A5029700405- Advanced Fluorescence Microscopy Techniques
- Genomics and Chromatin Dynamics
- Advanced Biosensing Techniques and Applications
- Retinoids in leukemia and cellular processes
- Biotin and Related Studies
- DNA Repair Mechanisms
- RNA Research and Splicing
- Advanced biosensing and bioanalysis techniques
- COVID-19 Clinical Research Studies
- SARS-CoV-2 and COVID-19 Research
- Single-cell and spatial transcriptomics
- Bacterial Genetics and Biotechnology
- SARS-CoV-2 detection and testing
- Bacteriophages and microbial interactions
- CRISPR and Genetic Engineering
- Force Microscopy Techniques and Applications
- bioluminescence and chemiluminescence research
- Protein Degradation and Inhibitors
- Monoclonal and Polyclonal Antibodies Research
- Nanofabrication and Lithography Techniques
- RNA and protein synthesis mechanisms
- DNA and Nucleic Acid Chemistry
- Click Chemistry and Applications
- Gene Regulatory Network Analysis
- Biosensors and Analytical Detection
University of California, Berkeley
2020-2025
Howard Hughes Medical Institute
2023-2025
Berkeley College
2024
California Institute for Regenerative Medicine
2024
Harvard University
2013-2021
Boston VA Research Institute
2020-2021
Rockefeller University
2019
Center for Systems Biology
2014-2018
Harvard University Press
2012
University of Cambridge
2010-2011
The parABS system is a widely employed mechanism for plasmid partitioning and chromosome segregation in bacteria. ParB binds to parS sites on plasmids chromosomes associates with broad regions of adjacent DNA, phenomenon known as spreading. Although essential function, the spreading remains poorly understood. Using single-molecule approaches, we discovered that Bacillus subtilis (Spo0J) able trap DNA loops. Point mutants Spo0J disrupt bridging are defective recruitment structural maintenance...
<h2>Summary</h2> Gene activation by mammalian transcription factors (TFs) requires multivalent interactions of their low-complexity domains (LCDs), but how such regulate remains unclear. It has been proposed that extensive LCD-LCD culminating in liquid-liquid phase separation (LLPS) TFs is the dominant mechanism underlying transactivation. Here, we investigated tuning amount and localization <i>in vivo</i> affects endogenous human genes. Quantitative single-cell single-molecule imaging...
How molecules interact governs how they move. Single-molecule tracking (SMT) thus provides a unique window into the dynamic interactions of biomolecules within live cells. Using transcription regulation as case study, we describe SMT works, what it can tell us about molecular biology, and has changed our perspective on inner workings nucleus. We also cannot yet new technical advances seek to overcome its limitations. This ongoing progress will be imperative address outstanding questions...
Transcription coactivators are proteins or protein complexes that mediate transcription factor (TF) function. However, they lack DNA-binding capacity, prompting the question of how engage target loci. Three non-exclusive hypotheses have been posited: recruited by complexing with TFs, binding histones through epigenetic reader domains, partitioning into condensates their extensive intrinsically disordered regions. Using p300 as a prototypical coactivator, we systematically mutated its...
Single-molecule imaging provides a powerful way to study biochemical processes in live cells, yet it remains challenging track single molecules while simultaneously detecting their interactions. Here, we describe novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), which one fluorophore (the ‘sender’) can reactivate second ‘receiver’) from dark state. PAPA requires proximity between the two fluorophores, operates at longer average intermolecular distance than Förster...
Summary Cells are built from vast networks of competing molecular interactions, most which have been impossible to monitor in vivo. We recently devised a new strategy, proximity-assisted photoactivation (PAPA), detect these interactions at single-molecule resolution live cells. Here we apply PAPA visualize the network that regulate central transcription elongation factor P-TEFb. between multiple pairs endogenous proteins, combined with fast tracking (fSMT), revealed inactive P-TEFb within...
Single-molecule pulling experiments on the folding of biomolecules are usually interpreted with one-dimensional models in which dynamics occurs ``pulling coordinate.'' Paradoxically, free-energy profile along this coordinate may lack a refolding barrier, yet barrier is known to exist for folding; thus, it has been argued that do not probe folding. Here, we show transitions monitored true but be hidden projection onto coordinate. However, theory using still yields physically meaningful energy...
Re-opening of communities in the midst ongoing COVID-19 pandemic has ignited new waves infections many places around world. Mitigating risk reopening will require widespread SARS-CoV-2 testing, which would be greatly facilitated by simple, rapid, and inexpensive testing methods. This study evaluates several protocols for RNA extraction RT-qPCR that are simpler less expensive than prevailing First, isopropanol precipitation is shown to provide an effective means from nasopharyngeal (NP) swab...
Abstract SARS coronavirus 2 (SARS-CoV-2) has caused an ongoing global pandemic with significant mortality and morbidity. At this time, the only FDA-approved therapeutic for COVID-19 is remdesivir, a broad-spectrum antiviral nucleoside analog. Efficacy moderate, improved treatment strategies are urgently needed. To accomplish goal, we devised strategy to identify compounds that act synergistically remdesivir in preventing SARS-CoV-2 replication. We conducted combinatorial high-throughput...
Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs chromatin is proposed be regulated by competition for limiting pool core RXR subunit. However, this mechanism has not yet been tested endogenous proteins live cells. Using single-molecule tracking (SMT) proximity-assisted photoactivation (PAPA), we...
Mechanical stretching of proteins modifies their folding kinetics and may also cause a switch mechanism from that at zero force. It is not clear the alone whether change continuous distortion force pathway or it occurs via "discrete switch" to an alternative pathway. We use molecular simulations dissect this as pulling applied protein G four different pairs residues, "pulling coordinates". Using statistical clustering approach based on pattern native contact formation, we find distinct...
Most bacteria utilize the highly conserved parABS partitioning system in plasmid and chromosome segregation. This depends on a DNA-binding protein ParB, which binds specifically to centromere DNA sequence parS adjacent non-specific over multiple kilobases phenomenon called spreading. Previous single-molecule experiments combination with genetic, biochemical computational studies have argued that ParB spreading requires cooperative interactions between dimers including bridging possible...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of disease 2019 (COVID-19), has emerged as a major global health threat. The COVID-19 pandemic resulted in over 168 million cases and 3.4 deaths to date, while number continues rise. With limited therapeutic options, identification safe effective therapeutics is urgently needed. repurposing known clinical compounds holds potential for rapid drugs against SARS-CoV-2. Here, we utilized library FDA-approved...