Over the last decade, we have been witnessing the rise of two-dimensional (2D) materials. Several 2D materials with outstanding properties have been theoretically predicted and experimentally synthesized. 2D materials are good candidates for sensing and detecting various biomolecules because of their extraordinary properties, such as a high surface-to-volume ratio. Silicene and germanene are the monolayer honeycomb structures of silicon and germanium, respectively. Quantum simulations have been very effective in understanding the interaction mechanism of 2D materials and biomolecules and may play an important role in the development of effective and reliable biosensors. This article focuses on understanding the interaction of DNA/RNA nucleobases with silicene and germanane monolayers and obtaining the possibility of using silicene and germanane monolayers as a biosensor for DNA/RNA nucleobases' sequencing using the first principle of Density Functional Theory (DFT) calculations with van der Waals (vdW) correction and nonequilibrium Green's function method. Guanine (G), Cytosine (C), Adenine (A), Thymine (T), and Uracil (U) were examined as the analytes. The strength of adsorption between the DNA/RNA nucleobases and silicene and germanane is G > C > A > T > U. Moreover, our recent work on the investigation of Au- and Li-decorated silicene and germanane for detection of DNA/RNA nucleobases is presented. Our results show that it is possible to get remarkable changes in transmittance due to the adsorption of nucleobases, especially for G, A, and C. These results indicate that silicene and germanene are both good candidates for the applications in fast sequencing devices for DNA/RNA nucleobases. Additionally, our present results have the potential to give insight into experimental studies and can be valuable for advancements in biosensing and nanobiotechnology.