Stretching DNA to Quantify Non-Specific Binding by the Lambda Repressor (ci)

Abstract

Non-specific binding of regulatory proteins to DNA can be an important mechanism for target search and for storage. This seems to be the case for the λ repressor protein (CI), which maintains lysogeny after bacteriophage infection. CI binds specifically at two distant regions along the viral genome and induces the formation of a repressive DNA loop. However, single-molecule experiments and kinetic measurements show that CI also binds to DNA non-specifically, and that this mode of binding may play an important role in maintaining lysogeny. Therefore, we have quantified non-specific CI binding by stretching DNA at various CI concentrations using magnetic tweezers. We recorded the decrease in DNA extension caused by CI (see Fig. 1). Then, we used a novel theory extending work by Zhang & Marko [PRE 77, 031916, (2008)] to calculate the change in CI binding from the measured decrease in DNA extension. In this presentation, we will interpret new stretching data at various CI concentrations using our novel theory. Furthermore, we will discuss the versatility of our method for characterizing gene regulation via non-specific protein binding.