Interaction between ciprofloxacin and DNA mediated by Mg2+-ions

The oligonucleotide duplex d(C1C2T3C4G5C6T7C8T9C10)·d(G11A12G13A14G15C16G17A18G19G20) has been titrated with the fluoroquinolone ciprofloxacin (CFX) using 1H 1D and 2D NMR spectroscopy to monitor the interaction pattern. The assignments of key intermolecular proton–proton crosspeaks in the NOESY map between the fluoroquinolone and the duplex prove the existence of predominantly minor groove CFX–duplex interactions. When MgCl2 was added to a solution of 1:1 CFX–duplex until a final concentration of Mg2+–[PO4]=1, the binding pattern did not change significantly. Theoretical calculations (Docking) carried out on a model of the ternary CFX–Mg2+–duplex adduct using a key interproton distance derived from the NOESY map as anchoring, produced an energetically favourable orientation of the CFX–Mg2+ in the minor groove.