Ph.D. 1969, Pennsylvania State University

Biophysical Chemistry/structural analysis of biomolecules/energy minimization and molecular dynamics calculations

Professor Krugh's group is interested in the three-dimensional structure of RNA oligomers, with an overall goal of relating structure to biological function. Two-dimensional NMR experiments are used to assign nucleic acid NMR resonances, and to measure intermolecular distances for energy minimization and molecular dynamics calculations used to determine three-dimensional structures. We are interested in the structure of RNA hairpins, which are single strands of RNA that fold to form a structure resembling a hairpin. In collaborative studies with Professor Douglas Turner and his group, we are investigating the structure of RNA duplexes containing various motifs. The overall goal of these structural studies is to provide a basis for correlation between sequence and structure.

Shankar, N., Xia, T., Kennedy, S. D., Krugh, T. R., Turner, D. H. "NMR Reveals Absence of Hydrogen Bonding in Adjacent UU and AG Mismatches in an Isolated Internal Loop From Ribosomal RNA," Biochemistry 2007, 46, 12665-12678. Tolbert, B. S., Kennedy, S. D., Schroeder, S. J., Krugh, T. R., Turner, D. H. "MR Structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: Probing the Structural Features That Shape the Thermodynamic Stability of GA Pairs," Biochemistry 2007, 46, 1511-1522. Chen, G., Kierzek, R., Yildirim, I., Krugh, T. R., Turner, D. H., Kennedy, S. D. "Stacking Effects on Local Structure in RNA: The Structure of Tandem GA Pairs Changes When Flanking GC Pairs are Replaced by isoG-isoC Pairs," Journal of Physical Chemistry B 2007, 24, 6718-6727. Shankar, N., Kennedy, S. D., Chen, G., Krugh, T. R., Turner, D. H. "The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50S ribosomal subunits," Biochemistry 2006, 45, 11776-11789. Shankar, N., Kennedy, S. D., Chen, G., Krugh, T. R., Turner, D. H. "The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50S ribosomal subunits," Biochemistry 2006, 45, 11776-11789. Chen, G., Kennedy, S. D., Qiao, J., Krugh, T. R., Turner, D. H. "An Alternating Sheared AA Pair and Elements of Stability for a Single Sheared Purine-Purine Pair Flanked by Sheared GA Pairs in RNA," Biochemistry 2006, 45, 6889-6903. Chen, G., Znosko, B. M., Kennedy, S. D., Krugh, T. R., Turner, D. H. "Solution Structure of an RNA Internal Loop with Three Consecutive Sheared GA Pairs," Biochemistry 2005, 44, 2845-2856. Znosko, B.M., Kennedy, S. D., Wille, P. C., J. D., Krugh, T. R., Turner, D. H. "Structural Features and Thermodynamics of the J4/5 Loop from the Candida albicans and Candida dubliniensis Group I Introns," Biochemistry 2004, 43, 15822-15837. Schroeder, S. J., Fountain, M. A., Kennedy, S. D., Lukavsky, P. J., Puglisi, J. D., Krugh, T. R., Turner, D. H. "Thermodynamic Stability and Structural Features of the J4/5 Loop in a Pneumocystis carinii Group I Intron," Biochemistry 2003, 42, 14184-14196.

Znosko, B. M., Barnes, T. W., III, Krugh, T. R., Turner, D. H. "NMR Studies of DNA Single Strands and DNA:RNA Hybrids With and Without 1-Propynylation at C5 of Oligopyrimidines," J. Amer. Chem. Soc. 2003, 125, 6090-6097.