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.
A three-dimensional (3D) simulation for micropowder blasting was carried out for the first time to predict the convex corner structure of a processed glass substrate with patterned mask erosion. The simulator utilized a cellular automaton algorithm which consisted of combinations of two orthogonal planes of two-dimensional (2D) cells and a solid particle erosion model. It was confirmed that the effect of erosion at the convex corner of the mask on the glass processing profile, which cannot be predicted in the previous 2D simulation, was successfully simulated using our 3D simulator.
We present a new rapid prototyping technique without a photolithography step to produce a glass chip with high aspect ratio channel for a micro total analysis system (µTAS). This technique consists of a powder blasting technique and direct laser patterning of Au nanoparticles dispersed polymer mask technique, and is useful in the development stage of a glass chip. The mask thickness and powder blasting condition were optimized for the fabrication of a glass chip with a higher aspect ratio channel. Under the optimized processing condition, the microchannel with a maximum aspect ratio of 2.1 in a glass substrate was successfully realized. The proposed technique was applied to a glass chip for electrophoresis and its performance for DNA separation analysis was confirmed.
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