Single-Molecule Studies of Doxorubicin-DNA Interactions using Optical Tweezers

Abstract

Understanding the binding mechanisms of cancer drugs to DNA at the single molecule level plays a key role to design new and improved cancer drugs for the future. We use counter-propagating laser beams in a dual-beam optical tweezers setup to quantify the binding properties of an anti-cancer drug, Doxorubicin, to DNA. Prior studies that used optical tweezers to study Doxorubicin interactions with DNA at low forces observed intercalation in the micromolar range. The dual-beam setup provides us the capabilities to extend these studies to higher forces. When the DNA was stretched past the over stretching transition in the presence of Doxorubicin, it was observed that melting the DNA felicitated more intercalation in the nanomolar concentration range. We use the lengthening of DNA upon binding to Doxorubicin in conjunction with the McGhee - von Hippel one dimensional lattice binding model to quantify the binding affinity. Our study suggests that during the transcription process when the DNA is under high tensions forming transcription bubbles Doxorubicin can effectively bind in lower concentrations than previously believed.