title: Nanomechanical DNA origami pH sensors.
abstract: 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.
authors.affiliation: Department of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate, Suita, Osaka 564-8680, Japan. kuzuya@kansai-u.ac.jp.
authors.forename: Akinori
authors.initials: A
authors.lastname: Kuzuya
authors.affiliation: Department of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate, Suita, Osaka 564-8680, Japan. k947410@kansai-u.ac.jp.
authors.forename: Ryosuke
authors.initials: R
authors.lastname: Watanabe
authors.affiliation: Department of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate, Suita, Osaka 564-8680, Japan. y7yamanaka@gmail.com.
authors.forename: Yusei
authors.initials: Y
authors.lastname: Yamanaka
authors.affiliation: Department of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate, Suita, Osaka 564-8680, Japan. tamaki.takuya@mw.nkchemical.co.jp.
authors.forename: Takuya
authors.initials: T
authors.lastname: Tamaki
authors.affiliation: Department of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate, Suita, Osaka 564-8680, Japan. k460583@kansai-u.ac.jp.
authors.forename: Masafumi
authors.initials: M
authors.lastname: Kaino
authors.affiliation: Department of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate, Suita, Osaka 564-8680, Japan. yohya@kansai-u.ac.jp.
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Ohya
mesh_terms: D015374:Biosensing Techniques / Q000379:methods*; D004247:DNA / Q000737:chemistry / Q000302:isolation & purification*; D006863:Hydrogen-Ion Concentration; D018625:Microscopy, Atomic Force; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA