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DNA Molecule in Confined Geometries

Salari, Hossein | 2017

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  1. Type of Document: Ph.D. Dissertation
  2. Language: Farsi
  3. Document No: 50105 (04)
  4. University: Sharif University of Technology
  5. Department: Physics
  6. Advisor(s): Ejtehadi, Mohammad Reza
  7. Abstract:
  8. DNA molecule is one of the most important macromolecules in cell, which carries genetic information for life. DNA is often in confined geometries, such as, packaging in cell and DNA-protein interactions. While DNA is nearly a stiff polymer, its elastic behaviour plays a crucial role on its functionalities.Therefore, investigating the elastic and mechanical properties of DNA is really important.The elastic behaviour of a long and free DNA can be predicted very accurately by ”worm-like chain“ (WLC) model. In WLC model, DNA is assumed as a elastic rod with harmonic potential of local bending and twist.Many structural properties of DNA have been ignored in this model. But in recent years, by developing the techniques in nano scales, a lot of single molecule experiments have been developed to study the elastic properties of DNA in confined geometries. The results of these experiments show that the WLC model is not able to explain elastic properties in short length scales and confinements. Therefore, we need to add some structural properties to the model in order to explain this anomalous effect.The constraints on DNA can be considered in this two ways: constraint on boundary conditions, and constraint on space dimensions. Here, we investigate three constraints on DNA. One of them is DNA in two dimensional confinement which a spatial constraint, and the others are looping probabilities of DNA and supercoiling of circular DNA, which are boundary constraints. Here, we show that the anisotropy in bending of DNA can increase the persistence length of DNA in two dimension (2D) in comparison with 3D persistence length. Also, we show that asymmetry in bending of DNA is responsible for kink formation in DNA and it increases several order of magnitude of the looping probability of short DNA (a few nano meter length). Furthermore, it is shown that excluded volume interactions and superhelix end loops can play role in configurations of supercoiled DNA. Our results in all of these works is in good agreement with experimental data. Here, we use Monte Carlo simulations with coarse-grained model at base pair level to exploit the elastic properties of DNA. We also use analytical methods with continuum models to find elastic and statistical behaviour
    of DNA molecule
  9. Keywords:
  10. Elastic Properties ; Wormlike Chain Model ; Bending Anisotropy ; DNA Molecule Elastic Properties ; Asymmetric Bending

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