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
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.
Zhang, H., Fountain, M. A., Krugh, T. R.
"Structural Characterization of a Six Nucleotide Hairpin Loop Found in E. coli: r(UUAAGU),"
Biochemistry
2001,
40,
9879-9886.
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.
2001,
78,
691-694.
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.
2000,
122,
6841-6847.