Research and Teaching Interests
Our research is focused on the development and application of state-of-the-art techniques of single molecule detection to study complex biological systems. We use an interdisciplinary approach that interweaves concepts from physics, chemistry and biology.
Conformational dynamics of biomolecules:
In contrast with the more conventional fluorescence techniques, where billions of molecules are sampled simultaneously, single molecule techniques allow the observation of subpopulations and rare events that would otherwise be hidden in the measured average. More importantly, the observation of an individual molecule allows for the study of dynamic aspects of conformational changes without the need to synchronize the entire sample. A related technique, Fluorescence Correlation Spectroscopy, is based on the analysis of the fluctuations in the fluorescent signal of a small number of molecules. Correlation analysis of the fluorescence fluctuations yields kinetic information about the dynamic processes that cause the changes in the fluorescent signal.
We use these concepts to investigate the dynamics, structure and kinetics of nucleoprotein assemblies. Specific projects in this line of research include the study of the dynamic aspects of DNA-protein interactions in nucleosomes. We are interested in characterizing the spontaneous DNA unwrapping and re-wrapping kinetics, and in the study of the effect of ATP-dependent remodeling enzymes.
Photophysical properties of fluorescent dyes commonly used in single molecule spectroscopy:
We are also interested in studying the photochemical and photophysical properties of fluorescent dyes that are commonly used for single-molecule applications. Photophysical processes are a source of artifacts that have not been thoroughly explored in many cases. Photochemical reactions, such as isomerizations, produce results that can be interpreted as conformational changes of the macromolecule to which the fluorophore is attached. A careful characterization of the photophysical properties of these fluorophores is critical for correct interpretation of experimental results.
"Photobleaching and Blinking of TAMRA Induced by Mn2+," E. M. S. Stennett, G. Kodis and M. Levitus, ChemPhysChem 13 909-913 (2012)
"Probing the Interaction Between Fluorophores and DNA Nucleotides by Fluorescence Correlation Spectroscopy and Fluorescence Quenching," S. Ranjit and M. Levitus, Photochem. Photobiol. 88 782-791 (2012)
"Real-time monitoring of RAG-catalyzed DNA cleavage unveils dynamic changes in coding end association with the coding end complex," G. Wang, K. Dhar, P. C. Swanson, M. Levitus and Y. Chang, Nucl. Acids Res. 40 6082-6096 (2012)
"Cy3-DNA Stacking Interactions Strongly Depend on the Identity of the Terminal Basepair," Justin Spiriti, Jennifer K. Binder, Marcia Levitus, Arjan van der Vaart, Biophysical Journal 100 1049-1057 (2011)
"Dynamics of Nucleosome Invasion by DNA Binding Proteins," Tims H.S., Gurunathan K, Levitus M and Widom J. , J. Mol. Biol. 411 430-448 (2011)