In our research we seek to understand how the structure, dynamics, and protein binding properties of nucleic acids contribute to their function. Projects underway include work on both RNA and DNA-containing systems. In the area of protein-DNA complexes our emphasis is on how DNA structure is modulated upon protein binding and how the resulting bending and other structural distortions lead to activation of gene expression. Methods used in this effort include a combination of molecular biological and NMR techniques. Since DNA bending is a widespread phenomenon in genetic control systems, there is a wide array of systems available for study, including proteins from both prokaryotic and eukaryotic organisms.

A major focus of our work with RNA is understanding structural motifs that augment simple double helix formation. For example, two complementary RNA stem loops involved in the control of plasmid DNA replication form a remarkably stable bent helical structure resulting from interaction of their complementary loops. In addition, spliced leader RNAs from primitive parasitic organisms provide a model for studying the structure and structural dynamics of RNAs which can convert rapidly between alternate conformations. Methodologies used in our studies of RNA include NMR investigations of 13C and 15N labeled samples, along with chemical and molecular biological approaches, such as footprinting and differential chemical reactivity.

RNA-protein interaction motifs are not as well understood as is the case for DNA. Problems under active study by NMR methods include the interaction of the RNA binding domain of HIV Tat protein with its RNA target and the ability of synthetic compounds to interfere with this interaction.

The broad educational emphasis in our group is on developing an understanding of how physical, chemical and molecular biological methods can be combined to elucidate biological function.

Selected References

"DNA-Binding Domains of Fos and Jun Do Not Induce DNA Curvature: An Investigation with Solution and Gel Methods," A. Sitlani and D. M. Crothers, Proc. Natl. Acad. Sci. U.S.A., 95, 1404-1409 (1998).

"Measurement of the DNA Bend Angle Induced by the Catabolite Activator Protein Using Monte Carlo Simulation of Cyclization Kinetics," J. D. Kahn and D. M. Crothers, J. Mol. Biol., 276, 287-309 (1998).

"Simultaneous Determination of Helical Unwinding Angles and Intrinsic Association Constants in Ligand-DNA Complexes: The Interaction between DNA and Calichearubicin B," S. M. Zeman, K. M. Depew, S. J. Danishefsky and D. M. Crothers, Proc. Natl. Acad. Sci. U.S.A., 95, 4327-4332 (1998).

"Bent Helix Formation Between RNA Hairpins with Complementary Loops" J. P. Marino, R. S. Gregorian, G. Csankovszki and D. M. Crothers, Science, 268, 1448-1454 (1995).