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

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

Soft Matter & Physics of Living Systems

Date

November 21, 2017 -
3:00pm to 4:00pm

Location

Klaus

Room

1116 West

Affiliation

Northeastern University

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.