3D structural analysis of aptamer and diagnostic platforms for detecting hepatocellular carcinoma

Background Alpha-fetoprotein (AFP) has been used as a biomarker for early diagnosis of hepatocellular carcinoma (HCC) for a long time. Aptamer is a type of material that is receiving attention as a new alternative in the diagnosis and treatment of diseases. Objective We applied aptamer to AFP detection and utilized in silico analysis techniques. Here, we describe the selection of aptamers that can bind to AFP as well as in vitro and in silico validation of the binding site. We also developed an aptamer-based detection platform called hybrid-aptablotting sandwich assay (Hybrid-ABSA) and a point-of-care AFP detection kit. Results To construct the AFP detection platform, we screened a total of 18 candidate AFP-binding aptamers and identified a pair of aptamers without non-overlapping-binding sites using dot blotting. We validated results of dot blotting using in silico 3D binding structure docking simulation analysis. The aptamer-based Hybris-ABSA for AFP detection using this pair of aptamers demonstrated superior detection performance to antibody-based ELISA detection methods. Furthermore, we confirmed that AFP could be detected using the developed point-of-care lateral flow In Vitro Diagnostic (IVD) kit. Conclusion Results of this study demonstrate that aptamer-based disease diagnostic technology has potential of replace conventional diagnostic methods. This study also confirms that in silico techniques have sufficient utility in biological assays.