title: Nanopore analysis of individual RNA/antibiotic complexes.
abstract: Nanopores in thin solid-state membranes are used to rapidly analyze individual RNA/drug complexes. The interactions of a truncated A-site RNA model of the prokaryotic ribosome with aminoglycoside antibiotics are characterized by passing individual molecules through a 3-3.5 nm diameter pore fabricated in a 8-10 nm thick silicon nitride membrane. Complexes of the A-site RNA with aminoglycosides can be distinguished from unbound A-site based on the ion current signatures produced as they pass through the nanopores. Counting the fraction of free and drug-bound molecules affords label-free drug-RNA binding isotherms consistent with literature reports and with data generated using independent fluorescence-based assays. Our measurements are supported by molecular dynamics simulations, which illustrate the relationship between the ionic current and complexation of the A-site RNA with paramomycin, a prototypical aminoglycoside antibiotic.
authors: Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States. wanunu@neu.edu
authors: Meni
authors: M
authors: Wanunu
authors: Swati
authors: S
authors: Bhattacharya
authors: Yun
authors: Y
authors: Xie
authors: Yitzhak
authors: Y
authors: Tor
authors: Aleksei
authors: A
authors: Aksimentiev
authors: Marija
authors: M
authors: Drndic
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry; D001665:Binding Sites; D004058:Diffusion; D018274:Electroporation / Q000379:methods*; D008422:Materials Testing; D008567:Membranes, Artificial; D049329:Nanostructures / Q000737:chemistry* / Q000648:ultrastructure*; D010303:Paromomycin / Q000737:chemistry*; D016062:Porosity; D012313:RNA / Q000737:chemistry*; D012666:Semiconductors
chemical_list: D000900:Anti-Bacterial Agents; D008567:Membranes, Artificial; D010303:Paromomycin; D012313:RNA