Novel DNA Target Site Search Mechanism for Sequence-Specific DNA Binding Proteins

Abstract

A significant subset of protein-DNA interactions occur between proteins that identify a specific target sequence amongst large sections of nonspecific DNA. The currently accepted model for this process states that sequence-specific DNA-binding proteins (SSDBPs) find their DNA targets by a ubiquitous process in which they bind loosely to DNA to scan DNA in 1-D, adopting a tightly bound state to the DNA only at the target sequence1. However, little consideration has been made for the vast array of properties exhibited by SSDBPs which could influence protein search behavior prior to finding the DNA target site. SSDBPs differ considerably in size, DNA target sequence length, function, and (in)dependence on cofactors. These properties affect protein activity at the target sites and may similarly affect protein search mechanisms.We propose that SSDBP search mechanisms may not be ubiquitously defined for all SSDBPs. We study protelomerase TelK, a cofactor-independent single-turnover protein responsible for the formation of DNA hairpins in prokaryotic DNA, and its mechanism of DNA target site identification2. High resolution optical trap studies show an unpredicted observation of nonspecific DNA condensation by TelK. TIRFM studies show that TelK 1D scanning of nonspecific DNA occurs only at low concentrations where TelK is a monomer. 1D scanning ceases at higher TelK concentrations, as TelK forms aggregates of multiple TelK units. This suggests that TelK searches for its target site while loosely bound to DNA as a monomer and aggregates once it encounters another TelK unit on DNA, before reaching the target site. These results suggest a mechanism contrary to the currently accepted model for SSDBP targeting mechanisms, indicating that these processes may vary from protein to protein.1. Halford et al. Nucl. Ac. Res 32, 3040 (2004).2. Aihara et al. Mol. Cell 27, 901 (2007).