Brent M. Znosko, Ph.D.
Professor; Associate Chair
Department of Chemistry
Courses Taught
CHEM 4610, 4620, 5620
Education
Allegheny College, B.S. in Chemistry, 1999
University of Rochester, M.S. in Chemistry, 2001
University of Rochester, Ph.D. in Chemistry, 2004
Research Interests
Biochemistry, Bioinformatics, Computational Chemistry, Thermodynamics and Structure of RNA
For more information, visit .
Labs and Facilities
Shannon 204/206
Publications and Media Placements
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:
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:
鈥�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:
鈥�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.
DOI:
44. Saon, Md. S., and Znosko, B. M. (2022) "Thermodynamic characterization of naturally
occurring RNA pentaloops," RNA 28, 832-841. DOI:
鈥�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:
鈥�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. DOI:
鈥�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.
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.
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.
38. Lisowiec-Wachnicka, J., Znosko, B. M., and Pasternak, A. (2019) "Contribution of 3鈥橳 and 3鈥橳T overhangs to the thermodynamic stability of model siRNA duplexes," Biophys. Chem. 246, 35-39.
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.
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.
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.
34. Jolley, E. A. and Znosko, B. M. (2017) 鈥淭he loss of a hydrogen bond: Thermodynamic contributions of a non-standard nucleotide,鈥� Nucleic Acids Res. 45, 1479-1487.
33. Richardson, K. E. and Znosko, B. M. (2016) 鈥淣earest-neighbor parameters for 7-deaza-adenosine路uridine base pairs in RNA duplexes,鈥� 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) 鈥淎nalysis of secondary structural elements in human microRNA hairpin precursors,鈥� BMC Bioinformatics 17, 112.
31. Jolley, E. A., Lewis, M., and Znosko, B. M. (2015) 鈥淎 computational model for predicting experimental RNA nearest-neighbor free energy rankings: Inosine-uridine pairs,鈥� Chem. Phys. Lett. 639, 157-160.
30. Tomcho, J. C., Tillman, M. R., and Znosko, B. M. (2015) 鈥淚mproved model for predicting the free energy contribution of dinucleotide bulges to RNA duplex stability,鈥� Biochemistry 54, 5290-5296.
29. Johnson, C. A., Hudson, G. A., Hardebeck, L. K. E., Jolley, E. A., Ren, Y., Lewis, M., and Znosko, B. M. (2015) 鈥淓ffect of intercalator substituent and nucleotide sequence on the stability of DNA- and RNA-naphthalimide complexes,鈥� Bioorg. Med. Chem. 23, 3586-3591.
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.
27. 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.
26. 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.
25. Chen, Z. and Znosko, B. M. (2013) Effect of sodium ions on RNA duplex stability, Biochemistry 52, 7477-7485.
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 鈥淐omment on 鈥淐omputational model for predicting experimental RNA and DNA nearest-neighbor free energy rankings,鈥欌�� J. Phys. Chem. B 116, 8333-8334.
22. Hausmann, N. Z. and Znosko, B. M. (2012) Thermodynamic characterization of RNA 2x3 nucleotide internal loops, Biochemistry 51, 5359-5368.
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.
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.
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.
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.
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.
16. Thulasi, P., Pandya, L. K., and Znosko, B. M. (2010) Thermodynamic characterization of RNA triloops, Biochemistry 49, 9058-9062.
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.
14. Sheehy, J. P., Davis, A. R., and Znosko, B. M. (2010) Thermodynamic characterization of naturally occurring RNA tetraloops, RNA 16, 417-429.
1. Christiansen, M. E. and Znosko, B. M. (2009) Thermodynamic characterization of tandem mismatches in naturally occurring RNA, Nucleic Acids Res. 37, 4696-4706.
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.
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.
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.
9. Davis, A. R. and Znosko, B. M. (2007) Thermodynamic characterization of single mismatches found in naturally occurring RNA,Biochemistry 46, 13425-13436.
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.
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.
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.
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.
4. Znosko, B. M., Barnes T. W., Krugh T. R., and Turner, D. H. NMR studies of DNA single strands and DNA:RNA hybrids with and without 1-propynylation at C5 of oligopyrimidines. (2003) J. Am. Chem. Soc. 125, 6090-6097.
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鈥�(rGGCAAGCCU)2, Biochemistry 41, 14978-14987.
2. Znosko, B. M., Burkard, M. E., Schroeder, S. J., Krugh, T. R., and Turner, D. H. (2002) Sheared Aanti脳础anti base pairs in a destabilizing 2x2 internal loop: The NMR structure of 5鈥�(rGGCAAGCCU)2, Biochemistry 41, 14969-14977.
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.
Honors and Awards
橘子视频School of Science and Engineering Undergraduate and Graduate Mentoring Award (2024)
橘子视频Arts and Sciences Award for Outstanding Service to Undergraduate Students (2008)
Professional Organizations and Associations
American Chemical Society