Kentaro Doi

DNA Manipulation and Separation in Sublithographic-Scale Nanowire Array

Electrokinetic manipulations of biomolecules using artificial nanostructures within microchannels have proven capability for controlling the dynamics of biomolecules. Because there is an inherent spatial size limitation to lithographic technology, especially for nanostructures with a small diameter and high aspect ratio, manipulating a single small biomolecule such as in DNA elongation before nanopore sequencing is still troublesome. Here we show the feasibility for self-assembly of a nanowire array embedded in a microchannel on a fused silica substrate as a means to manipulate the dynamics of a single long T4-DNA molecule and also separate DNA molecules. High-resolution optical microscopy measurements are used to clarify the presence of fully elongated T4-DNA molecules in the nanowire array. The spatial controllability of sublithographic-scale nanowires within microchannels offers a flexible platform not only for manipulating and separating long DNA molecules but also for integrating with other nanostructures to detect biomolecules in methods such as nanopore sequencing.

Development of coarse-graining DNA models for single-nucleotide resolution analysis

Recently, analytical techniques have been developed for detecting single-nucleotide polymorphisms in DNA sequences. Improvements of the sequence identification techniques has attracted much attention in several fields. However, there are many things that have not been clarified about DNA. In the present study, we have developed a coarse-graining DNA model with single-nucleotide resolution, in which potential functions for hydrogen bonds and the π-stack effect are taken into account. Using Langevin-dynamics simulations, several characteristics of the coarse-grained DNA have been clarified. The validity of the present model has been confirmed, compared with other experimental and computational results. In particular, the melting temperature and persistence length are in good agreement with the experimental results for a wide range of salt concentrations.

Role of an Aluminum Atom on Graphene for Hydrogen Adsorption

The effects of an aluminum atom on the hydrogen adsorption onto graphene are investigated. An aluminum atom can be attached on a graphene sheet by a bond with both covalent and ionic properties. Then, the electric charge is transferred from the aluminum atom to the graphene. The activation energy for the hydrogen adsorption is significantly lowered by the addition of the aluminum atom for both atomic and molecular adsorptions. The hydrogen adsorption energy is also lowered significantly by the aluminum atom.

Molecular dynamics study of solvation effect on diffusivity changes of DNA fragments

DNA sequence analyzing and base pair separation techniques have attracted much attention, such as denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and capillary electrophoresis. However, details of sequence separation mechanisms in electrophoresis are not clarified enough. Understanding and controlling flow characteristics of DNA are important not only for fundamental research but also for further developments of bio-nano technologies. In the present study, we theoretically discuss the relationship between diffusivity and hydrated structures of DNA fragments in water solvent using molecular dynamics methods. In particular, influence of base pair substitutions on the diffusivity is investigated, focusing on an adenine-thymine (AT) rich B–DNA decamer 5’-dCGTATATATA-3’. Consequently, it is found that water molecules that concentrate on dissociated base pairs form hydrated structures and change the diffusivity of DNA decamers. The diffusion coefficients are affected by the substitution of GC for AT because of the different manner of interactions between the base molecules and water solvent. This result predicts a possibility of base pair separation according to differences in the diffusivity.

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

This study has investigated the formation patterns resulting from the self-assembly of deoxyribonucleic acid (DNA) on highly oriented pyrolytic graphite (HOPG), using both experimental and molecular dynamics approaches. Under optimized conditions based on pretreatment of HOPG surface and specific solution concentrations, DNA is found to self-assemble to form various patterned networks. The associated self-assembly mechanism is elucidated using coarse-grained molecular dynamics simulations and fractal dimension analysis. The results of this work demonstrate an effective technique allowing the formation of arrays of negatively charged biomacromolecules on negatively charged HOPG surfaces.

Tailoring particle translocation via dielectrophoresis in pore channels

Understanding and controlling electrophoretic motions of nanoscopic objects in fluidic channels are a central challenge in developing nanopore technology for molecular analyses. Although progress has been made in slowing the translocation velocity to meet the requirement for electrical detections of analytes via picoampere current measurements, there exists no method useful for regulating particle flows in the transverse directions. Here, we report the use of dielectrophoresis to manipulate the single-particle passage through a solid-state pore. We created a trap field by applying AC voltage between electrodes embedded in a low-aspect-ratio micropore. We demonstrated a traffic control of particles to go through center or near side surface via the voltage frequency. We also found enhanced capture efficiency along with faster escaping speed of particles by virtue of the AC-mediated electroosmosis. This method is compatible with nanopore sensing and would be widely applied for reducing off-axis effects to achieve single-molecule identification.

