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Method for obtaining stable DNA tetrahedron synthesis parameters based on modeling

An acquisition method and tetrahedron technology are applied in the field of acquisition of stable DNA tetrahedron synthesis parameters, which can solve the problems such as the inability to improve the space capacity of DNA tetrahedrons, and achieve the effects of not cumbersome design, wide application and low cost.

Active Publication Date: 2020-09-08
SHANDONG UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

After research by the inventors of the present invention, it has been found that for the simulation calculation of DNA polyhedrons, two simulation softwares, Amber and NAMD, are mainly used at present, and the existing reports only carry out modeling and calculation from a single angle, and there is no explanation at the level of mathematical theory , there are certain limitations and deficiencies in the process from the initial model construction to the dynamic simulation, and it is impossible to evaluate the integrity and stability of the DNA tetrahedron, so that the space capacity of the DNA tetrahedron cannot be improved.

Method used

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  • Method for obtaining stable DNA tetrahedron synthesis parameters based on modeling
  • Method for obtaining stable DNA tetrahedron synthesis parameters based on modeling
  • Method for obtaining stable DNA tetrahedron synthesis parameters based on modeling

Examples

Experimental program
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Effect test

Embodiment 1

[0080] (1) Using CorelDRAW 12 software to draw a mathematical chain link with specific topological properties figure 1 TD, such as figure 1 As shown, its link graph contains 4 branches, and the number of intersections on each edge is 2.

[0081](2) According to the chain link diagram, use the PolygenDNA model software to set the apex connector to be composed of 5 thymidines. By adjusting the module parameters in the program, construct a DNA tetrahedron nanocage all-atom model, such as figure 2 As shown, name it 1TD.pdb.

[0082] Wherein: the double helix edge torsion number of the DNA tetrahedral cage model obtained by constructing is respectively 1, corresponds to the crossing number of the mathematical link diagram in the step (1), and its all-atom model structure atom number is respectively 4586, constitutes a tetrahedron The number of nucleotides in the structure is 144, which is a standard DNA tetrahedron all-atom structure.

[0083] (3) Using Gromacs 5.1.2 software, ...

Embodiment 2

[0096] (1) Using CorelDRAW 12 software to draw a mathematical chain link with specific topological properties figure 1 TD, such as figure 1 As shown, its link graph contains 4 branches, and the number of crossings on each edge is 4.

[0097] (2) According to the chain link diagram, use the PolygenDNA model software to set the apex connector to be composed of 5 thymidines. By adjusting the module parameters in the program, construct a DNA tetrahedron nanocage all-atom model, such as figure 2 As shown, name it 2TD.pdb.

[0098] Wherein: the double helix edge torsion number of the DNA tetrahedral cage model obtained by constructing is respectively 2, corresponds to the intersection number of the mathematical link diagram in the step (1), and its all-atom model structure atom number is respectively 8393, constitutes a tetrahedron The number of nucleotides in the structure is 264, which is a standard DNA tetrahedron all-atom structure.

[0099] (3) Using Gromacs 5.1.2 software,...

Embodiment 3

[0112] (1) Using CorelDRAW 12 software to draw a mathematical chain link with specific topological propertiesfigure 1 TD, such as figure 1 As shown, its chain-ring graph contains 4 branches, and the number of crossings on each edge is 6.

[0113] (2) According to the chain link diagram, use the PolygenDNA model software to set the apex connector to be composed of 5 thymidines. By adjusting the module parameters in the program, construct a DNA tetrahedron nanocage all-atom model, such as figure 2 As shown, name it 3TD.pdb.

[0114] Wherein: the double helix edge torsion number of the DNA tetrahedral cage model obtained by constructing is respectively 3, and corresponding to the intersection number of the mathematical link diagram in the step (1), its all-atom model structure atom number is respectively 11825, constitutes a tetrahedron The number of nucleotides in the structure is 372, which is a standard DNA tetrahedron all-atom structure.

[0115] (3) Using Gromacs 5.1.2 so...

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Abstract

The invention discloses a method for obtaining stable DNA tetrahedron synthesis parameters based on modeling. The method comprises the following steps: counting the number of branches of a DNA tetrahedron and the number of intersections on each side of the DNA tetrahedron; constructing a DNA tetrahedron nanocage all-atom model by utilizing a mathematical chain ring diagram; processing the DNA tetrahedron nano-cage all-atom model by using Gromacs software, carrying out integrity and stability detection on the constructed model to obtain the number of branches, the number of intersections and the total number of nucleotides of the DNA tetrahedron with integrity and stability. According to the method, the synthesis parameters of a stable DNA tetrahedron can be obtained, and the synthesis of the stable DNA tetrahedron can be guided according to synthesis parameters.

Description

technical field [0001] The invention relates to a method for obtaining synthesis parameters of a stable DNA tetrahedron based on modeling. Background technique [0002] The information disclosed in this background section is only intended to increase the understanding of the general background of the present invention, and is not necessarily to be regarded as an acknowledgment or any form of suggestion that the information constitutes the prior art already known to those skilled in the art. [0003] DNA, also known as deoxyribonucleic acid, is composed of two intertwined complementary single strands and plays an important role in the growth and development of all known organisms and many viruses. The main function of DNA in living organisms is information storage, conveying instructions for building intracellular compounds such as proteins and ribonucleic acid. Professor N.C. Seeman of New York University designed the nucleic acid linker in 1982. He used a specific oligonuc...

Claims

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Application Information

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IPC IPC(8): G16B5/00
CPCG16B5/00
Inventor 刘淑雅白慧李佳
Owner SHANDONG UNIV
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