Self-assembly of 50 bp poly(dA)·poly(dT) DNA on highly oriented pyrolytic graphite via atomic force microscopy observation and molecular dynamics simulation

Doi, Kentaro; Takeuchi, Hiroshi; Nii, Ryosuke; Akamatsu, Shingo; Kakizaki, Toshiya

doi:10.1063/1.4818595

Cited by 17 publications

(17 citation statements)

References 45 publications

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“…In a previous study, we investigated the transport of deoxyribonucleic acid (DNA) in nanochannels that have negative charges in electrolyte solutions [12][13][14] . By applying an potential difference, DNA molecules were found to be transported by electrophoresis in an electroosmotic flow.…”

Section: Development Of Glass Microelectrodes For Local Electric Fielmentioning

confidence: 99%

Development of glass micro-electrodes for local electric field, electrical conductivity, and pH measurements

Doi

Asano

2020

Sci Rep

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In micro- and nanofluidic devices, liquid flows are often influenced by ionic currents generated by electric fields in narrow channels, which is an electrokinetic phenomenon. Various technologies have been developed that are analogous to semiconductor devices, such as diodes and field effect transistors. On the other hand, measurement techniques for local electric fields in such narrow channels have not yet been established. In the present study, electric fields in liquids are locally measured using glass micro-electrodes with 1-μm diameter tips, which are constructed by pulling a glass tube. By scanning a liquid poured into a channel by glass micro-electrodes, the potential difference in a liquid can be determined with a spatial resolution of the size of the glass tip. As a result, the electrical conductivity of sample solutions can be quantitatively evaluated. Furthermore, combining two glass capillaries filled with buffer solutions of different concentrations, an ionic diode that rectifies the proton conduction direction is constructed, and the possibility of pH measurement is also demonstrated. Under constant-current conditions, pH values ranging from 1.68 to 9.18 can be determined more quickly and stably than with conventional methods that depend on the proton selectivity of glass electrodes under equilibrium conditions.

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Section: Development Of Glass Microelectrodes For Local Electric Fielmentioning

confidence: 99%

Development of glass micro-electrodes for local electric field, electrical conductivity, and pH measurements

Doi

Asano

2020

Sci Rep

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“…As a result, our device can make a significantly fast EHD flow compared to previous results [14]. Further progresses based on the present results are expected to be developed not only for translocation velocity control of single molecules but also for arbitrary molecular pattern fabrications [15]. Co., Ltd., Tokyo, Japan) was employed in this experiment.…”

Section: Introductionmentioning

confidence: 59%

Observation of Electrohydrodynamic Flow through a Pore in Ion-Exchange Membrane

Yano¹,

Doi²

2015

IJCEA

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Liquid flows driven by electric force is known as electrohydrodynamics (EHD). EHD flows are expected to be applied to micropumps, microactuators, and mixing devices. However, it is known that conventional EHD flows require at least tens of volts of the applied voltage. In this study, a novel device is developed to generate an EHD flow under a constant current condition with a few voltages. An ion-exchange membrane that has a small pore is set in a reservoir to separate the flow path of anion and cation. The reservoir is filled with NaOH aqueous solution and a constant electric current is applied across the membrane. When the cross sectional area of the ion-exchange membrane is 200 times larger than that of the pore, EHD flows observed in the pore become faster than those in previous studies. The maximum value of the flow velocity reaches 3 mm/s by applying a constant current of 0.8 mA.

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“…The separation and velocity control of short-chain singlestranded DNA (ssDNA) is currently an important issue in DNA sequencing, and our own group has developed coarse-grained models of DNA to assist in investigating transport properties (14,(20)(21)(22). In this prior work, the time spans and folded structures of dsDNA passing through nanogaps (14) or nanowire arrays (6) were determined, using practical spatial and temporal dimensions.…”

Section: Introductionmentioning

confidence: 99%

Effects of Polymer Length and Salt Concentration on the Transport of ssDNA in Nanofluidic Channels

Qian

Doi

2017

Biophysical Journal

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Electrokinetic phenomena in micro/nanofluidic channels have attracted considerable attention because precise control of molecular transport in liquids is required to optically and electrically capture the behavior of single molecules. However, the detailed mechanisms of polymer transport influenced by electroosmotic flows and electric fields in micro/nanofluidic channels have not yet been elucidated. In this study, a Langevin dynamics simulation was used to investigate the electrokinetic transport of single-stranded DNA (ssDNA) in a cylindrical nanochannel, employing a coarse-grained bead-spring model that quantitatively reproduced the radius of gyration, diffusion coefficient, and electrophoretic mobility of the polymer. Using this practical scale model, transport regimes of ssDNA with respect to the ζ-potential of the channel wall, the ion concentration, and the polymer length were successfully characterized. It was found that the relationship between the radius of gyration of ssDNA and the channel radius is critical to the formation of deformation regimes in a narrow channel. We conclude that a combination of electroosmotic flow velocity gradients and electric fields due to electrically polarized channel surfaces affects the alignment of molecular conformations, such that the ssDNA is stretched/compressed at negative/positive ζ-potentials in comparatively low-concentration solutions. Furthermore, this work suggests the possibility of controlling the center-of-mass position by tuning the salt concentration. These results should be applicable to the design of molecular manipulation techniques based on liquid flows in micro/nanofluidic devices.

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Self-assembly of 50 bp poly(dA)·poly(dT) DNA on highly oriented pyrolytic graphite via atomic force microscopy observation and molecular dynamics simulation

Cited by 17 publications

References 45 publications

Development of glass micro-electrodes for local electric field, electrical conductivity, and pH measurements

Development of glass micro-electrodes for local electric field, electrical conductivity, and pH measurements

Observation of Electrohydrodynamic Flow through a Pore in Ion-Exchange Membrane

Effects of Polymer Length and Salt Concentration on the Transport of ssDNA in Nanofluidic Channels

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