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Nanopore Analysis of Individual RNA/Antibiotic Complexes

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Meni Wanunu†*, Swati Bhattacharya‡, Yun Xie§, Yitzhak Tor§, Aleksei Aksimentiev‡*, and Marija Drndic†

^† Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States

^‡ Department of Physics, University of Illinois, Urbana, Illinois 61801, United States

^§ Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States

Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania

ACS Nano, 2011, 5 (12), pp 9345–9353

DOI: 10.1021/nn203764j

Publication Date (Web): November 8, 2011

*Address correspondence to wanunu@neu.edu, aksiment@illinois.edu, drndic@physics.upenn.edu.

Section:

Pharmacology

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.