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.
We measured single molecule ssDNA binding by SSB proteins from different systems, E. coli SSB, T4 gene 32, and LINE-1 ORF1p. All showed surprising initial compaction then decompaction. This allows them to dissociate rapidly in response to crowding, as we show in QRB Discovery doi.org/10.1017/qrd….
— Mark Williams single molecule biophysics lab (@williamslabneu.bsky.social) January 22, 2025 at 6:05 PM
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When B DNA is overstretched, it converts to melted DNA or S-DNA. Overstretching has been controversial because the transitions are similar for the two states. With the Westerlund and Wilhelmsson labs, we show in NAR the B-to-S transition is much faster than melting academic.oup.com/nar/article/…
— Mark Williams single molecule biophysics lab (@williamslabneu.bsky.social) January 18, 2025 at 12:17 PM
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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.
Retrotransposon replication
LINE1 ORF1p perform multiple functions to facilitate LINE1 retrotransposition. It also facilitates replication of other retrotransposons. We show that it does this through multiple binding modes, including the ability to bind multiple nucleic acids at once.
Nucleosome chaperone protein function
Like other HMGB proteins, human FACT destabilizes nucleosomes to facilitate transcription. Why is the rest of this large protein needed? We show that the SSRP1 HMGB domain coordinates with the SPT16 domain to facilitate nucleosome reassembly after disruption