Molecular dynamics simulations of the DNA interaction with metallic nanoparticles and TiO₂ surfaces

The understanding of the mechanism of DNA interactions and bindingwith metallic nanoparticles (NPs) and surfaces represents a great interestin today medicine applications due to diagnostic and treatment ofoncology diseases. Recent experimental and simulation studies involvethe DNA interaction with highly localized proton beams or metallic NPs(such as Ag, Au, etc.), aimed on targeted cancer therapy through the injectionof metal micro- or nanoparticles into the tumor tissue with conse- quent local microwave or laser heating. The effects of mutational structurechanges in DNA and protein structures could result in destroying ofnative chemical (hydrogen) bonds or, on the contrary, creating of newbonds that do not normally exist there. The cause of such changes mightbe the alteration of one or several nucleotides (in DNA) or the substitutionof specific amino acid residues (in proteins), that can brought to theessential structural destabilization or unfolding. At the atomic or molecularlevel, the replacement of one nucleotide by another (in DNA doublehelices)or replacement of one amino acid residue by another (in proteins)cause essential modifications of the molecular force fields of theenvironment that break locally important hydrogen bonds underlying thestructural stability of the biological molecules. In this work, the moleculardynamics (MD) simulations were performed on four DNA modelsand the flexibilities of the purine and pyrimidine nucleotides during theinteraction process with the metallic NPs and TiO₂ surface were clarified.