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Thomas R. Krugh
Structure Determination of Nucleic Acids by NMR
Professor of Chemistry
Ph.D. 1969, Pennsylvania State University

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. The sequence and structure of an RNA hairpin containing a loop of six bases is shown in Figure 1. The G4 and A9 bases are part of the loop, and form hydrogen bonds to one another. The remaining bases in the loop do not form base-to-base hydrogen bonds. 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.

Relevant Publications
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  20064511776-11789.
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  2006456889-6903.
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  2005442845-2856.
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  20044315822-15837.
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  20034214184-14196.
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.  20031256090-6097.
Zhang, H., Fountain, M. A., Krugh, T. R.  "Structural Characterization of a Six Nucleotide Hairpin Loop Found in E. coli: r(UUAAGU),"  Biochemistry  2001409879-9886.
Werner, T.C., Lichter, R. L., Krugh, T. R.  "The National Conferences on Undergraduate Research (NCUR): Conference History and the Role of Chemistry,"  J. Chem. Educ.  200178691-694.
Guckian, K. M., Krugh, T. R., Kool, E. T.  "Solution Structure of a Nonpolar, Non-Hydrogen-Bonded Base Pair Surrogate in DNA,"  J. Am. Chem. Soc.  20001226841-6847.

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