Abstract

Molecular Dynamics Study on Cluster Damaged DNA Containing Apurinic/Apyrimidinic Sites on the Same Strand

DNA has susceptibility to alkylation, oxidation, and irradiation, which can lead damage to the molecular structures such as base damage, apurinic/apyrimidinic site (AP site), and strand breaks. These damages are usually repaired by enzymes in the cell. However, when the damages are locally crowded and clustered, the enzymatic repair cannot work adequately, which can lead to cell death and cancer. In this work, we carried out MD simulations of DNA with AP sites; we particularly focused on a situation in which two AP sites are positioned at the same strand. The results found that the presence of AP sites in DNA significantly changes the structure of DNA, which possibly make a significant effect on the enzymatic repair.

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Molecular Dynamics Simulation of Cluster Damaged DNA Composed of Apurinic/Apyrimidinic Sites

DNA has susceptibility to alkylation, oxidation, and irradiation, which can produce damage to the molecular structures such as 8-oxoguanine, apurinic/apyrimidinic site (AP site), and strand breaks. These damages are usually repaired by enzymes in the cell. However, when the damages are locally crowded and clustered, the enzymatic repair cannot work adequately, which can lead to cell death and cancer. In this work, we carried out MD simulations of DNA with AP sites, and here we particularly focused on a situation in which two AP sites are positioned at the same strand. From the analysis of the DNA structural changes, we will clarify why effect of the AP sites is different between the same and complementary strands.

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The role of DNA sequence in the stability of double-stranded structure

The separation process of double-stranded DNA was examined for three different base sequences using molecular dynamics simulations. We applied an external force to an atom on the DNA backbone and calculated the work required to pull the double strands away. A DNA fragment consisting of guanine-cytosine pairs shows a sharper change in work than DNA fragments consisting of adenine-thymine pair . This fact is attributed to the difference in the number of hydrogen bonds between base pairs. Meanwhile, even between the same base pairs, the ease of breaking hydrogen bonds differs depending on the surrounding sequence.

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Molecular Dynamics Study of Polymer-Water Interaction in Zwitterionic Polymer Brush-Water Interface

In the medical fields, zwitterionic polymer brushes have received considerable attention owing to their highly antifouling effect. The structure of hydrated polymer brushes and the dynamics of hydrated water have been recognized as important factors for antifouling in recent studies. Molecular dynamics simulations of the all-atom models composed of zwitterionic polymer brushes and water are performed to clarify the effect of polymer brush tacticity on the dynamics of interfacial water. Our simulations show that shape of polymer brushes and dynamics of water differ between syndiotactic zwitterionic polymer brushes and isotactic ones. It is also found that the lifetime for hydrogen bond of syndiotactic model is longer than that of isotactic model. It is concluded that there is certainly difference in the dynamics of interfacial water depending on the tacticity of polymer brushes.

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Investigation of phase behavior of bolaamphiphilic solution using dissipative particle dynamics simulation

We study the phase behavior of bolaamphiphilic solution performing the dissipative particle dynamics simulations of coarse-grained bolaamphiphilic molecules with explicit solvent molecules. The phase structure becomes a micellar phase at a low concentration of bolaamphiphilic molecules in water, and that it changes to complex mesophases as the concentration increases. Our simulations show that there are six kinds of phases: isotropic micellar, micellar, rod-shaped micellar, hexagonal, network-structure and lamellar. The network-structure and the lamellar phases disappear when the restoring potential against the bending of bolaamphiphilic molecules in our simulation model is excluded; and the isotropic micellar and the hexagonal phases disappear when the restoring potential is included. This suggests that the strength of the restoring potential against the bending of bolaamphiphilic molecules has an important role in the formation of the mesophases.

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Simulation study of the structural formation in systems with short-range interaction

By carrying out the molecular dynamics simulations of 100 short polymer chains, each of which consists of 20 CH₂ groups, we show that the orientationally ordered structure at low temperature is formed from a random structure at high temperature by a sudden cooling. The essentially extended chains form a monolayer structure. The ratio of the lattice constants a/b takes the hexagonal value 3^1/2 at 400 K and decreases as the temperature decreases. From detailed analysis of the local orientational order, it is found that the growth of the local ordered clusters proceeds in a stepwise fashion. From the analysis of the molecular mobility, we find that the longitudinal chain motion increases dramatically with increasing temperature while the transverse chain motion is not so dependent on the temperature variation.

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Simulation study of the structural formation in thermodynamically closed systems

By carrying out the molecular dynamics simulations of a single polymer chain with 500 segments, we show that the orientationally ordered structure at low temperature is formed from a random-coil structure at high temperature by a stepwise cooling. The radii of gyration and the orientational order parameters show that the transition temperature region from the random-coil structure to the orientationally ordered structure is 350<T<550 K. From detailed analyses of the orientationally ordered structure at T=100 K, it is found that the lengths of stems and each fold region along the principal axis with the smallest moment of inertia are around 20 A and 10 A, respectively.

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Simulational and Analytic Studies of Anomalous Relaxation in Disordered Systems

Anomalous relaxations observed in various kinds of disordered systems are discussed. In particular, the structural relaxations in supercooled liquids are studied by making use of molecular dynamics simulations. On the belief that the essential aspects of anomalous relaxations are explained in the framework of one-body pictures, we carry out analytic and simulational studies both of the fractal time random walk and of random walks in spaces of fractal and non-fractal dimensions, from which we show that the anomalous relaxations of the stretched-exponential type as well as of the Cole-Cole type take place even in these systems.

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