Effect of a Photolithography Polymer Mask's Dynamic Viscoelasticity on Microchannel Cross-Sectional Shapes of Glass Processed by Micropowder Blasting.

In this study, a micropowder blasting system with varying processing temperatures was proposed to control the cross-sectional shape of a channel processed on a glass substrate. Based on an analysis of the processing temperature-dependence of the dynamic viscoelastic properties of a commercial mask material for micropowder blasting, a processing temperature control system that can be installed in a micropowder blasting machine was designed. The erosion of the mask during micropowder blasting depended on the loss tangent in dynamic viscoelasticity, and showed a maximum value at a processing temperature of 100 °C. Moreover, we confirmed that the maximum decrease in the width of the processed microchannel was 30 µm (12%) by mask erosion, and this change was large compared with the maximum change in the thickness of the eroded mask. These results clarified that varying the processing temperature using a mask could control the cross-section of the processed line pattern profile on glass, and a small-width channel was realized at a processing temperature of 109 °C.

Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design.

DNA nick can be used as a design motif in programming the shape and reconfigurable deformation of synthetic DNA nanostructures, but its mechanical properties have rarely been systematically characterized at the level of base sequences. Here, we investigated sequence-dependent mechanical properties of DNA nicks through molecular dynamics simulation for a comprehensive set of distinct DNA oligomers constructed using all possible base-pair steps with and without a nick. We found that torsional rigidity was reduced by 28-82% at the nick depending on its sequence and location although bending and stretching rigidities remained similar to those of regular base-pair steps. No significant effect of a nick on mechanically coupled deformation such as the twist-stretch coupling was observed. These results suggest that the primary structural role of nick is the relaxation of torsional constraint by backbones known to be responsible for relatively high torsional rigidity of DNA. Moreover, we experimentally demonstrated the usefulness of quantified nick properties in self-assembling DNA nanostructure design by constructing twisted DNA origami structures to show that sequence design of nicks successfully controls the twist angle of structures. Our study illustrates the importance as well as the opportunities of considering sequence-dependent properties in structural DNA nanotechnology.

Coarse-Grained Molecular Dynamics Model of Double-Stranded DNA for DNA Nanostructure Design.

A new coarse-grained molecular dynamics double-stranded DNA model (nCG-dsDNA model) using an improved beads-spring model was proposed. In this model, nucleotide comprising phosphate, sugar, and base group were replaced by a single bead. The double stranded model with 202 base pairs was created to tune the parameters of the bond, the nonbond, stack, angle bending, and electrostatic interaction. The average twisted angle and the persistence length of the model without electrostatic interaction were calculated at 35.3° and 120.3 bp, confirming that the proposed model successfully realized the experimentally observed double-stranded DNA structure. Moreover, the model with electrostatic interaction was discussed. From calculation results, we confirmed that the dependency of the salt concentration on the persistence length of the nCG-dsDNA model at the 30% charge is in good agreement with the Poisson-Boltzmann theoretical model.