Below is a sampling of research projects to which the Znosko Laboratory has contributed. Each section provides a brief overview along with representative recent publications.
Thermodynamic characterization of RNA secondary structure motifs
Research in the Znosko Laboratory has primarily focused on the thermodynamic characterization of RNA secondary structure motifs, an area that has historically received limited experimental attention. We have systematically measured thermodynamic parameters for a diverse set of naturally occurring RNA motifs, including internal loops, bulge loops, and hairpin loops. These experimental data have been used to develop improved predictive models for RNA motifs lacking direct thermodynamic measurements.
Our goal is to incorporate these experimentally derived parameters and models into RNA secondary structure prediction software, thereby enhancing the accuracy of structure predictions from sequence alone. This work has the potential to impact more than 25,000 users of RNAstructure and the broader community that relies on RNA secondary structure prediction to design and interpret nucleic acid experiments. A representative sampling of our publications in this area is provided below.
Saon, Md. S., and Znosko, B. M. (2022) "Thermodynamic characterization of naturally occurring RNA pentaloops," RNA 28, 832-841.
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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
DOI: 10.1021/acs.biochem.5b00474
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Murray, M. H., Hard, J. A., and Znosko, B. M. (2014) "Improved model to predict the free energy contribution of trinucleotide bulges to RNA duplex stability," Biochemistry 53, 3502-3508.
DOI: 10.1021/bi500204e
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Sheehy, J. P., Davis, A. R., and Znosko, B. M. (2010) "Thermodynamic characterization of naturally occurring RNA tetraloops," RNA 16, 417-429.
DOI: 10.1261/rna.1773110
RNA thermodynamics in buffers that better mimic biological conditions
Recognizing that the buffers traditionally used in RNA thermodynamic studies often poorly reflect biological and biochemical conditions, the Znosko Laboratory has investigated RNA thermodynamics in solution environments that more closely mimic those found in cells and experimental systems. By measuring thermodynamic parameters under biologically relevant conditions, this work aims to improve the accuracy and applicability of RNA secondary structure predictions. The resulting insights have the potential to benefit more than 25,000 users of RNAstructure and the broader community that relies on RNA structure prediction from sequence to guide nucleic acid experiments. A representative sampling of our publications in this area is provided below.
Arteaga, S. J., Dolenz, B. J., and Znosko, B. M. (2024) "Competitive influence of alkali metals in the ion atmosphere on nucleic acid duplex stability," ACS Omega 9, 1287-1297.
DOI: doi.org/10.1021/acsomega.3c07563
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Arteaga, S. J., Adams, M. S., Meyer, N. L., Richardson, K. E., Hoener, S., and Znosko, B. M. (2023) "Thermodynamic determination of RNA duplex stability in magnesium solutions," Biophys. J. 122, 565-576.
DOI: 10.1016/j.bpj.2022.12.025
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Adams, M. S. and Znosko, B. M. (2019) "Thermodynamic characterization and nearest neighbor parameters for RNA duplexes under molecular crowding conditions," Nucleic Acids Res. 47, 3658-3666.
DOI: 10.1093/nar/gkz019
Thermodynamic characterization of short RNA oligonucleotides containing common non-standard nucleotide
Because non-standard nucleotides are prevalent in natural RNAs, the Znosko Laboratory has conducted systematic thermodynamic studies of short RNA oligonucleotides containing commonly occurring non-standard nucleotides. Current software for predicting RNA stability and secondary structure from sequence cannot directly accommodate these modified bases, limiting the accuracy of predictions for many biologically relevant RNAs. Incorporation of our experimentally derived thermodynamic parameters will enable structure prediction for sequences containing non-standard nucleotides and expand the applicability of RNA secondary structure prediction tools. A representative sampling of our publications in this area is provided below.
Hopfinger, M. C., Kirkpatrick, C. C., and Znosko, B. M. (2020) "Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides," Nucleic Acids Res. 48, 8901-8913.
DOI: 10.1093/nar/gkaa654
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Wright, D. J., Force, C. R., and Znosko, B. M. (2018) "Stability of RNA duplexes containing inosine-cytoside pairs," Nucleic Acids Res. 46, 12099-12108.
DOI: 10.1093/nar/gky907
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Jolley, E. A. and Znosko, B. M. (2016) "The loss of a hydrogen bond: Thermodynamic contributions of a non-standard nucleotide," Nucleic Acids Res. 45, 1479-1487.
DOI: 10.1093/nar/gkw830
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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.
Structural characterization of short RNA oligonucleotides by NMR
Much of PI Znosko’s early research focused on the structural characterization of short RNA oligonucleotides using nuclear magnetic resonance (NMR) spectroscopy. These oligonucleotides contained biologically relevant secondary structure motifs or base modifications, enabling detailed analysis of their three-dimensional architectures. This work resulted in the deposition of 10 NMR-derived RNA structures in the Protein Data Bank, contributing valuable structural data to the RNA research community. A representative sampling of publications in this area is provided below.
Levengood, J. D., Rollins, C., Mishler, C. H., Johnson, C. A., Miner, G., Rajan, P., Znosko, B. M., and Tolbert, B. S. (2012) "Solution structure of the HIV-1 exon splicing silencer 3," J. Mol. Biol. 415, 680-698.
DOI: 10.1016/j.jmb.2011.11.034
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Chen, G., Znosko, B. M., Kennedy, S. D., Krugh, T. R., and Turner, D. H. (2005) "Solution structure of an RNA internal loop with three consecutive sheared GA pairs," Biochemistry 44, 2845-2856.
DOI: 10.1021/bi048079y
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Znosko, B. M., Kennedy, S. D., Wille, P. C., Krugh, T. R., and Turner, D. H. (2004) "Structural features and thermodynamics of the J4/5 loop from the Candida albicans and Candida dubliniensis group I introns," Biochemistry 43, 15822-15837.
DOI: 10.1021/bi049256y
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Znosko, B. M., Barnes T. W., Krugh T. R., and Turner, D. H. (2003) "NMR studies of DNA single strands and DNA:RNA hybrids with and without 1-propynylation at C5 of oligopyrimidines," J. Am. Chem. Soc. 125, 6090-6097.
DOI: 10.1021/ja021285d
Identifying, annotating, and comparing RNA secondary structure motifs in 3D structures
Recent projects in the Znosko Laboratory have focused on identifying, annotating, and comparing RNA secondary structure motifs within three-dimensional RNA structures. By defining sequence families that adopt similar structural features, this work enables the inference of structural characteristics for RNAs whose structures have not yet been determined by NMR or X-ray crystallography. The resulting insights provide a foundation for improving RNA tertiary structure prediction directly from sequence. A representative sampling of publications in this area is provided below.
Saon, Md. S., Kirkpatrick, C. C., and Znosko, B. M. (2023) "Identification and characterization of RNA pentaloop sequence families," NAR Genom. Bioinform. 5, lqac102.
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Richardson, K. E., Kirkpatrick, C. C., and Znosko, B. M. (2020) "RNA CoSSMos 2.0: An improved searchable database of secondary structure motifs in RNA three-dimensional structures," Database 2020, baz153.
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Richardson, K. E., Adams, M. S., Kirkpatrick, C. C., Gohara, D. W., and Znosko, B. M. (2019) "Identification and characterization of new RNA tetraloop sequence families," Biochemistry 58, 4809-4820.
DOI: 10.1021/acs.biochem.9b00535
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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.
DOI: 10.1093/nar/gkr943