Assistant Professor Saint Louis University Department of Chemistry 3501 Laclede Ave. Saint Louis, MO 63103 Office Phone: (314) 977-8567 Dept. Fax:  (314) 977-2521   email:  znoskob@slu.edu

RESEARCH ZNOSKO PUBLICATIONS VIEW AN NMR STRUCTURE Znosko Curriculum Vitae GROUP MEMBER LIST RESEARCH POSITIONS BS & BA PROGRAMS IN BIOCHEMISTRY AT SLU JOURNAL LINKS LAB PROTOCOLS LAB PHOTO ALBUM

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, the lack of experimental parameters for non-Watson-Crick regions is a major limitation of these algorithms. 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 investigate structural features of common RNA motifs by one- and two-dimensional proton NMR. 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), and the use of NMR to identify structural properties of underrepresented RNA motifs in the PDB. A SLU summer research award, the SLU Beaumont Faculty Development Fund, Sigma Xi GIAR awards, and an NIH AREA grant have funded this project.

Thermodynamic, Energetic, and Structural Characterization of Short RNA Oligomers Containing Inosine. We are beginning to understand the thermodynamics, dynamics, and structures of various RNA secondary structure motifs containing the standard nucleotides. Understanding motifs containing non-standard nucleotides is also important, because they too play an important biological role. However, many non-standard nucleotides, such as inosine (I), have not yet been characterized. Inosine occurs naturally and is a result of the deamination of adenosine, which leads to a wide variety of functional consequences, including the creation of splice sites, the sequestering of RNA in the nucleus, and the regulation of gene expression in mammalian brain. Surprisingly, there is little published data available on the thermodynamics, dynamics, and structures of RNA motifs containing inosine. We were able to characterize the stability of RNA oligonucleotides containing I·U pairs. In order to further characterize I·U pairs and better understand the thermodynamic trends observed, computational methods and NMR are being used to investigate the energetics and structural properties of ribonucleotides containing I·U pairs. In addition, the thermodynamic, energetic, and structural studies are being extended to ribonucleotides containing I·C and I·A pairs. Research Corporation Cottrell College Science Awards and grants from the National Center for Supercomputing Applications have funded this project. Some of this work is in collaboration with Dr. Mike Lewis at SLU.

Investigating the Role of Substituent-Substituent Interactions in DNA/RNA Base Stacking and in DNA/RNA-Intercalator Stacking. While many therapeutic treatments of cancer have been developed, the number of cancer cases diagnosed and the number of deaths due to cancer have remained constant over the past ten years. Therefore, there is a growing interest and pressing need to develop improved therapeutic treatments of cancer. In order to design and develop novel chemotherapeutic agents, a better understanding of the physical properties, structural orientations, and thermodynamics of potential therapeutic agents is required. Thus, the broad, long-term objective of this research is to investigate the role of substituent-substituent interactions in DNA/RNA base stacking and in DNA/RNA-intercalator stacking. The specific aims of the proposed research are to: (1) to thermodynamically, structurally, and electrostatically characterize the effects of substituent-substituent interactions in DNA/RNA base stacking and (2) to synthesize intercalators and then thermodynamically, structurally, and electrostatically characterize intercalator binding to DNA/RNA duplexes and the role of subsitutent-substituent interactions. The research design and methods for achieving these goals include: the development of a set of rules for predicting the binding energy between substituted aromatics and DNA bases depending on the substitution pattern of the aromatics by using ab initio molecular orbital theory, the synthesis of DNA binding substrates with substituted aromatics, the thermodynamic analysis of DNA-substrate complexes using UV spectroscopy, and structural analysis using NMR. This project is a collaboration with Dr. Mike Lewis at SLU.

Five Recent Publications:

1.    Davis, A. R. and Znosko, B. M. (2008) Thermodynamic characterization of naturally occurring RNA single mismatches with G-U nearest neighbors, Biochemistry 47, 10178-10187. article pdf

2.    Christiansen, M. E. and Znosko, B. M. (2008) Thermodynamic characterization of the complete set of sequence symmetric tandem mismatches in RNA and an improved model for predicting the free energy contribution of sequence asymmetric tandem mismatches, Biochemistry 47, 4329-4336. article pdf

3.     Badhwar, J., Karri, S., Cass, C. K., Wunderlich, E. W., and Znosko, B. M. (2007) Thermodynamic characterization of RNA duplexes containing naturally occurring 1x2 nucleotide internal loops, Biochemistry 46, 14715-14724. article pdf

4.     Davis, A. R. and Znosko, B. M. (2007) Thermodynamic characterization of single mismatches found in naturally occurring RNA, Biochemistry 46, 13425-13436. article pdf

5.    Wright, D. J., Rice, J. L., Yanker, D. M., and Znosko, B. M. (2007) Nearest neighbor parameters for inosine-uridine pairs in RNA duplexes, Biochemistry 46, 4625-4634. article pdf

Last updated 15 May 2009