Nonequilibrium Ionic Response of Biased Mechanically Controllable Break Junction (MCBJ) Electrodes

Novel experimental techniques allow for the manipulation and interrogation of biomolecules between metallic probes immersed in micro/nanofluidic channels. The behavior of ions in response to applied fields is a major issue in the use of these techniques in sensing applications. Here, we experimentally and theoretically elucidate the behavior of background currents in these systems. These large currents have a slowly decaying transient response, as well as noise that increases with ionic concentration. Using mechanically controllable break junctions (MCBJ), we study the ionic response in nanogaps with widths ranging from a few nanometers to millimeters. Moreover, we obtain an expression for the ionic current by solving time-dependent Nernst–Planck and Poisson equations. This expression shows that after turning on an applied voltage, ions rapidly respond to the strong fields near the electrode surface, screening the field in the process. Ions subsequently translocate in the weak electric field and slowly relax within the diffusion layer. Our theoretical results help to explain the short- and long-time behavior of the ionic response found in experiments, as well as the various length scales involved.

Theoretical Study of the Transpore Velocity Control of Single-Stranded DNA

The electrokinetic transport dynamics of deoxyribonucleic acid (DNA) molecules have recently attracted significant attention in various fields of research. Our group is interested in the detailed examination of the behavior of DNA when confined in micro/nanofluidic channels. In the present study, the translocation mechanism of a DNA-like polymer chain in a nanofluidic channel was investigated using Langevin dynamics simulations. A coarse-grained bead-spring model was developed to simulate the dynamics of a long polymer chain passing through a rectangular cross-section nanopore embedded in a nanochannel, under the influence of a nonuniform electric field. Varying the cross-sectional area of the nanopore was found to allow optimization of the translocation process through modification of the electric field in the flow channel, since a drastic drop in the electric potential at the nanopore was induced by changing the cross-section. Furthermore, the configuration of the polymer chain in the nanopore was observed to determine its translocation velocity. The competition between the strength of the electric field and confinement in the small pore produces various transport mechanisms and the results of this study thus represent a means of optimizing the design of nanofluidic devices for single molecule detection.

Structures and Electronic States of Gadolinium Oxide Clusters

We have carried out ab initio quantum chemical calculations for gadolinium oxide clusters and clarified the most suitable combination of a theoretical method, basis sets, and effective core potentials for large systems of gadolinium oxides. We confirmed the reliability of our calculation by computing the electronic state of GdO molecule whose bond length and binding energy are well known. In order to examine how the electronic states depend on the size of clusters, we calculated several cluster series: GdOn clusters (n=2–4) with negative net charge, (GdO)n colinear and zigzag chain clusters (n=1–4), (GdO)n square pillar clusters (n=4,6,8), and large clusters based on the Gd2O3 cubic crystal (Gd4O1824-8Q3+ and Gd4O1926-8Q3+), where Q denotes the point charge. New images of electronic stresses in the clusters can be visualized in terms of the electronic stress tensor density based on the regional density functional theory.

Electrohydrodynamic Flow through a 1 mm2 Cross-Section Pore Placed in an Ion-Exchange Membrane

In recent years, the control of ionic currents has come to be recognized as one of the most important issues related to the efficient transport of single molecules and microparticles in aqueous solutions. However, the complicated liquid flows that are usually induced by applying electric potentials have made it difficult to address a number of unsolved problems in this area. In particular, the nonequilibrium phenomena that occur in electrically non-neutral fields must be more thoroughly understood. Herein, we report on the development of a theoretical model of liquid flows resulting from ion interactions while focusing on the so-called electrohydrodynamic (EHD) flow. We also discuss the development of an experimental system to optically and electrically observe EHD flows using a 1 mm(2) cross-section pore placed in an ion-exchange membrane where cation and anion flows can be separated without the use of a charged environment. Although micro/nanosized flow channels are usually applied to induce electric double layer overlaps to utilize strong electroosmotic effects, our system does not require such laborious fabrication processes. Instead, we visualize EHD flows by using a millimeter size pore immersed in an alkaline aqueous solution. In this setup, liquid flows passing through the pore along the direction of ion flow, whose velocity reaches on the order of 1 mm/s, can be clearly observed by applying a few volts of electric potential. Furthermore, the transient phenomena associated with ionic responses are theoretically elucidated.