Concentration and Length Dependence of DNA Looping in Transcriptional Regulation

TL;DR

This study investigates how DNA looping, influenced by repressor concentration and binding site distance, affects transcriptional regulation, revealing two distinct looped states and providing quantitative insights into DNA flexibility and looping energetics.

Contribution

It provides the first detailed single-molecule analysis of DNA looping in the lac operon, quantifying the effects of concentration and distance on loop formation and energetics.

Findings

DNA loops form at shorter spacings than the DNA persistence length.

Two distinct looped states depend on repressor concentration and site distance.

A simple statistical model quantifies the free energy of DNA looping.

Abstract

In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA loops: Binding at two or more sites on the DNA results in the formation of a loop, which can bring the transcription factor into the immediate neighborhood of the relevant promoter. Though there have been a variety of insights into the combinatorial aspects of transcriptional control, the mechanism of DNA looping as an agent of combinatorial control in both prokaryotes and eukaryotes remains unclear. We use single-molecule techniques to dissect DNA looping in the lac operon. In particular, we measure the propensity for DNA looping by the Lac repressor as a function of the concentration of repressor protein and as a function of the distance between repressor binding sites. As with earlier single-molecule studies, we find (at least) two distinct looped states and demonstrate that the presence of these two states depends both upon the concentration of repressor protein and the distance between the two repressor binding sites. We find that loops form even at interoperator spacings considerably shorter than the DNA persistence length, without the intervention of any other proteins to prebend the DNA. The concentration measurements also permit us to use a simple statistical mechanical model of DNA loop formation to determine the free energy of DNA looping, or equivalently, the J-factor for looping.