Efficient one-step immobilization of DNA probes on 1DZnO nanoplatforms targeting a low-mutation region of SARS-CoV-2.

Abstract

Fabricating cost-effective biosensors with rapid response times is highly desirable during pandemic scenarios, where accuracy, swift detection, and portability are crucial for making prompt decisions. The design and conceptualization of these devices at early stages are critical for enhancing their output responses. In this work, we implemented a one-step immobilization strategy for DNA probes targeting a low-mutation region from the envelope protein of SARS-CoV-2 onto one-dimensional ZnO nanostructures (1DZnO) to achieve high detection efficiency. First, DNA probes were designed to select a highly conserved region (L28-A36) among SARS-CoV-2 subvariants using bioinformatic analysis. Then, dynamic simulations were performed to estimate the binding affinity of DNA to 1DZnO, where phosphate molecules were identified as the functional groups with the highest affinity to the ZnO surface, followed by the sugar rings and the base pairs. In addition, linear interaction energies (LIEs) and their average contributions were calculated for the ssDNA/ZnO interfaces. Computational simulations were correlated to experimental techniques, where suitable DNA immobilization and target detection were confirmed by FTIR, photoluminescence (PL), transmission electron microscopy (TEM), and elemental mapping, corroborating the adsorption of DNA across the entire 1DZnO surface. Intense peaks related to C-C, C=C, C=N, P-O, and N-H were identified as the most important by FTIR characterizations, whereas PL showed a distinctive shift in Deep Level Emission band (DLE) between 520-530 nm, with a partial quenching of the Near Band Emission signal, obtaining as well variations in the calculated bandgap. In summary, it is suggested that structural oxygen vacancies of 1DZnO nanoplatforms provide a significant proportion of active available sites for an easy and strong interaction with the phosphate backbone of DNA, enhancing physical adsorption. Furthermore, molecular validation by PCR confirmed the long-term stability of immobilized DNA probes, probing their suitability for further biosensing devices.