Nanomechanical DNA Origami pH Sensors

• Main Authors: Akinori Kuzuya, Ryosuke Watanabe, Yusei Yamanaka, Takuya Tamaki, Masafumi Kaino, Yuichi Ohya
• Format: Article
• Language: English
• Published: MDPI AG 2014-10-01
• Series: Sensors
• Subjects: DNA Origami; DNA Nanotechnology; Proton Detection; pH Sensors; i-motif; AFM; nanomechanical devices; Single-Molecule Sensors
• Online Access: http://www.mdpi.com/1424-8220/14/10/19329

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.