Revolving Vernier Mechanism Controls Size of Linear Homomultimer

Abstract

A new kind of the Vernier mechanism that is able to control the size of linear assembly of DNA origami nanostructures is proposed. The mechanism is realized by mechanical design of DNA origami, which consists of a hollow cylinder and a rotatable shaft in it connected through the same scaffold. This nanostructure stacks with each other by the shape complementarity at its top and bottom surfaces of the cylinder, while the number of stacking is limited by twisting angle of the shaft. Experiments have shown that the size distribution of multimeric assembly of the origami depends on the twisting angle of the shaft; the average lengths of the multimer are decamer, hexamer, and tetramer for 0°, 10°, and 20° twist, respectively. In summary, it is possible to affect the number of polymerization by adjusting the precise shape and movability of a molecular structure.

1D Colloidal chains: recent progress from formation to emergent properties and applications

“…Behind the vast range of colloids, the factors that really matter in the process of assembling chains are the type of materials, surface properties, shapes and geometries. Almost all kinds of colloids made of metal, [76][77][78] metallic chalcogenide, [79][80][81] semiconductor, [82][83][84] nonmetallic oxide (mainly silica), [85][86][87] carbon nanomaterials, [88][89][90] polymer, [91][92][93] biomacromolecules 73,94,95 and their hybrids [96][97][98][99] have been utilized as building blocks. Apart from giving nanochains extraordinary electrical, magnetic, optical, and mechanical properties, the intrinsic nature of building blocks can also be applied to assemble 1D chains.…”

“…For instance, adding a non-solvent for a selected patch of multicompartment patchy micelles can induce supracolloidal polymerization to form compartmentalized nanochains as the patches gradually turn insoluble. 72,92 Surfactants, [147][148][149] polymers, [150][151][152] peptides, [153][154][155] proteins, 75,156,157 and DNA 74,94,158 are able to assemble into soft or rigid 1D tubular, rodlike, and filiform nanostructures. Using these 1D nanostructures or carbon 159,160 and polymer 161 fibrils as templates, nanochains can be fabricated by encapsulating, attracting and grafting building blocks to the templates via simple physical embedding, or electrostatic and covalent interactions.…”

How to Develop Students’ Creativity?—A Case of Student Competition of Biomolecular Design

“…In this project, students of Tohoku University tried to design and fabricate DNA nanostructure module capable of controlling their stacking number. This work is later published as a journal paper [5].…”

Web Server with a Simple Interface for Coarse-grained Molecular Dynamics of DNA Nanostructures

“…Among them, caDNAno [13] is one of the most popular tools for modeling 2D and 3D structures of DNA origami. Complicated structures have been designed using this software; for instance, rotaxane and a heptagonal module were developed in our laboratory [14,15]. One of the advantages of caDNAno is that the design information of DNA origami is abstracted as a 2D blueprint where DNA strands are represented as simple lines.…”