Simulative Analysis Of A Family Of DNA Tetrahedral Nanocages

DNA as the main genetic material,the editability of its nucleic acid sequence,the high controllability of base pairing and its own good biocompatibility make it a highly versatile biological nanomaterial.In the past few decades,DNA nanocages with different polyhedron geometries have been synthesized in large quantities in experiments,and are widely used in molecular diagnostics,bioimaging,drug delivery and other fields.Therefore,how to reveal the physical and chemical properties of DNA nanocage self-assembly from a theoretical perspective has become one of the important scientific issues.Based on the mathematical theory of DNA polyhedrons,this thesis carried out molecular dynamics simulation and analysis on a family of DNA tetrahedrons.The contents are as follows:In chapter 1,We introduced the chemical composition and physicochemical properties of DNA,as well as the existing three conformations of deoxyribonucleic acid,and,based on different synthesis strategies,we introduced the experimental research progress of DNA polyhedra.In addition,we also give The research progress of MD simulation of DNA polyhedra.Finally,some mathematical concepts related to DNA polyhedra are introducedIn chapter 2,Starting from molecular dynamics simulation,we elaborated on the development process of dynamics calculation technology,and further introduced the force field of dynamics calculation and its built-in force field function,and compared the applicable systems of these force fields.In addition,we listed the dynamic simulation software that can be used in biological macromolecules in recent years,focusing on the detailed description of the simulation process of GROMACS software,configuration file parameters,energy minimization and energy balance.In chapter 3,We performed a classical molecular dynamics simulation of a family of tetrahedral nanocages produced by changing the twist number of each double helix.The polyhedron of this family is composed of three(truncated)connectors of 5T and a tetrahedral cage with twists of 1,2 and 3 on the double helix.We calculated the RMSD values of the three parts of the tetrahedral cage full atom structure,double helix edge and thymidine connector.Further,for the double helix side part,we calculated the Cross-Correlation coefficient of the Local RMSF and Global RMSF values.For the joint connector part,H-bond and Cluster analysis of the tetrahedral truncated area is developed.The simulation results show that the three tetrahedral cages are stable throughout the simulated trajectory,and each has complex behavior.At the same time,the 2TD and 3TD cages have undergone large conformational changes,and the internal space is larger.It further illustrates that the twist number of the double helix plays an important role in determining the structural variability of the tetrahedral cage and expanding its capacity space.