Joseph A Piccirilli

Our group is broadly interested in the chemistry and biochemistry of nucleic acids with particular emphasis on RNA and RNA catalysis. The laboratory integrates areas of organic chemistry, physical chemistry, enzymology and molecular biology to gain a fundamental understanding of nucleic acid structure and mechanisms of RNA catalysis. Using the principles and techniques of organic chemistry and molecular biology, we manipulate the structure of RNA molecules at precise locations in ways that are designed to answer very specific questions about biological function.

We employ these approaches toward gaining a fundamental understanding of the role that divalent metal ions play in phosphoryl transfer reactins that occur during RNA splicing, a fundamental step in genetic expression. One experimental system that we are using to address these issues is the self-splicing intervening sequence RNA of the ciliated protozoan Tetrahymena. Shortened forms of this RNA can act as enzymes, catalyzing the sequence specific cleavage of RNA and DNA substrates with multiple turnover. We have used sulfur substitution of the oxygen substituents on the phosphoryl group undergoing transfer to reveal the transition state interactions between the ribozyme and the scissile phosphate.

Another area of interest is the development of new methods and model systems for studying RNA molecules. For example, we have recently designed hydrogen atom is replaced by CH3, CH2F, CHF2, or CF3 . These analogues provide a systematic way to perturb the acidity of the 2'-OH group, thereby allowing us to probe the all important role of this functional group in RNA mediated biological processes.

Our group is broadly interested in the chemistry and biochemistry of nucleic acids with particular emphasis on RNA and RNA catalysis. The laboratory integrates areas of organic chemistry, physical chemistry, enzymology and molecular biology to gain a fundamental understanding of nucleic acid structure and mechanisms of RNA catalysis. Using the principles and techniques of organic chemistry and molecular biology, we manipulate the structure of RNA molecules at precise locations in ways that are designed to answer very specific questions about biological function.

We employ these approaches toward gaining a fundamental understanding of the role that divalent metal ions play in phosphoryl transfer reactins that occur during RNA splicing, a fundamental step in genetic expression. One experimental system that we are using to address these issues is the self-splicing intervening sequence RNA of the ciliated protozoan Tetrahymena. Shortened forms of this RNA can act as enzymes, catalyzing the sequence specific cleavage of RNA and DNA substrates with multiple turnover. We have used sulfur substitution of the oxygen substituents on the phosphoryl group undergoing transfer to reveal the transition state interactions between the ribozyme and the scissile phosphate.

Another area of interest is the development of new methods and model...

Ye, J. D., Tereshko, V., Frederiksen, J., Koide, A., Fellouse, F., Sidhu, S., Koide, S., Kossiakoff, T., and Piccirilli Joseph, A. (2008) Synthetic antibodies for specific recognition and crystallization of structured RNA. Proc Natl Acad Sci U S A 105, 82-87. 

Korennykh, A. V., Plantinga, M. J., Correll, C. C., and Piccirilli, J. A. (2007) Linkage between Substrate Recognition and Catalysis during Cleavage of Sarcin/Ricin Loop RNA by Restrictocin. Biochemistry 46, 12744-12756 

Dai, Q., Fong, R., Saikia, M., Stephenson, D., Yu, Y. T., Pan, T., and Piccirilli, J. A. (2007) Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine. Nucleic Acids Res 35, 6322-6329 

Ye, J. D., Li, N. S., Dai, Q., and Piccirilli, J. A. (2007) The mechanism of RNA strand scission: an experimental measure of the Bronsted coefficient, beta nuc. Angew Chem Int Ed Engl 46, 3714-7. 

Gordon, P. M., Fong, R., and Piccirilli, J. A. (2007) A Second Divalent Metal Ion in the Group II Intron Reaction Center. Chem Biol 14, 607-612. 

Korennykh, A. V., Piccirilli, J. A., and Correll, C. C. (2006) The electrostatic character of the ribosomal surface enables extraordinarily rapid target location by ribotoxins. Nat Struct Biol 13, 436-443 

Das, S. R., and Piccirilli, J. A. (2005) General acid catalysis by the hepatitis delta virus ribozyme. Nat Chem Biol 1, 45-52. 

Hougland, J. L., Kravchuk, A. V., Herschlag, D., and Piccirilli, J. A. (2005) The ol'switcheroo shows how an RNA enzyme splices itself. PLoS Biology 3, 1512. 

Ye, J. D., Tereshko, V., Frederiksen, J., Koide, A., Fellouse, F., Sidhu, S., Koide, S., Kossiakoff, T., and Piccirilli Joseph, A. (2008) Synthetic antibodies for specific recognition and crystallization of structured RNA. Proc Natl Acad Sci U S A 105, 82-87. 

Korennykh, A. V., Plantinga, M. J., Correll, C. C., and Piccirilli, J. A. (2007) Linkage between Substrate Recognition and Catalysis during Cleavage of Sarcin/Ricin Loop RNA by Restrictocin. Biochemistry 46, 12744-12756 

Dai, Q., Fong, R., Saikia, M., Stephenson, D., Yu, Y. T., Pan, T., and Piccirilli, J. A. (2007) Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine. Nucleic Acids Res 35, 6322-6329 

Ye, J. D., Li, N. S., Dai, Q., and Piccirilli, J. A. (2007) The mechanism of RNA strand scission: an experimental measure of the Bronsted coefficient, beta nuc. Angew Chem Int Ed Engl 46, 3714-7. 

Gordon, P. M., Fong, R., and Piccirilli, J. A. (2007) A Second Divalent Metal Ion in the Group II Intron Reaction Center. Chem Biol 14, 607-612.