General Area:
My laboratory investigates the thermodynamics and kinetics of protein-induced conformational changes in DNA and the structures of nucleo-protein assemblies relevant to transcriptional regulation. The goal is to understand the molecular features of regulatory mechanisms. We use single molecule experimentation, in particular the tethered particle motion technique with and without magnetic tweezers. We also use scanning force microscopy in collaboration with
David Dunlap in the
Cell Biology Department.
Current Projects:
We are currently studying the epigenetic switch of λ bacteriophage and of 186 coliphage. Both λ and 186 are temperate phages which infect
E. coli bacteria. Upon infection, the newly injected viral DNA can either integrate in the bacterial genome and be passively replicated with it or circularize and be actively replicated. In the first case, the virus will be quiescent, until an external event triggers it. In the second case it will cause the lysis and death of the bacteria and the spreading of viral progeny. What determines the choice between these two behaviors is one repressor protein, which interacts with multiple binding sites on the DNA. Such interaction leads to dynamic structures, where the DNA loops or wraps around the protein, which allow stable lysogeny and, simultaneously, efficient switch to lysis if necessary. We are interested in studying the molecular mechanism at the basis of these switches. This involves understanding the different interaction modes of repressor with DNA and the nature of the different nucleoprotein complexes that are possible, and characterizing the kinetics and thermodynamics of complex formation and breakdown. Furthermore, we are interested in studying how supercoiling affects DNA looping/wrapping and contributes to transcriptional regulation.
In collaboration with
Dr. Lucchesi in the
Biology Department, we are also studying the molecular properties of the Male Specific Lethal (MSL) complex of
Drosophila. This complex enhances the level of transcription of numerous genes on the X chromosome of
Drosophila males and ensures dosage compensation in males and females. Dosage compensation is a fundamental problem of transcriptional regulation, epigenetics and developmental biology. The MSL complex contains an ATP-dependent RNA/DNA helicase (MLE). In
Drosophila males, the complex assembles on the X chromosomes at specific sites and then spreads to numerous additional sites. From these sites, complexes target activated genes in order to increase their level of expression. Our laboratory uses single-molecule assays and bulk biophysical techniques to characterize the parameters that are responsible for the translocation of the MSL complex along DNA.
Finally, we collaborate with Dr. Dunlap in the Cell Biology Department to study how variations in the bending rigidity of DNA may affect motor proteins.
Instrumentation Development: This is an active area of investigation in the laboratory, since questions often require new instrumentation. For example, we recently developed a novel single molecule microscope that allows simultaneous observation of DNA conformations and protein activity to determine how certain motor enzymes are affected by protein-induced conformational changes in DNA.
Theory: We formulate
ad hoc computational and analytical models independently and in collaboration with theoretical physicists in order to validate, explain and interpret the experimental data.
Website: www.physics.emory.edu/faculty/finzi/
