Monitoring Structural Transitions of a DNA Holliday Junction Using an Acoustic Wave Sensor

Abstract

Structural DNA nanotechnology deals with building DNA molecules with particular geometrical features; creating nanoscale shapes and patterns using long DNA scaffolds, as in DNA origami, or changing DNA shape in a controlled way and in response to an external stimulus, as in molecular switches. Such nanomachines can perform computation, actuation and diagnostic tasks.We took advantage of a biomolecular structure comprising a four-way DNA (Holliday) junction which belongs to a molecular machines group capable of moving between distinct states. This particular molecular switch exists in either an open (extended) or closed (coaxially stacked) conformation and it is proposed to be used as a principle for sequence-specific nucleic acid recognition. In this study we used the quartz crystal microbalance with energy dissipation (QCM-D) to study the applicability of this structure to detect DNA hybridization on a device surface and test its potential to act as a controllable switch.We present a novel way of monitoring in real time both oligonucleotide binding and the transition from the closed to the open state of the junction. This transition can be reversed and repeated indefinitely in a fully controllable way.View Large Image | View Hi-Res Image | Download PowerPoint Slide