研究领域

Biochemistry/Physical Chemistry

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.

近期论文

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"ATP and Magnesium Promote Cotton Short-Form Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) Activase Hexamer Formation at Low Micromolar Concentrations". Agnieszka M. Kuriata, Manas Chakraborty,J. Nathan Henderson, Suratna Hazra, Andrew J. Serban, Tuong V. T. Pham, Marcia Levitus., Rebekka M. Wachter Biochemistry 2014. in press "Protein Oligomerization Equilibria and Kinetics Investigated by Fluorescence Correlation Spectroscopy: a Mathematical Treatment". Kanno, D.M., Levitus, M. J. Phys. Chem. B 2014. in press "A Designed Buried Salt Bridge Modulates Heterodimerization of a Membrane Peptide". Shinde, S., Binder, J. K., Goyal, B., Woodrum, B., De Munari, S., Levitus, M.and Ghirlanda, G. Biopolymers 2014. in press "Intrinsic stability and oligomerization dynamics of DNA processivity clamps". Binder, J. K., Douma, L.G., Ranjit, S., Kanno D.M., Chakraborty, M., Bloom, L.B., and Levitus M Nucl. Acids. Res. 2014. 42, 6476-6486. "Photophysical and Dynamical Properties of Doubly Linked Cy3-DNA Constructs". Stennett, E. M. S., Ning, M., van der Vaart, A, and Levitus M J. Phys. Chem. B 2014. 1, 152-163. "Manganese-Induced Triplet Blinking and Photobleaching of Single Molecule Cyanine Dyes". Ciuba, M.and Levitus M ChemPhysChem 2013. 14, 3495-3502. "Photophysical processes in single molecule organic fluorescent probes". Stennett, E.M.S., Ciuba, M.and Levitus M Chem. Soc. Rev. 2013. Advance Article. "Protein Oligomerization Monitored by Fluorescence Fluctuation Spectroscopy: Self-Assembly of Rubisco Activase". Chakraborty,M., Kuriata, A.M., Henderson, J.N., Salvucci, M.E., Wachter, R.M.and Levitus M Biophys. J. 2012. 103, 949-958. Featured as New and Notable "Real-time monitoring of RAG-catalyzed DNA cleavage unveils dynamic changes in coding end association with the coding end complex". Wang G., Dhar K., Swanson P.C., Levitus M, and Chang Y. Nucl. Acids Res. 2012. 40, 6082-6096 "Probing the interaction between fluorophores and DNA nucleotides by fluorescence correlation spectroscopy and fluorescence quenching". Ranjit S., Levitus M Photochem. Photobiol. 2012. 88,782-791 "Photobleaching and Blinking of TAMRA Induced by Mn2+". Stennett E.M.S., Kodis G, Levitus M ChemPhysChem 2012. 13,909-913 "Dynamics of Nucleosome Invasion by DNA Binding Proteins". Tims H.S., Gurunathan K, Levitus M and Widom J. J. Mol. Biol. 2011. 411,430-448 "Cy3-DNA Stacking Interactions Strongly Depend on the Identity of the Terminal Basepair". Spiriti J, Binder JK, Levitus M and van der Vaart A. Biophys. J. 2011. 100, 1049-1057. "Chemical Kinetics at the Single-Molecule Level". Levitus M J. Chem. Ed. 2011. 88, 162-166. "Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments". Levitus M and Ranjit S. Q. Rev. Biophys. 2010. 44, 123-151. "Relaxation Kinetics by Fluorescence Correlation Spectroscopy: Determination of Kinetic Parameters in the Presence of Fluorescent Impurities". Levitus M. J. Phys. Chem. Lett 2010. 1, 1346-1350. "FRET Fluctuation Spectroscopy of Diffusing Biopolymers: Contributions of Conformational Dynamics and Translational Diffusion". Gurunathan K, Levitus M. J. Phys. Chem. B 2010. 114, 980-986. "Single-Molecule Fluorescence Studies of Nucleosome Dynamics". Gurunathan K, Levitus M. Curr. Pharm. Bio. 2009. 10, 559-568. Hot Topic issue:Single-Molecule Workshop ASPEN 2009. "DNA Sequence-Dependent Enhancement of Cy3 Fluorescence". Harvey B.J., Perez C., Levitus M. Photochem. Photobiol. Sci. 2009. 8, 1105-1110. "Photophysics of Backbone Fluorescent DNA Modifications: Reducing Uncertainties in FRET". Ranjit S., Gurunathan K., Levitus M. J. Phys. Chem. B 2009. 113, 7861-7866. (featured in cover). "Nucleobase-Specific Enhancement of Cy3 Fluorescence". Harvey B., Levitus M. J. Fluoresc. 2009. 19, 443-448.