The effect of secondary structures on the generation of characteristic events during the translocation of DNA hybrid through α-hemolysin

Abstract

Nanopore has been developed to be a powerful, single-molecule analytical tool for sensing ions, small organic molecules and biomacromolecules such as proteins and DNAs. Generally, the identity of the analyte can be revealed by current amplitude changes and mean dwell time of the analyte binding events. In some cases, generation of highly characteristic current events affords an alternative way of analyte determination with high confidence level. However, we found that secondary structures in DNA/RNA hybrids might severely hinder the generation of signature events during their translocation through α-hemolysin nanopore. In this report, we propose a strategy to add a certain concentration of urea in the buffer solution for single channel recordings and validate that low concentration of urea can effectively denature the secondary structures in DNA hybrids and recover the generation of signature events. This finding might be useful in other secondary structure-related nanopore sensing activities. © 2015 Science China Press and Springer-Verlag Berlin Heidelberg