Molecular dynamics (MD) simulations were used to investigate the interaction of norfloxacin with the DNA oligonucleotide d[ATATCGATAT]₂. The initial binding structure was built with molecular modeling based on the experimental results. A 2 ns MD calculation was performed to study the norflox-acin-DNA complex and the results indicated that norfloxacin was inserted in the minor groove of DNA, binding to the region of duplex TCGA bases. The possible H-bonds between carbonyl and carboxyl group of norfloxacin and amine group of the guanine base support a minor-groove complex for the compound in GC DNA sequence. Molecular dynamics studies complement the structural analysis and provide a clear picture of the norfloxacin-DNA complex.

Key words: norfloxacin, DNA, molecular modeling, molecular dynamics simulation