title: Nanopore-based conformational analysis of a viral RNA drug target.
abstract: Nanopores are single-molecule sensors that show exceptional promise as a biomolecular analysis tool by enabling label-free detection of small amounts of sample. In this paper, we demonstrate that nanopores are capable of detecting the conformation of an antiviral RNA drug target. The hepatitis C virus uses an internal ribosome entry site (IRES) motif in order to initiate translation by docking to ribosomes in its host cell. The IRES is therefore a viable and important drug target. Drug-induced changes to the conformation of the HCV IRES motif, from a bent to a straight conformation, have been shown to inhibit HCV replication. However, there is presently no straightforward method to analyze the effect of candidate small-molecule drugs on the RNA conformation. In this paper, we show that RNA translocation dynamics through a 3 nm diameter nanopore is conformation-sensitive by demonstrating a difference in transport times between bent and straight conformations of a short viral RNA motif. Detection is possible because bent RNA is stalled in the 3 nm pore, resulting in longer molecular dwell times than straight RNA. Control experiments show that binding of a weaker drug does not produce a conformational change, as consistent with independent fluorescence measurements. Nanopore measurements of RNA conformation can thus be useful for probing the structure of various RNA motifs, as well as structural changes to the RNA upon small-molecule binding.
authors.affiliation: Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States.
authors.forename: Carolyn
authors.initials: C
authors.lastname: Shasha
authors.affiliation: Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States.
authors.forename: Robert Y
authors.initials: RY
authors.lastname: Henley
authors.affiliation: Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States.
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Stoloff
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States.
authors.forename: Kevin D
authors.initials: KD
authors.lastname: Rynearson
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States.
authors.forename: Thomas
authors.initials: T
authors.lastname: Hermann
authors.affiliation: Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States.
authors.forename: Meni
authors.initials: M
authors.lastname: Wanunu
mesh_terms: D001665:Binding Sites; D004566:Electrodes; D004573:Electrolytes; D031541:Fluorescence Resonance Energy Transfer; D016174:Hepacivirus; D006863:Hydrogen-Ion Concentration; D008968:Molecular Conformation; D053758:Nanoparticles / Q000737:chemistry*; D058608:Nanopores; D036103:Nanotechnology / Q000379:methods*; D009693:Nucleic Acid Hybridization; D012313:RNA / Q000737:chemistry; D012367:RNA, Viral / Q000737:chemistry; D012270:Ribosomes / Q000737:chemistry; D013696:Temperature
chemical_list: D004573:Electrolytes; D012367:RNA, Viral; D012313:RNA