Saint Louis University
Department of Chemistry
3501 Laclede Ave.
Saint Louis, MO 63103
Office Phone: (314) 977-8567
Understanding the Thermodynamics and Structure of RNA Secondary Structure Motifs. While many important RNA sequences have been determined, there is little definitive secondary and three-dimensional structure information about RNA. Several computer algorithms have been developed to predict RNA secondary structure from sequence; however, these programs have several limitations. NMR and X-ray crystallography are powerful tools to determine RNA three-dimensional structure; however, these techniques are time and labor intensive. Thus, there is a need for reliable, rapid methods to predict secondary and three-dimensional structures of RNA from sequence. Therefore, one broad, long-term objective of my laboratory is to improve RNA secondary and tertiary structure prediction from sequence. In order to achieve this long-term objective, it is essential to understand RNA thermodynamics and structure and how these properties are related. Improved nearest neighbor parameters derived from thermodynamic data can improve secondary structure prediction from sequence. In order to improve tertiary structure prediction, knowledge about the structural features of secondary structure motifs in previously solved three-dimensional structures and NMR data for previously unstudied motifs would be beneficial. Therefore, this project begins to investigate the thermodynamics and structures of common RNA secondary structure motifs. The specific objectives of this project are: (1) to investigate the major limitations of the current algorithms used to predict secondary structure from sequence, (2) to comprehensively identify, annotate and compare secondary structure motifs in three-dimensional structures, and (3) to better understand stability-structure relationships via compuational techniques. The methods for achieving these goals include: optical melting experiments, an in-depth search and analysis of RNA structures in the Protein Data Bank (PDB), the use of NMR to identify structural properties of underrepresented RNA motifs in the PDB, and calculations on a supercomputer to investigate the strength of hydrogen bonding and base stacking. A SLU Summer Research Award, the SLU Beaumont Faculty Development Fund, Sigma Xi GIAR awards, and an NIH AREA grant have funded this project.
Understanding DNA-Intercalator Complexes Using Substituted Naphthalimides as a Model System. Nucleic acid base stacking plays a major role in stabilizing nucleic acid duplexes and nucleic acid complexes; however, very little is understood about these stacking interactions and other binding properties. In order to better understand and begin to predict these properties, we are investigating DNA-naphthalimide complexes with a variety of substituted naphthalimides. The focus of this work is the synthesis of these intercalators followed by the thermodynamic and structural characterization of the DNA-intercalator complexes. The specific aims of the proposed research are to: (1) to synthesize various substituted naphthalimide analogs, (2) to use optical melting studies to investigate the thermodynamics of DNA-naphthalimide complexes, and (3) to use NMR, molecular modeling, and footprinting studies to investigate the structural features of various DNA-intercalator complexes. A President's Research Fund award from SLU has funded this project. This project is a collaboration with Dr. Mike Lewis at SLU.
Five Recent Publications:
1. Hardebeck, L. K. E., Johnson, C. A., Hudson, G. A., Ren, Y., Watt, M., Kirkpatrick, C. C., Znosko, B. M., and Lewis M. (2013) Predicting DNA-intercalator binding: The development of an arene-arene stacking parameter from SAPT analysis of benzene-substituted benzene complexes, J. Phys. Org. Chem. 26, 879-884.
2. Hudson, G. A., Bloomingdale, R. J., and Znosko, B. M. (2013) Thermodynamic contribution and nearest neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides, RNA 19, 1474-1482.
3. Chen, Z. and Znosko, B. M. (2013) Effect of sodium ions on RNA duplex stability, Biochemistry 52, 7477-7485.
4. Grohman, J. K., Gorelick, R. J., Lickwar, C. R., Lieb, J. D., Bower, B. D., Znosko, B. M., and Weeks, K. M. (2013) A guanosine-centric mechanism for RNA chaperone function, Science 340, 190-195.
5. Johnson, C. A., Bloomingdale, R. J., Ponnusamy, V. E., Tillinghast, C. A., Znosko, B. M., and Lewis, M. (2012) Reply to "Comment on 'Computational model for predicting experimental RNA and DNA nearest-neighbor free energy rankings,'"J. Phys. Chem. B 116, 8333-8334.
Last updated 9 May 2014