Znosko Publications

Refereed

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.  

13.     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. (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.

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.

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.

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.