Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex
Journal article, 2014

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 Delta, Delta-[mu-bidppz-(phen)(4)Ru-2]4(+) (Delta, Delta-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 Delta, Delta-P intercalation K-d is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Delta-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 Delta, Delta-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.


A. A. Almaqwashi

Northeastern University

T. Paramanathan

Bridgewater State University

Northeastern University

Per Lincoln

Chalmers, Chemical and Biological Engineering, Physical Chemistry

I. Rouzina

University of Minnesota

Fredrik Westerlund

Chalmers, Chemical and Biological Engineering, Physical Chemistry

M. C. Williams

Northeastern University

Nucleic Acids Research

0305-1048 (ISSN) 1362-4962 (eISSN)

Vol. 42 18 11634-11641

Areas of Advance

Nanoscience and Nanotechnology (2010-2017)

Life Science Engineering (2010-2018)

Subject Categories

Biochemistry and Molecular Biology



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