Cooperative stabilization of Zn2+: DNA complexes through netropsin binding in the minor groove of FdU-substituted DNA

The simultaneous binding of netropsin in the minor groove and Zn2+ in the major groove of a DNA hairpin that includes 10 consecutive FdU nucleotides at the 3-terminus (3FdU) was demonstrated based upon NMR spectroscopy, circular dichroism (CD), and computational modeling studies. The resulting Zn2+/netropsin: 3FdU complex had very high thermal stability with aspects of the complex intact at 85 degrees C, conditions that result in complete dissociation of Mg2+ complexes. CD and F-19 NMR spectroscopy were consistent with Zn2+ binding in the major groove of the DNA duplex and utilizing F5 and O4 of consecutive FdU nucleotides as ligands with FdU nucleotides hemi-deprotonated in the complex. Netropsin is bound in the minor groove of the DNA duplex based upon 2D NOESY data demonstrating contacts between AH2 H-1 and netropsin H-1 resonances. The Zn2+/netropsin: 3FdU complex displayed increased cytotoxicity towards PC3 prostate cancer (PCa) cells relative to the constituent components or separate complexes (e.g. Zn2+:3FdU) indicating that this new structural motif may be therapeutically useful for PCa treatment.An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:32