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Nucleic Acids Res. 2014 Oct;42(18):11634-41. doi: 10.1093/nar/gku859. Epub 2014 Sep 22.

Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex.

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Department of Physics, Northeastern University, Boston, MA 02115, USA.
Department of Physics, Northeastern University, Boston, MA 02115, USA Department of Physics, Bridgewater State University, Bridgewater, MA 02324, USA.
Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden.
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
Department of Physics, Northeastern University, Boston, MA 02115, USA


DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Δ,Δ-[μ-bidppz-(phen)4Ru2]4+ (Δ,Δ-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that results in one ligand intercalated at almost every DNA base stack. The zero force Δ,Δ-P intercalation Kd is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Δ-P). The force-dependent kinetics analysis reveals a mechanism that requires DNA elongation of 0.33 nm for association, relaxation to an equilibrium elongation of 0.19 nm, and an additional elongation of 0.14 nm from the equilibrium state for dissociation. In cells, a molecule with binding properties similar to Δ,Δ-P may rapidly bind DNA destabilized by enzymes during replication or transcription, but upon enzyme dissociation it is predicted to remain intercalated for several hours, thereby interfering with essential biological processes.

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