The Simulation Study On Dynamics Of The Conformation Transition In DNA-salt Solution

The polymer deoxyribonucleic acid chain formed by the polymerization of deoxyribonucleic acid,known as DNA.DNA is one of the basic biopolymers,which plays a vital role in the life activities,is the key material to carry genetic information in plant cell.DNA,as a marker of genetic information,as well as the guidance of the function of the living body,its structure in the cell is dynamically variable.Many studies have shown that DNA has a wide range of conformational changes,such as the small perturbation in the current conformation,and the unwinding of DNA.DNA has many conformations.The stability of DNA depends not only on the chemical composition of the chemical modification of the DNA sequence and the clip,but also by the influence of the solution conditions.Since DNA is often accompanied by regular conformational changes in the process of DNA replication,transcription and translation,the researchers believe that the physiological function of the system is through the change of conformation.In addition,the DNA is physically treated as a general molecular design of nano scale structure,due to its proper sequence can be folded into a DNA column two level structure defined,DNA is expected to develop into a mobile component of nano devices,such as nano pliers.DNA based molecular controlled machinery can be driven by the conversion between different conformations of DNA.Therefore,more attention has been paid to the study of conformational transition of DNA.The B conformation of DNA is the most thermodynamically stable state of DNA under physiological conditions.However,the double helix structure of DNA is also endowed with sufficient structural flexibility.The conformation of A relatively compact structure to be considered not only in gene expression plays an important role,but also as a recognition motif in-DNA protein complexes.DNA's A/B conformational interconversion process is consideredto be one of the protein-DNA identification model,at the same time is also considered to promote self DNA the assembly,and the main driving force of the shell by the virus protein.For this reason,the study of conformational changes of A-B is very extensive in many studies of DNA conformation.Previous studies have shown that the alkali metal ions in the solution can play an important role in the conformational transition of A-B-DNA.In addition,we found that there is a stable A-DNA conformation in the high concentration salt solution.Therefore,it is assumed that the initial A-DNA configuration of the high concentration salt solution can be stable with time.Based on the principle of molecular dynamics,the GROMACS5.1.4 software package was used to simulate the conformational changes of A-DNA and B-DNA in high concentration salt solution.The results are as follows: 1.Comparing the various molecular dynamics simulations,the Charmm36 force field is most suitable for this system.2,Na,K,Rb and other alkali metal ions were simulated and compared,found in the ability to hinder the ability to change the conformation of K<Rb<Na.3.The simulation of the ion system with different concentration of 3M is more than that of 1M.It is found that there is a stable conformation of class A in the concentration range.In the lower salt concentration solution,the initial B conformation remains stable,while the A conformation changes to the B conformation,which is in agreement with the experimental data.It was found that the aggregation of Na+ions in the DNA channel may be an important reason for preventing the conformational transition.This study enriches the understanding of the molecular dynamics simulation of the conformational transition of DNA molecules in salt solutions.However,the need to pay attention to the molecular dynamics simulation of the force field parameters are not perfect,in a variety of stress field simulation of the final conformation are non A conformation,DNA molecules appear base pair separation and so on in the simulation process.