Single-Molecule Counting of Nucleotide by Electrophoresis with Nanochannel-Integrated Nano-Gap Devices.

Takahito Ohshiro,Yuki Komoto,Masateru Taniguchi

doi:10.3390/mi11110982

Abstract

We utilized electrophoresis to control the fluidity of sample biomolecules in sample aqueous solutions inside the nanochannel for single-molecule detection by using a nanochannel-integrated nanogap electrode, which is composed of a nano-gap sensing electrode, nanochannel, and tapered focusing channel. In order to suppress electro-osmotic flow and thermal convection inside this nanochannel, we optimized the reduction ratios of the tapered focusing channel, and the ratio of inlet 10 μm to outlet 0.5 μm was found to be high performance of electrophoresis with lower concentration of 0.05 × TBE (Tris/Borate/EDTA) buffer containing a surfactant of 0.1 w/v% polyvinylpyrrolidone (PVP). Under the optimized conditions, single-molecule electrical measurement of deoxyguanosine monophosphate (dGMP) was performed and it was found that the throughput was significantly improved by nearly an order of magnitude compared to that without electrophoresis. In addition, it was also found that the long-duration signals that could interfere with discrimination were significantly reduced. This is because the strong electrophoresis flow inside the nanochannels prevents the molecules’ adsorption near the electrodes. This single-molecule electrical measurement with nanochannel-integrated nano-gap electrodes by electrophoresis significantly improved the throughput of signal detection and identification accuracy.

Highlights

The nanochannel is a key part of micro/nano-machine devices that is widely used in various research fields, such as the analytical sensing and/or mechanical engineering fields, because it provides indispensable functions such as sample-introduction, separation, and purification [1,2]
It seems that the backflow is a typical electro-osmotic flow (EOF) that is induced by the movement of the solvent by the counter ions of the nanochannel surface charge
Several kinds of surfactants, such as polyethylene-glycol, polyvinyl-pyrrolidone, polyvinyl-alcohol, and Triton X-100, are reported in order to suppress the negative charge inside the nanochannel [24,25], surfactants with a π-conjugated ring are not suitable for this study because the size of surfactants with a π-conjugated ring is comparable to those of DNA and RNA bases, which have a pyrimidine or purine ring, so that signals of surfactant molecules itself could resemble those signals of DNA and RNA samples

Summary

Introduction

The nanochannel is a key part of micro/nano-machine devices that is widely used in various research fields, such as the analytical sensing and/or mechanical engineering fields, because it provides indispensable functions such as sample-introduction, separation, and purification [1,2]. One of the most attractive research fields is micro total analytical systems (μTAS), in which the chemical analysis system is miniaturized by micromachining, and nanochannels seamlessly combine various kinds of functional units with various sensors so that they provide the developments of medical application fields such as blood analysis and drug evaluation systems [3,4,5]. The detection principle is as follows: When sample molecules pass between the nano-gap electrodes that work as sensors, a tunnel phenomenon induces electron transfer through the molecules, resulting in the detection of individual electrical conductivity due to the electronic state of each of the molecules

Methods

Results

Discussion

Conclusion