Research Overview

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.

Research Interests

• Biophysical chemistry
• structural analysis of biomolecules, energy minimization and molecular dynamics calculations

Selected Publications

• 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.