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DONALD M. CROTHERS

Understanding how the properties of nucleic acids and agents that bind to them relate to function.
A subject of considerable interest in our lab is DNA bending which can result from intrinsic properties of the DNA sequence or from protein binding. We study these related phenomena in a variety of ways including chemical and enzymatic synthesis of specific sequences and comparison of their subsequent effects on electrophoretic properties and protein binding, as well as by using NMR spectroscopy to study structure and dynamics. Students in the laboratory have pioneered in the use of gel electrophoretic methods to separate and characterize discrete intermediates both in the interaction of proteins with DNA and in the process of initiation of RNA transcription. Experiments now in progress should help characterize the relationship between DNA bending and its various functions and shed some light on the possible mechanisms of control of gene expression.

RNA conformation and RNA-protein interactions are issues of wide importance in molecular biology. The role of RNA conformation and protein binding in processes such as regulation of gene expression, RNA splicing, and viral replication can be better understood with knowledge of structural features, as well as from thermodynamic stability and kinetic information for molecular interactions. Physiochemical and molecular biological methods along with NMR spectroscopy are being used by students in the lab to characterize biologically interesting RNAs and RNA-protein complexes aiming to gain further insight into their functions.

Other investigations of the properties of nucleic acids include the characterization of DNA-drug interactions using electrophoretic and NMR spectroscopy techniques. In addition, a series of RNA-DNA hybrid duplex and triplex molecules consisting of a polypurine-polypyrimidine motif are being characterized by NMR in combination of other spectroscopy techniques to determine how their specific structural differences give rise to their observed differences in global conformation and thermodynamic properties. The problems studied in our lab are addressed by a combination of physiochemical, molecular biological, spectroscopic, and computational methods offering students a broadly based training to draw on in future research.

Selected References
Kinetic Consequences of Covalent Linkage of DNA Binding Polyamides, R. Baliga, E. E. Baird, D. M. Herman, C. Melander, P. B. Dervan and D. M. Crothers, Biochemistry 40, 3-8 (2001).

Nucleic Acids: Structures, Properties, and Functions, V. A. Bloomfield, D. M. Crothers,and I. T. Tinoco, Jr., University Science Books, Sausalito, CA (2000)

Global Structure and Mechanical Properties of a 10-bp Nucleosome Positioning Motif, M.Roychoudhury, A. Sitlani, J. Lapham and D. M. Crothers, Proc. Natl. Acad. Sci. U.S.A. 97, 13608-13613 (2000)

RNA Folding Pathways, D. M. Crothers, Curr. Protocols in Nucleic Acid Chem.11.1.1-11.1.5 (2000)

The Kinetic Basis for Sequence Discrimination by Distamycin A, R. Baliga and D. M.Crothers, J. Am. Chem. Soc. 122, 11751-11752 (2000)

Last updated 2001