Nanomechanical DNA origami pH sensors.

Single-molecule pH sensors have been developed by utilizing molecular imaging of pH-responsive shape transition of nanomechanical DNA origami devices with atomic force microscopy (AFM). Short DNA fragments that can form i-motifs were introduced to nanomechanical DNA origami devices with pliers-like shape (DNA Origami Pliers), which consist of two levers of 170-nm long and 20-nm wide connected at a Holliday-junction fulcrum. DNA Origami Pliers can be observed as in three distinct forms; cross, antiparallel and parallel forms, and cross form is the dominant species when no additional interaction is introduced to DNA Origami Pliers. Introduction of nine pairs of 12-mer sequence (5'-AACCCCAACCCC-3'), which dimerize into i-motif quadruplexes upon protonation of cytosine, drives transition of DNA Origami Pliers from open cross form into closed parallel form under acidic conditions. Such pH-dependent transition was clearly imaged on mica in molecular resolution by AFM, showing potential application of the system to single-molecular pH sensors.

Precise structure control of three-state nanomechanical DNA origami devices.

Precise structure switching between all of the three forms of three-state nanomechanical DNA origami devices has been accomplished. A nanomechanical DNA origami device called DNA origami pliers, which consists of two levers of 170-nm long, 20-nm wide, and 2-nm thick connected at a Holliday-junction fulcrum, takes three conformations: closed parallel, closed antiparallel, and open cross forms. They were previously applied to construct detection systems for biomolecules in single-molecular resolution by observing the structure switching between cross form and one of the other two forms under atomic force microscope (AFM). We redesigned DNA origami pliers in this study to let them freely switch between all of the three states including parallel-antiparallel direct switching without taking cross form. By the addition of appropriate switcher strands to the solution, hybridization and dehybridization of particular binder strands that fix the levers into predetermined state were selectively triggered as programmed in their sequence. Circuit structure switching through all of the three states in both of the two opposite direction was even successful with the new design.