| With the advent of structural DNA nanotechnology, more and more researchers are putting much effort into this new community. However, it is very different from conventional "up bottom" fabrication method, the new tendency is creating "bottom up" fabrication method. Therefore, based on the design and fabrication of DNA tile, the new "bottom up" technology got a big progress recently. However, there still are lots of issues regarding to its function, application, mechanism and shortcomings. There are two representative issues:1. why similar tile structures lead to various nanoribbon? Why 2-dimensional cross tile lead to 3-dimensional nanotube. In order to fully understand the mechanism of DNA tile, normal mode analysis is introduced to acquire the physical insights such tiles. After simulation of the mode shapes and natural frequencies corresponding to the low frequency. Lots of physical insights are supplied to resolve the current issues. The main contents are summarized as below:Firstly, since the premise of Normal Mode Analysis is the minimum energy state of the given structure. Thus, somewhat adjustment for the given ideal structure is done before the dynamic modeling. In particular, the minimum state of DNA can be represented by the average equilibrium "rest" parameters. So the conventional overcomplicated molecular dynamics procedure was replaced by the current geometric adjustment. Based on the sequence-dependent statistics in this field and the planar assumption of base pairs, the whole adjustment can coded in Robotic Kinematic model with regards to the rigid body manipulation, such as translation and rotation. Consequently, the fine structure of the DNA tile is the given structure for the succeeding process.Secondly, the given structure should be coded in Coarse-grained Elastic Network Model. Since the fast Brownian motions of atoms are not the main concern, the overcomplicated full-atom model is improper now. By assuming the interactions among atoms are harmonic potential and selecting the presentative atoms, the whole structure mimics a spring network. After deriving the dynamic equations, an eigen matrix can be generated finally. Where the calculated eigenvalue indicate the vibration frequencies and the eigenvector indicate the normal mode. Because the low frequency vibrations correspond to the significant collective motions of the macromolecule, all the low frequency modes should pay much attention to.Thirdly, the single coupled DNA tile is the most basic one in the DNA tile family. The Normal Mode Analysis for single coupled DNA is especially important. Here 4 types of single coupled DNA tile, DX1, DX2, DX3, DX4, with same structure but different sequence are analyzed. After Normal Mode Analysis, the first assembling unit containing DX1 and DX2 has consistent lower frequencies than the other assembling unit which contains DX3 and DX4. Which demonstrate the first assembling unit has the higher rigidity with regard to the similar mass of both units. Such conclusion explained the big difference of the size for NANO fabrication.Fourthly, the cross DNA tile is another very common used type. Although the fabrication of nano tube with this tile is succeed several years ago. However, the mechanism of nano formation is still the tricky problem. After the normal mode analysis for the quadruplet structure, the lowest three modes are simulated. The first mode has obvious bending curvature, and this deformed conformation can deduce the formation of nanotube in term of longitudinal growth and contour growth. This is the definite bright insight for nanotube fabrication.
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