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.
