TCB Publications - Abstract

S. Wanunu, S. Bhattacharya, Y. Xie, Y. Tor, A. Aksimentiev, and M. Drndic. Nanopore analysis of individual RNA/antibiotic complexes. ACS Nano, 5:9345-9353, 2011.

WANU2011-AA 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 33.5 nm diameter pore fabricated in a 810 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.

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