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.

Keywords:

• Diazinon
• docking
• DNA–ligand interaction
• G-quadruplex aptamer
• molecular dynamics

Acknowledgments

The authors gratefully acknowledge spiritual and financial support from the Entomology and Toxicology Department, agriculture collage of Urmia University (Urmia, Iran) and Department of Pharmacy, Mashhad University of Medical Sciences (Mashhad, Iran); as part of the PhD thesis. We thank Mrs Mitra Jokar, Dr Rahmani, and Scribendi© (online editing and proofreading company www.scribendi.com) for editing the manuscript.