title: DFT and MD study of the divalent-cation-mediated interaction of ochratoxin A with DNA nucleosides.
abstract: Aptamers are ligand-binding nucleic acids with affinities and selectivities that make them useful for the detection of a variety of compounds, including ochratoxin A. Theoretical methods can be applied to study the recognition interaction between aptamers and the ochratoxin A molecule. In this work, molecular dynamics simulations and quantum chemical calculations performed at the DFT level of theory were used to study the structures and energies of aptamers and aptamer-ochratoxin A complexes. The optimal structures as well as the interaction energies of these structures were elucidated. Divalent cations in the water solvent were shown to be an important influence on the structures and stabilities of the complexes.
authors.affiliation: Department of Nuclear Physics and Biophysics, Comenius University in Bratislava, Bratislava, Slovakia.
authors.forename: Jozef
authors.initials: J
authors.lastname: Motyčka
authors.forename: Pavel
authors.initials: P
authors.lastname: Mach
authors.forename: Milan
authors.initials: M
authors.lastname: Melicherčík
authors.forename: Jan
authors.initials: J
authors.lastname: Urban
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001665:Binding Sites; D004735:Energy Transfer; D006151:Guanosine / Q000737:chemistry*; D008024:Ligands; D008274:Magnesium / Q000737:chemistry*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009793:Ochratoxins / Q000737:chemistry*; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D009793:Ochratoxins; D012997:Solvents; D014867:Water; D006151:Guanosine; C025589:ochratoxin A; D008274:Magnesium