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- Type of Document: M.Sc. Thesis
- Language: Farsi
- Document No: 47804 (04)
- University: Sharif University of Technology
- Department: Physics
- Advisor(s): Ejtehadi, Mohammad Reza
- Abstract:
- Our bodies are made from billions of individual cells and DNA is the control central of each cell. In addition to linear DNAs, there are circular DNAs in nature. Circular DNAs cause new topological structures such as knots and catenanes. These topological structures form during biological proccesses such as replication. For example during replication, two daughter circular DNAs may link together and form catenanes. Anzymes named topoisomerases can simplify the topology of circular DNAs. Type 2 topoisomerases is used for simplification of catenanes. These anzymes do it with breaking a double-strand DNA and passing through another one. In comparison with DNAs, topoisomerases are very small and access local information. They can’t recognize topology of DNAs because it is a global property. Therefore, type 2 topoisomerase form both catenanes and decatenanes. In addition, these biological procceses occur in confined invironments such as nucleus of DNA, virus and bacteria. In this thesis, we study two circular chains in a spherical confined geometry with molecular dynamic simulation and calculate probability of catenation in diffrent radiuses of sphere. We show that probability of catenation is more than decatenation with calculating vanderwaals energy between two circular chains. Also, we calculate gyration radius of each circular chain and show gyration radius of each chain in catenation is larger than decatenation
- Keywords:
- Molecular Dynamic Simulation ; Circular DNAs ; Catenane ; Type2 Topoisomerase ; Confined Geometry ; MOLECULAR DYNAMIC SIMULATION
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