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Sensors 2014, 14(10), 19329-19335;

Nanomechanical DNA Origami pH Sensors

Department of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate, Suita, Osaka 564-8680, Japan
PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
Authors to whom correspondence should be addressed.
Received: 25 August 2014 / Revised: 30 September 2014 / Accepted: 8 October 2014 / Published: 16 October 2014
(This article belongs to the Special Issue Single Biomolecule Detection)
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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. View Full-Text
Keywords: DNA Origami; DNA Nanotechnology; Proton Detection; pH Sensors; i-motif; AFM; nanomechanical devices; Single-Molecule Sensors DNA Origami; DNA Nanotechnology; Proton Detection; pH Sensors; i-motif; AFM; nanomechanical devices; Single-Molecule Sensors

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Kuzuya, A.; Watanabe, R.; Yamanaka, Y.; Tamaki, T.; Kaino, M.; Ohya, Y. Nanomechanical DNA Origami pH Sensors. Sensors 2014, 14, 19329-19335.

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