Probing Protein-DNA Interactions by Unzipping a Single DNA Double Helix

Abstract

We present unzipping force analysis of protein association (UFAPA) as a novel and versatile method for detection of the position and dynamic nature of protein-DNA interactions. A single DNA double helix was unzipped in the presence of DNA-binding proteins using a feedback-enhanced optical trap. When the unzipping fork in a DNA reached a bound protein molecule we observed a dramatic increase in the tension in the DNA, followed by a sudden tension reduction. Analysis of the unzipping force throughout an unbinding “event” revealed information about the spatial location and dynamic nature of the protein-DNA complex. The capacity of UFAPA to spatially locate protein-DNA interactions is demonstrated by noncatalytic restriction mapping on a 4-kb DNA with three restriction enzymes ( BsoBI, XhoI, and EcoRI). A restriction map for a given restriction enzyme was generated with an accuracy of ∼25 bp. UFAPA also allows direct determination of the site-specific equilibrium association constant ( K A) for a DNA-binding protein. This capability is demonstrated by measuring the cation concentration dependence of K A for EcoRI binding. The measured values are in good agreement with previous measurements of K A over an intermediate range of cation concentration. These results demonstrate the potential utility of UFAPA for future studies of site-specific protein-DNA interactions.