Nucleic Acid Thermodynamics: My lab studies the biophysical effects of cellular metabolites, potential drug compounds, and small molecule effectors on nucleic acid (DNA and RNA) structure and stability. Our principle experimental tool is temperature-dependent UV-Vis spectroscopy, although we utilize a variety of biochemical techniques, as needed.
RNA Group I Introns: My lab has developed novel RNA catalysts, based on autocatalytic RNA group I introns, which can recombine RNA in predetermined ways. Using this technology, our group has sequence-specifically repaired mutations in functional RNA transcripts. Questions that remain with this and other recently developed catalysts include how to develop them for effective cellular activity, how they fold and function, and how they can be exploited for the development of new biotechnologies. Methods used in these projects involve molecular biology (for example, PCR, cloning, site-directed mutagenesis, and gel electrophoresis).
Dotson, II, P. P., Hart, J., Noe, C., and Testa, S. M. (2012) “Ribozyme-Mediated Trans Insertion-Splicing into Target RNAs” Ribozymes: Methods and Protocols, Methods in Molecular Biology, vol 848.
Hart, J. L., Harris, Z. M., and Testa, S. M. (2010) “Analyzing and predicting the thermodynamic effects of the metabolite trehalose on nucleic acids”, Biopolymers, 93 (12) 1085-1092.
Dotson II, P. P., Sinha, J., and Testa, S. M. (2008) “A Pneumocystis carinii group I intron-derived ribozyme utilizes an endogenous guanosine as the first reaction step nucleophile in the trans excision-splicing reaction”, Biochemistry 47, 4780-4787.
Dotson II, P. P., Johnson, A. K., and Testa, S. M. (2008) "Tetrahymena thermophila and Candida albicans Group I intron-derived ribozymes can catalyze the trans-excision-splicing reaction", Nucleic Acids Research, 36, 5281-5289.
- Dotson II, P. P., Johnson, A. K., and Testa, S. M. (2008) "Tetrahymena thermophila and Candida albicans Group I intron-derived ribozymes can catalyze the trans-excision-splicing reaction", Archives of Biochemistry and Biophysics.
- Dotson II, P. P., Sinha, J., and Testa, S. M. (2008) “A Pneumocystis carinii group I intron-derived ribozyme utilizes an endogenous guanosine as the first reaction step nucleophile in the trans excision-splicing reaction”, FEBS Journal, 275 (12), 3110-3122.
- Dotson II, P. P. Testa, S. M. (2006) "Group I Intron-Derived Ribozyme Recombination Reactions" Recent Developments in Nucleic Acids Research, 2(2006): 307-324 ISBN: 81-7895-192-4.
- Johnson, A. K., Sinha, J., Testa, S. M. (2005) "Ribozyme-Catalyzed Insertion of Targeted Sequences into RNAs", RNA 11, 897-905.
- Alexander, R. C., Baum, D. A., Testa, S. M. (2005) "5' Transcript Replacement in vitro Catalyzed by a Group I Intron-Derived Ribozyme", Biochemistry 44, 1067-1077.
- Bell, M. A., Sinha, J., Johnson, A. K., Testa, S. M. (2004) "Enhancing the Second Step of the Trans Excision-Splicing Reaction of a Group I Ribozyme by Exploiting P9.0 and P10 for Intermolecular Recognition", Biochemistry 41, 15327-15333.
- Disney, M. D., Testa, S. M., Turner, D. H. (2000) "Targeting a Pneumocystis carinii Group I Intron with Methylphosphonate Oligonucleotides: Backbone Charge is Not Required for Binding or Reactivity",Biochemistry 39, 6991-7000.
- Testa, S. M., Turner, D. H., Kierzek, R. (1999) "Thermodynamics of RNA-RNA Duplexes with 2- or 4-Thiouridines: Implications for Antisense Design and Targeting a Group I Intron", Biochemistry 38, 16655-16662.
- Testa, S. M, Gryaznov, S. M., Turner, D. H. (1999) "In Vitro Suicide inhibition of self-splicing of a group I intron from Pneumocystis carinii by an N3'->P5' phosphoramidate hexanucleotide", Proc. Natl. Acad. Sci. U.S.A. 96, 2734-2739.
- Testa, S. M., Gryaznov, S. M., Turner, D. H. (1998) "Antisense Binding Enhanced by Tertiary Interactions: Binding of Phosphorothioate and N3'-> P5' Phosphoramidate Hexanucleotides to the Catalytic Core of a Group I Ribozyme from the Mammalian Pathogen Pneumocystis carinii", Biochemistry 37, 9379-9385.
- Testa, S. M. , Haidaris, C. G., Gigliotti, F., Turner, D. H. (1997) "A Pneumocystis carinii Group I Intron Ribozyme that Does Not Require 2' OH Groups on its 5' Exon Mimic for Binding to the Catalytic Core", Biochemistry 36, 15303-15314.
- Profenno, L., Kierzek, R., Testa, S. M., Turner, D. H. (1997) "Guanosine Binds to the Tetrahymena Ribozyme in More than One Step, and Its 2' OH and the Nonbridging pro-Sp Phosphoryl Oxygen at the Cleavage Site Are Required for Productive Docking", Biochemistry 36, 12477-12485.
- Testa, S. M, Gilham, P. T. (1993) "Analysis of Oligonucleotide Structure using Hyperchromism Measurements at Long Wavelengths", Nucleic Acids Res. 21, 3907-3908.