Single Molecule DNA-protein Interactions: From Retroviral Restriction to Nucleosome Stability

Abstract

Optical tweezers allow us to probe the interactions of proteins with single DNA molecules and apply very small forces. Measurement of force-dependent DNA conformations allows us to quantify interactions that govern cellular function. Here we investigate the DNA interactions of human APOBEC3G, an innate antiviral immunity protein that functions as a cytidine deaminase.

Our results show that the process of interconversion between monomeric and dimeric states regulates APOBEC3G’s deamination-dependent and deamination-independent inhibition of HIV-1 replication. I will then discuss the role of eukaryotic HMGB proteins in determining nucleosome accessibility, an important mechanism for regulating protein expression.

We construct an array of nucleosomes on a single DNA molecule, measuring nucleosome stability in the presence of HMGB proteins. We find significant unwrapping of nucleosomes due to HMBG-DNA binding, the extent of which differs between different types of HMGB proteins. The extent of observed destabilization correlates with the presence of nucleosome-free regions in cells, revealing distinct functions for regulation of nucleosome accessibility by different HMGB proteins.