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...

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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:
AFM
Online Access:http://www.mdpi.com/1424-8220/14/10/19329
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spelling doaj-3f1f1349ee4b41008907a2c925cddfee2020-11-24T21:51:47ZengMDPI AGSensors1424-82202014-10-011410193291933510.3390/s141019329s141019329Nanomechanical DNA Origami pH SensorsAkinori Kuzuya0Ryosuke Watanabe1Yusei Yamanaka2Takuya Tamaki3Masafumi Kaino4Yuichi Ohya5Department of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate, Suita, Osaka 564-8680, JapanDepartment of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate, Suita, Osaka 564-8680, JapanDepartment of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate, Suita, Osaka 564-8680, JapanDepartment of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate, Suita, Osaka 564-8680, JapanDepartment of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate, Suita, Osaka 564-8680, JapanDepartment of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate, Suita, Osaka 564-8680, JapanSingle-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.http://www.mdpi.com/1424-8220/14/10/19329DNA OrigamiDNA NanotechnologyProton DetectionpH Sensorsi-motifAFMnanomechanical devicesSingle-Molecule Sensors
collection DOAJ
language English
format Article
sources DOAJ
author Akinori Kuzuya
Ryosuke Watanabe
Yusei Yamanaka
Takuya Tamaki
Masafumi Kaino
Yuichi Ohya
spellingShingle Akinori Kuzuya
Ryosuke Watanabe
Yusei Yamanaka
Takuya Tamaki
Masafumi Kaino
Yuichi Ohya
Nanomechanical DNA Origami pH Sensors
Sensors
DNA Origami
DNA Nanotechnology
Proton Detection
pH Sensors
i-motif
AFM
nanomechanical devices
Single-Molecule Sensors
author_facet Akinori Kuzuya
Ryosuke Watanabe
Yusei Yamanaka
Takuya Tamaki
Masafumi Kaino
Yuichi Ohya
author_sort Akinori Kuzuya
title Nanomechanical DNA Origami pH Sensors
title_short Nanomechanical DNA Origami pH Sensors
title_full Nanomechanical DNA Origami pH Sensors
title_fullStr Nanomechanical DNA Origami pH Sensors
title_full_unstemmed Nanomechanical DNA Origami pH Sensors
title_sort nanomechanical dna origami ph sensors
publisher MDPI AG
series Sensors
issn 1424-8220
publishDate 2014-10-01
description 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.
topic DNA Origami
DNA Nanotechnology
Proton Detection
pH Sensors
i-motif
AFM
nanomechanical devices
Single-Molecule Sensors
url http://www.mdpi.com/1424-8220/14/10/19329
work_keys_str_mv AT akinorikuzuya nanomechanicaldnaorigamiphsensors
AT ryosukewatanabe nanomechanicaldnaorigamiphsensors
AT yuseiyamanaka nanomechanicaldnaorigamiphsensors
AT takuyatamaki nanomechanicaldnaorigamiphsensors
AT masafumikaino nanomechanicaldnaorigamiphsensors
AT yuichiohya nanomechanicaldnaorigamiphsensors
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