PUBLICATIONS
Work at Saint Louis University
49. Arteaga, S. J. and Znosko, B. M. (2026) "Structural analysis of uridine modifications in solved RNA structures," NAR Genom. Bioinform. 8, lqaf197.
DOI: doi.org/10.1093/nargab/lqaf197
48. 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
47. Sieg, J. P., Arteaga, S. J., Znosko, B. M., and Bevilacqua, P. C. (2023) "MeltR software provides facile determination of nucleic acid thermodynamics," Biophys. Rep. 3, 100101.
DOI: 10.1016/j.bpr.2023.100101
46. 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
45. Saon, Md. S., Kirkpatrick, C. C., and Znosko, B. M. (2023) "Identification and characterization of RNA pentaloop sequence families," NAR Genom. Bioinform. 5, lqac102.
44. Saon, Md. S., and Znosko, B. M. (2022) "Thermodynamic characterization of naturally occurring RNA pentaloops," RNA 28, 832-841.
43. 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
42. 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.
41. 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
40. Ferreira, I., Jolley, E. A., Znosko, B. M., and Weber, G. (2019) "Replacing salt correction factors with optimized RNA nearest neighbor enthalpy and entropy parameters," Chem. Phys. 521, 69-76.
DOI: 10.1016/j.chemphys.2019.01.016
39. Adams, M. S., and Znosko, B. M. (2019) "Thermodynamic characterization and nearest neighbor parameters for RNA duplexes under molecular crowding conditions," Nucleic Acids Res. 23, 3658-3666.
DOI: 10.1093/nar/gkz019
38. Lisowiec-Wachnicka, J., Znosko, B. M., and Pasternak, A. (2019) "Contribution of 3’T and 3’TT overhangs to the thermodynamic stability of model siRNA duplexes," Biophys. Chem. 246, 35-39.
DOI: 10.1016/j.bpc.2018.12.006
37. Wright, D. J., Force, C. R., and Znosko, B. M. (2018) "Stability of RNA duplexes containing inosine-cytosine pairs," Nucleic Acids Res. 46, 12099-12108.
DOI: 10.1093/nar/gky907
36. Jolley, E. A., Hardebeck, L. K. E., Ren, Y., Adams, M. S., Lewis, M., and Znosko, B. M. (2018) "The effects of varying the substituent and DNA sequence on the stability of 4-substituted DNA-naphthalimide complexes," Biophys. Chem. 239, 29-37.
DOI: 10.1016/j.bpc.2018.04.008
35. Berger, K. D., Kennedy, S. D., Schroeder, S. J., Znosko, B. M., Sun, H., Mathews, D. H., and Turner, D. H. (2018) "Surprising sequence effects on GU closure of symmetric 2x2 nucleotide RNA internal loops," Biochemistry 57, 2121-2131.
DOI: 10.1021/acs.biochem.7b01306
34. 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.
DOI: 10.1093/nar/gkw830
33. 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.
32. 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 Bioinform. 17, 112.
DOI: 10.1186/s12859-016-0960-6
31. 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.
DOI: 10.1016/j.cplett.2015.09.005
30. 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
29. Johnson, C. A., Hudson, G. A., Hardebeck, L. K. E., Jolley, E. A., Ren, Y., Lewis, M., and Znosko, B. M. (2015) "Effect of intercalator substituent and nucleotide sequence on the stability of DNA- and RNA-naphthalimide complexes," Bioorg. Med. Chem. 23, 3586-3591.
DOI: 10.1016/j.bmc.2015.04.030
28. 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
27. Chen, Z. and Znosko, B. M. (2013) "Effect of sodium ions on RNA duplex stability," Biochemistry 52, 7477-7485.
DOI: 10.1021/bi4008275
26. 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.
DOI: 10.1002/poc.3184
25. 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.
24. 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.
23. 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.
DOI: 10.1021/jp303191v
22. Hausmann, N. Z. and Znosko, B. M. (2012) "Thermodynamic characterization of RNA 2x3 nucleotide internal loops," Biochemistry 51, 5359-5368.
DOI: 10.1021/bi3001227
21. Vanegas, P. L., Horwitz, T. S., and Znosko, B. M. (2012) "Effects of non-nearest neighbors on the thermodynamic stability of RNA GNRA hairpin tetraloops," Biochemistry 51, 2192-2198.
DOI: 10.1021/bi300008j
20. 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
19. 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
18. Johnson, C. A., Bloomingdale, R. J., Ponnusamy, V. E., Tillinghast, C. A., Znosko, B. M., and Lewis, M. (2011) "Computational model for predicting experimental RNA and DNA nearest-neighbor free energy rankings," J. Phys. Chem. B 115, 9244-9251.
DOI: 10.1021/jp2012733
17. Davis, A. R., Kirkpatrick, C. C., and Znosko, B. M. (2011) "Structural characterization of naturally occurring RNA single mismatches," Nucleic Acids Res. 39, 1081-1094.
DOI: 10.1093/nar/gkq793
16. Thulasi, P., Pandya, L. K., and Znosko, B. M. (2010) "Thermodynamic characterization of RNA triloops,"
Biochemistry 49, 9058-9062.
DOI: 10.1021/bi101164s
15. Davis, A. R. and Znosko, B. M. (2010) "Positional and neighboring base pair effects on the thermodynamic stability of RNA single mismatches," Biochemistry 49, 8669-8679.
DOI: 10.1021/bi100146z
14. 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
13. Christiansen, M. E. and Znosko, B. M. (2009) "Thermodynamic characterization of tandem mismatches in naturally occurring RNA," Nucleic Acids Res. 37, 4696-4706.
DOI: 10.1093/nar/gkp465
12. 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.
DOI: 10.1021/bi800471z
11. 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.
DOI: 10.1021/bi7020876
10. Badhwar, J., Karri, S., Cass, C. K., Wunderlich, E. L., and Znosko, B. M. (2007) "Thermodynamic characterization of RNA duplexes containing naturally occurring 1x2 nucleotide internal loops," Biochemistry 46, 14715-14724.
DOI: 10.1021/bi701024w
9. Davis, A. R. and Znosko, B. M. (2007) "Thermodynamic characterization of single mismatches found in naturally occurring RNA," Biochemistry 46, 13425-13436.
DOI: 10.1021/bi701311c
8. 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.
DOI: 10.1021/bi0616910
Work prior to Saint Louis University
7. 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
6. 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
5. Chen, G., Znosko, B. M., Jiao, X., and Turner, D. H. (2004) "Factors affecting thermodynamic stabilities of RNA 3x3 internal loops," Biochemistry 43, 12865-12876.
DOI: 10.1021/bi049168d
4. 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
3. Znosko, B. M., Burkard, M. E., Krugh, T. R., and Turner, D. H. (2002) "Molecular recognition in purine-rich internal loops: Thermodynamic, structural, and dynamic consequences of purine for adenine substitutions in 5’(rGGCAAGCCU)2," Biochemistry 41, 14978-14987.
DOI: 10.1021/bi0203278
2. Znosko, B. M., Burkard, M. E., Schroeder, S. J., Krugh, T. R., and Turner, D. H. (2002) "Sheared Aanti×Aanti base pairs in a destabilizing 2x2 internal loop: The NMR structure of 5’(rGGCAAGCCU)2," Biochemistry 41, 14969-14977.
DOI: 10.1021/bi020326f
1. Znosko, B. M., Silvestri, S. B., Volkman, H., Boswell, B., and Serra, M. J. (2002) "Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges," Biochemistry 41, 10406-10417.
DOI: 10.1021/bi025781q