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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.

SUBMITTER: Wanunu M

PROVIDER: S-EPMC3253136 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature

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Nanopore analysis of individual RNA/antibiotic complexes.

Wanunu Meni M Bhattacharya Swati S Xie Yun Y Tor Yitzhak Y Aksimentiev Aleksei A Drndic Marija M

ACS nano 20111116 12

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 throu ...[more]

PMID: 22067050

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