Docking Simulation and Sandwich Assay for Aptamer-Based Botulinum Neurotoxin Type C Detection

Abstract

Aptamers are biomaterials that bind to a target molecule through a unique structure, and have high applicability in the diagnostic and medical fields. To effectively utilize aptamers, it is important to analyze the structure of the aptamer binding to the target molecule; however, there are difficulties in experimentally identifying this structure. In the modern pharmaceutical industry, computer-driven docking simulations that predict intermolecular binding models are used to select candidates that effectively bind target molecules. Botulinum toxin (BoNT) is the most poisonous neurotoxin produced from the Clostridium botulinum bacteria, and BoNT/C, one of the eight serotypes, causes paralysis in livestock. In this study, the aptamers that bound to BoNT/C were screened via the systematic evolution of ligands by exponential enrichment, and the binding affinity analysis and binding model were evaluated to select optimal aptamers. Based on surface plasmon resonance analysis and molecular operating environment docking simulation, a pair of aptamers that had high binding affinity to BoNT/C and were bound to different BoNT/C sites were selected. A sandwich assay based on this aptamer pair detected the BoNT/C protein to a concentration as low as ~0.2 ng Ml−1. These results show that docking simulations are a useful strategy for screening aptamers that bind to specific targets.

Aptamer–Protein Interactions: From Regulation to Biomolecular Detection

“…These limitations mean that, in applicability, none of the above approaches are versatile structural analysis tools for accessing the detailed structural features of aptamer–protein complexes described to date. Recently, with the rapid development of computer science, various molecular docking simulation programs have also been utilized to study aptamer–protein interactions, such as molecular operating environment (MOE) and collaborative computational project number 4 (CCP4). ,− These computer simulation procedures are generally performed to predict potential interaction sites and interaction modes. In some cases where structural characteristics of aptamer–protein complexes are not available, simulation software may help us to better understand how aptamers interact with target proteins.…”

Rapid SERS Detection of Botulinum Neurotoxin Type A

“…Tok and Fischer [ 16 ] developed several DNA aptamers for BoNT serotype A (aldehyde-inactivated full-length protein) with high affinity (K D values were in the range of 3 to 51 nM). Oh et al [ 17 ] developed DNA aptamers to the recombinant light chain of BoNT serotype C with superior affinity (K D values were in the range of 0.7 to 43 nM). Furthermore, RNA aptamers were selected by Chang et al [ 18 ] for the recombinant light chain of BoNT serotype A with K D in the range of 90 to 190 nM.…”

Structure Based Innovative Approach to Analyze Aptaprobe-GPC3 Complexes in Hepatocellular Carcinoma

“…SELEX technology has been developed as an in vitro selection method to screen aptamers, which are nucleic acid ligands with prominent functionalities. Aptamers are short single-stranded nucleic acid oligomers (ssDNA, RNA, or amino acids) that can fold into or around a target [27][28][29][30]. In addition, aptamers can bind to their targets (nanomolar to picomolar range) with high a nity and speci city and display low to no immunogenicity.…”