Nanopore-based conformational analysis of a viral RNA drug target.

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.

Recent trends in nanopores for biotechnology.

Nanopore technology employs a nanoscale hole in an insulating membrane to stochastically sense with high throughput individual biomolecules in solution. The generality of the nanopore detection principle and the ease of single-molecule detection suggest many potential applications of nanopores in biotechnology. Recent progress has been made with nanopore fabrication and sophistication, as well as with applications in DNA/protein mapping, biomolecular structure analysis, protein detection, and DNA sequencing. In addition, concepts for DNA sequencing devices have been suggested, and computational efforts have been made. The state of the nanopore field is maturing and given the right type of nanopore and operating conditions, nearly every application could revolutionize medicine in terms of speed, cost, and quality. In this review, we summarize progress in nanopores for biotechnological applications over the past 2-3 years.