Research Summary

The Williams lab specializes in the development of single molecule methods for quantitatively probing nucleic acid interactions in order to understand the role of these interactions in processes such as replication and transcription. At the heart of these studies is the search for the mechanism by which proteins interact with nucleic acids to alter their biophysical properties, thereby achieving their specific biological activity. These studies are done in collaboration with experts in each biological system, and the activities of the proteins are monitored in a variety of in vitro and in vivo studies to determine how the observed biophysical mechanism is manifested on the level of a complete biological system.

One of the Biophysics Groups at Northeastern University

Single molecule studies of biological interactions

Molecular mechanisms of retroviral and retrotransposon replication interactions

This work probes the interactions of nucleic acids with proteins that are involved in HIV-1 replication, including the innate human immune system APOBEC3 proteins, primarily focusing on APOBEC3G and APOBEC3H, which both inhibit HIV-1 replication in the absence of the viral protein Vif. We also probe the interactions of LINE1 ORF1p, a protein essential for retrotransposon replication.

Nucleosome accessibility and eukaryotic transcription regulatory proteins

We have developed single molecule DNA stretching methods to study DNA-protein interactions of eukaryotic regulatory proteins such as HMGB proteins, including the study of single nucleosome arrays. We find that nucleosomes are destabilized by HMGB proteins, and ongoing studies probe the much larger FACT protein, which also facilitates nucleosome reassembly.

Mechanism of DNA binding by proteins from model replication systems

By monitoring DNA binding using optical tweezers, combined with the ability to dynamically switch the binding template from double-stranded DNA to single-stranded DNA, we have determined the mechanisms by which several proteins facilitate replication in their biological systems. We probe the dynamics of replication interactions from bacteriophages as well as those involved in E. coli replication.

Thermodynamics and structural dynamics of small molecule binding to DNA

Our methods reveal the thermodynamics and structural dynamics of DNA as the small molecules bind, revealing the energy landscape of the interaction. These studies include groundbreaking work to understand the anti-cancer drug Actinomycin D, the activity of a series of ruthenium-based compounds that have complex DNA threading binding mechanisms, and the cisplatin-based intercalator phenanthriplatin.


HIV-1 replication interactions

This recent study shows how HIV-1 nucleocapsid protein condenses DNA, providing a mechanism to regulate the timing of capsid uncoating.

human FACT coordinates to facilitate both disassembly and reassembly of nucleosomes

Nucleosome accessibility in eukaryotic systems

This study shows how the human nucleosome chaperone protein FACT helps disassemble and reassemble nucleosomes to facilitate transcription.

Small molecule binding to DNA

We characterize the energy landscape of small molecule-DNA interactions to optimize characteristics for potential anti-cancer drugs. This study shows intercalation followed by covalent binding by the promising anti-cancer drug phenanthriplatin.