FRET based aptamer assay for sensitive detection of Salmonella paratyphi A and revealing its molecular interaction with DNA gyrase: An in silico accessment

Rapid pathogen detection and identification of its serovars are crucial to provide essential treatment during pandemic circumstances. Herein, we developed a facile and versatile FRET-based aptasensor for rapid Salmonella paratyphi A detection. The ssDNA aptamers specific towards pathogenic Salmonella paratyphi A were generated via whole-cell SELEX. The aptamer was conjugated onto quantum dot (QD) that served as the molecular beacon and graphene oxide (GO) was used as fluorescence quencher. The detection of Salmonella paratyphi A leads to the quenching of QD fluorescence due to the non-covalent interaction between GO and CdTe quantum dot. The assay shows a detection limit up to 10 cfu{middle dot}mL-1 with no cross-reactivity towards closely related species. The spiking analysis demonstrated an inter-assay coefficient of variance less than 8 % and recovery rate between 85%-102% mitigates assay reliability. Further analysis with commercially available ELISA kit validated the reliability of the developed aptasensor. Furthermore, molecular dynamics simulation was used to establish the mechanism of action of generated aptamer against bacterial DNA gyrase protein. The strong non-bonded interaction energies along with hydrogen bonds between the aptamer and protein inhibit the function of the bacteria.