A single molecule study of protein-DNA interactions

All the cells in our body contain the same genetic information encoded in the DNA molecule, but they differ in the subset of the genes they express, i.e. use to make functional proteins, which confers them their diverse function and appearance. The first step in the process of gene expression is the binding of transcription factors (TFs), which are sequence-specific DNA binding proteins that initiate the transcription cascade. In this talk, I will describe how we use optical tweezers to study binding of TFs to DNA, and show that it is a complex biophysical process modulated by multiple factors. By applying a mechanical force and “unzipping” a single DNA molecule we are able to detect the binding of an individual TF and follow its binding kinetics in real time. We also follow, simultaneously, the dynamics of nucleosomes, the basic building block of the chromatin. Our experiments show that the thermodynamics and kinetics of the binding process are affected by variations in the core binding site sequence, the flanking sequences, DNA methylation and the structure of chromatin. Together, our findings reveal novel regulatory mechanisms to fine-tune the expression of genes.

PhD seminar under the supervision of Prof. Ariel Kaplan