Single-molecule investigation of G-quadruplex folds of the human telomere sequence in a protein nanocavity

The bacterial protein α-hemolysin (α-HL) can form a mushroom-shaped ion channel by self-assembling across a lipid bilayer, allowing capture of a single DNA molecule inside its nanometer-scale vestibule in an electric field. Interactions between the protein nanocavity and DNA molecules generate characteristic current signals that reveal structural information. We harnessed such analytical power to investigate various G-quadruplex conformations adopted by the human telomeric sequence, namely hybrid, basket, and propeller folds that are formed under different physical conditions. Results presented here demonstrate the ability of α-HL to distinguish these G-quadruplexes based on their overall shapes and sizes and also to monitor their unraveling kinetics at different locations in the protein channel, expanding the applicability of the nanopore technology.