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Information × Registration Number 0224U002674, 0123U102290 , R & D reports Title Structural transformations of the DNA double helix under the influence of biologically active molecules and ions popup.stage_title Head Volkov Serhii N., Доктор фізико-математичних наук Registration Date 24-02-2024 Organization М.М.Bogolyubov Institute of Theoretical Physics of the National Academy of Sciences of Ukraine popup.description2  The following tasks were solved within the framework of the project: The molecular dynamics method was used to study the conformational flexibility of polyamine molecules interacting with the DNA double helix. In particular, a detailed analysis of the conformational space of spermidine3+ molecules both in solution and in close contact with DNA was carried out. It was shown that all possible conformations of the spermidine3+ molecule, and there are more than 2000 of them, can be classified into seven families, which were named conformational modes. The number of conformational modes corresponds to the number of dihedral angles formed by the atoms in the backbone chain of the spermidine3+ molecule. It was found that the relative population of these conformational modes is strongly influenced by the interaction of spermidine3+ with DNA. In particular, three of the seven dihedral angles of the spermidine3+ molecule are predominantly in the trans conformation (with or without DNA), while the other four dihedral angles switch between the trans, gauche+, and gauche– states. Two of the seven conformational modes of the spermidine3+ molecule appear only in complex with DNA and characterize its significantly bent state. The double helix can undergo significant transformations in response to the addition of a polyamine molecule, which is manifested in the extreme narrowing of the DNA minor groove. The possibility of formation of complexes of the hydrogen peroxide molecule with DNA nucleic bases was analyzed. Stable complexes were found. Their optimal geometries and interaction energies were determined using the methods of quantum chemistry. It is shown that complexes with hydrogen peroxide are energetically more stable than similar complexes with water molecule. These results may contribute to the understanding of the mechanisms of ion therapy of cancer diseases. An integrable nonlinear dynamical system of gauge-coupled intrasite excitations and lattice vibrations on an infin Product Description popup.authors Vakhnenko Oleksii O. Volkov Serhii N. Kanevska Polina P. Kriachko Yevhen S. Perepelytsia Serhii M. Piatnitskyi Dmytro V. popup.nrat_date 2024-02-24 Close