Exploring the fascinating interplay of epigenetically modified DNA bases with two dimensional bare and P-doped Si2BN and BN sheets for biosensing applications: A compelling DFT perspective

Abstract

Detecting epigenetically modified (EM) bases is crucial for disease detection, biosensing, and DNA sequencing. Two-dimensional P-doped Si₂BN and BN sheets are used as sensing substrates in density functional theory (DFT) studies. Both the sheets are doped with a phosphorous atom at various atomic sites to examine the sheet's potential in detecting 5-hydroxymethylcytosine (5hmc), 5-methylcytosine (5mc), 7-methylguanine (7mg) and 8-oxoguanine (8oxg) bases. Doping of the P atom in the Si₂BN sheet improves the adsorption energy (E_ad) of Ab+5hmc (-107.16 kcal/mol) and Ab+5mc (-78.36 kcal/mol), As+7mg (-84.31 kcal/mol) in the gas and aqueous phase Ab+5hmc (-93.28 kcal/mol), An+7mg (-78.92 kcal/mol) and As+5mc (-77.52 kcal/mol) respectively. Standard deviation (θ) indicates that As complexes have high θ values ranging from 4.55 to 37.77, suggesting a high likelihood of distinguishing the bases. The P-doped BN complexes exhibit noticeable work functional shifting (Δϕ%) recommended that they can be used as ϕ-based sensors. Time-dependent DFT results suggest that when EM bases interact with P-doped Si₂BN complexes, significant blue shifts (hypsochromic) and red shifts (bathochromic) are observed in the visible and near-infrared spectrum. Hence, the above finding suggests that P-doped Si₂BN sheets are highly effective for sensing EM bases and are recommended for DNA/RNA sequencing applications.

Keywords: Biosensors; Epigenetically modified bases; Si(2)BN.