Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

Quantifying Force-dependent and Zero Force DNA Intercalation by Single Molecule Stretching

In this work, we use single DNA molecule stretching to investigate DNA intercalation by several ligands, including the classical intercalator ethidium, three mononuclear ruthenium complexes, and a binuclear ruthenium complex. These intercalators exhibit a large range in intercalation strength. By stretching DNA and measuring ligand-induced DNA elongation at different ligand concentrations, we obtain DNA titration curves and determine the ligand-DNA binding constant and site size as a function of force. Both quantities depend strongly on force, and in the limit of zero force converge to the known bulk solution values, when available. The DNA stretching approach allows us to distinguish the intercalative mode of ligand binding from other binding modes and allows characterization of any intercalation from strong to very weak, with binding constant measurements ranging over eight orders of magnitude in these studies, including ligands that do not intercalate under experimentally accessible solution conditions. As ligand concentration increases, the DNA stretching curves saturate at a limiting force-extension curve that determines the maximum amount of ligand intercalation. The results show that the applied force partially relieves normal intercalation constraints. In addition, while simple intercalators rapidly establish equilibrium binding as the DNA is stretched, the binuclear complexes exhibit binding that is very slow on the time scale of the stretching experiment.

Mark C. Williams1, 2, *
Ioana D. Vladescu1
Thayaparan Paramanathan1
Fredrik Westerlund3
Micah J. McCauley1
Per Lincoln3
Megan E. Nuñez4
Ioulia Rouzina5

1Department of Physics
Northeastern University
Boston, MA 02115, USA
2Center for Interdisciplinary Research on Complex Systems
Northeastern University
Boston, Massachusetts 02115, USA
3Department of Chemical and Biological Engineering
Chalmers University of Technology
4Department of Chemistry
Mount Holyoke College
South Hadley, Massachusetts 01075, USA
5Department of Biochemistry
Molecular Biology and Biophysics
University of Minnesota
Minneapolis, Minnesota 55455, USA

*Phone: 617-373-7323
Fax: 617-373-2943
Email: mark@neu.edu