Quantifying Binding Kinetics of DNA-Ruthenium Complexes

When: Wednesday, March 14, 2012 at 12:00 pm
Where: DA 114
Speaker: Meriem Bahira
Organization: Northeastern University
Sponsor: Introduction to Physics Research

Ruthenium complexes are small synthetic molecules with a wide range of uses including cancer therapy, and as a research tool to understand chemical carcinogenesis. Specifically, [μ-bidppz(phen)4Ru2]4+ has been engineered to have a high affinity for DNA and a low dissociation rate. The complex consists of two Ru(phen)2- moieties connected by a flexible linker. Strong binding inhibits replication of DNA in target cancer cells. To quantify the rate at which DNA-ligand binding occurs, double-stranded DNA is stretched with optical tweezers, and exposed to the ligand under a fixed applied force. When binding to DNA, the two Ru(phen)2- moieties intercalate between base pairs. Intercalation results in an increase in the length of the target DNA, and this change depends exponentially upon the applied force. Surprisingly, a fast and a slow binding mode are revealed, indicating multi-step binding. Both the fast and the slow rates are dependent on force, and each binding event contributes equally to the extension change. These studies demonstrate the capability of optical tweezers to elucidate the mechanism of complex DNA-ligand interactions, which may facilitate the rational design of DNA binding ligands with specific DNA interaction properties.