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 virus and retrotransposon replication interactions
This work probes the interactions of nucleic acids with proteins that are involved in HIV-1 replication, including the HIV-1 nucleocapsid protein and the innate human immune system APOBEC3 proteins. We also probe the interactions of LINE1 ORF1p, a protein essential for retrotransposon replication. Finally, recent studies examine the SARS-CoV-2 N protein, which is a critical component of SARS-CoV-2 replication. SARS-CoV-2 is the virus responsible for the COVID-19 pandemic.
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 long dsDNA from reverse transcription is required for HIV-1 uncoating, likely due to mechanical pressure regulated by the nucleocapsid protein.