Apta-nanosensor preparation and in vitro assay for rapid Diazinon detection using a computational molecular approach

Abstract

Aptamers (ss-DNA or ss-RNA), also known as artificial antibodies, have been selected in vitro median to bind target molecules with high affinity and selectivity. Diazinon is one of the most widely used organophosphorus insecticides in developing and underdeveloped countries as insecticide and acaricide. Diazinon is readily absorbed from the gastrointestinal system and rapidly distributed throughout the body. Thus, the design of clinical and laboratory diagnostics using nanobiosensors is necessary. A computational approach allows us to screen or rank receptor structure and predict interaction outcomes with a deeper understanding, and it is much more cost effective than laboratory attempts. In this research, the best sequence (high affinity bind Diazinon-ssDNA) was ranked among 12 aptamers isolated from SELEX experimentation. Docking results, as the first virtual screening stage and static technique, selected frequent conformation of each aptamer. Then, the quantity and quality of aptamer-Diazinon interaction were simulated using molecular dynamics as a mobility technique. RMSD, RMSF, radius of gyration, and the number of hydrogen bonds formed between Diazinon-aptamer were monitored to assess the quantity and quality of interactions. G-quadruplex DNA aptamer (DF20) showed to be a reliable candidate for Diazinon biosensing. The apta-nanosensor designed using simulation results allowed with linearity detection in the range of .141-.65 nM and a LOD of 17.903 nM, and it was validated using a computational molecular approach.

Rolling Circle Amplification-based Copper Nanoparticle Synthesis on Cyclic Olefin Copolymer Substrate and Its Application in Aptasensor

“…In this study, we described a label-free fluorescent aptasensor, based on RCA and self-assembled CuNPs, to detect DZN on a COC substrate. A recent report featuring the properties of DZN-specific aptamer [45] was referred to while devising this detection strategy. The DF probe was designed for efficient RCA reactions, enabling a series of reactions to detect DZN on non-modified COC substrates.…”

Selective Binding and Elution of Aptamers for Pesticides Based on Sol-Gel-Coated Nanoporous Anodized Aluminum Oxide Membrane

“…For the aptamer binding assay, the diazinon-specific aptamer labeled with Texas Red was obtained by chemical synthesis and HPLC-purified by Bioneer Corporation (Daejeon, Korea). The anti-diazinon aptamer was a 72-mer oligonucleotide with the following sequence: 5′-ATC CGT CAC ACC TGC TCT AAT ATA GAG GTA TTG CTC TTG GAC AAG GTA CAG GGA TGG TGT TGG CTC CCG TAT-Texas Red-3′, as described in a previous report [ 29 ]. The aptamer solution was prepared in 1 × SELEX buffer (50 mM Tris-HCl, 150 mM NaCl, 25 mM KCl, 5 mM MgCl 2 , 1 mM CaCl 2 , 0.01% Tween-20, and pH 7.5) and used at a final concentration of 1 μM.…”

Aptamer-Based Biosensors for Environmental Monitoring

“…An alternative approach involved the development of a fluorescent biosensor. Arvand et al described the use of an NH 2 -C6-modified aptamer (Jokar et al, 2017) conjugated quantum dots and graphene oxide to generate a sensing system for the detection of diazinon which had a linear dynamic range of 1.05-205.83 nM and a LOD of 0.13 nM (Arvand and Mirroshandel, 2019). Moreover, the recovery of diazinon from spiked river water, apple, and cucumber samples was demonstrated between 91.0 and 102%.…”