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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) improve algorithms used to predict RNA secondary structure from sequence, (2) identify patterns of secondary strutcure motifs in three-dimensional structures, and (3) test the relationship between RNA stability and structure on a molecular level via computations and 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), 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.
Characterization of DNA-Intercalator Complexes Using Substituted Naphthalimides as a Model System. Nucleic acids are attractive target molecules for therapeutics as they direct replication, transcription, and translation. The ability to rationally design drugs that target nucleic acids, therefore, is important in developing pharmaceuticals to combat cancer, tumor growth, etc. Naphthalimides are DNA intercalating agents that are useful as therapeutic agents due to their conjugated pi system and ability for moiety attachment. Due to the success of the originally studied 1,8-naphthalimides, different analogues continue to be investigated for therapeutic activity. With the ongoing study of naphthalimide intercalators and their derivatives, there is still a need to understand these molecules and their ability to interact with DNA. While most studies focus on developing new intercalating compounds, few studies focus on the effects of small changes to a core intercalator structure. Also, most studies of naphthalimide derivatives use either calf thymus or salmon testes DNA as the target nucleic acid. By using such large DNA, it is difficult to understand DNA-intercalator interactions that are a result of the specific DNA sequence. Our team has recognized the need to understand intercalator interactions with short oligonucleotides. To evaluate the interactions important in DNA-intercalator complexes, we are performing systematic studies with mono- and di-substituted naphthalimides. The results of this work will provide a framework for more detailed studies of other known intercalators, as well as aid in the rational design of novel intercalators that may serve as therapeutic agents. The specific aims of the proposed research are to: (1) synthesize mono- and di-substituted naphthalimides, (2) characterize DNA-naphthalimide complexes using biochemical approaches (wavelength scans, NMR, CD, optical melting, footprinting, X-ray crystallography), and (3) characterize DNA-naphthalimide complexes using computational approaches (QM calculations and docking simulations). A President's Research Fund award from SLU has funded this project. This project is a collaboration with Drs. Chris Arnatt and Mike Lewis at SLU.
Five Recent Publications:
1. Jolley, E. A. and Znosko, B. M. (2017) The loss of a hydrogen bond: Thermodynamic contributions of a non-standard nucleotide, Nucleic Acids Res. 45, 1479-1487.
2. Richardson, K. E. and Znosko, B. M. (2016) Nearest-neighbor parameters for 7-deaza-adenosine-uridine base pairs in RNA duplexes, RNA 22, 934-942.
3. Liu, B., Childs-Disney, J. L., Znosko, B. M., Wang, D., Fallahi, M., Gallo, S. M., and Disney, M. D. (2016) Analysis of secondary structural elements in human microRNA hairpin precursors, BMC Bioinformatics 17, 112.
4. Jolley, E. A., Lewis, M. and Znosko, B. M. (2015) A computational model for predicting experimental RNA nearest-neighbor free energy rankings: Inosine-uridine pairs, Chem. Phys. Lett. 639, 157-160.
5. Tomcho, J. C., Tillman, M. R., and Znosko, B. M. (2015) Improved model for predicting the free energy contribution of dinucleotide bulges to RNA duplex stability, Biochemistry 54, 5290-5296.
The RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database allows users to search all three-dimensional RNA structures deposited in the Protein Data Bank for secondary structure motifs such as (a)symmetric loops, hairpin loops, and bulge loops. The database is online, freely accessible, and updated weekly. Users of the RNA CoSSMos database are encouraged to cite: Vanegas, P. L., Hudson, G. A., Davis, A. R., Kelly, S. C., Kirkpatrick, C. C., and Znosko, B. M. (2012) RNA CoSSMos: Characterization of Secondary Structure Motifs - A searchable database of secondary structure motifs in RNA three-dimensional structures, Nucleic Acids Res. 40, D439-D444.
Last updated 23 June 2017