Real-time label-free detection of dynamic aptamer–small molecule interactions using a nanopore nucleic acid conformational sensor

• DOI: 10.1073/pnas.2108118120
• Publication Date: 2023-06-05T19:16:24Z
• Authors: Rugare G. Chingar...; Kai Tian; Yu Kuang; Aby Sarangee; Chengrui Hou; Emily Ma; Jarett Ren; Sam Hawkins; Joshua Kim; Ray Adelstein; Sally Chen; Kevin D. Gillis; Li-Qun Gu
• Keywords: Aptamer; Conformational change; Nucleic acid structure; Nanopore; Riboswitch; Docking (animal)

Nucleic acids can undergo conformational changes upon binding small molecules. These be exploited to develop new therapeutic strategies through control of gene expression or triggering cellular responses and also used sensors for molecules such as neurotransmitters. Many analytical approaches detect dynamic change nucleic acids, but they need labeling, are expensive, have limited time resolution. The nanopore approach provide a snapshot each acid molecule detected, has not been reported in response -molecule binding. Here we demonstrate modular, label-free, acid-docked capable revealing time-resolved, molecule-induced, single transitions with millisecond By using the dopamine-, serotonin-, theophylline-binding aptamers testbeds, found that these scaffolds noncovalently docked inside MspA protein pore by cluster site-specific charged residues. This docking mechanism enables ion current characteristically vary aptamer undergoes changes, resulting sequence fluctuations report release ligand from aptamer. tool quantify specific ligands neurotransmitters, elucidate acid-ligand interactions, pinpoint motifs binding, showing potential biosensing, drug discovery assayed via RNA DNA design artificial riboswitch effectors synthetic biology.