An AFM/Rotaxane Molecular Reading Head for Sequence-Dependent DNA Structure

摘要

A nanomechanical molecular “tape reader” is assembled and tested by threading a β-cyclodextrin ring onto a DNA oligomer and pulling it along with an AFM tip. The formation and mechanical operation of the system is confirmed by measuring the forces required to unfold secondary structures in the form of hairpins. Unfolding induced by this 0.7 nm aperture requires 40 times more force than that reported for pulling on the ends of the DNA. A kinetic analysis shows that much less strain is required to destabilize the double helix in this geometry. Consequently, much more force is required to provide the free energy needed for opening. DNA secondary structure may prove to be a significant obstacle both for enzymes that process DNA though an orifice, and for the passage through nanopores proposed for some novel sequencing schemes.