Joseph Piccirilli's Publications

Original peer reviewed articles

 

 1.        Mattay, J., Runsink, J., Piccirilli, J. A., Jans, A. W. H. and Cornelisse, J.  Photochemical Cycloadditions of 1,3-Dioxoles to Anisole. J. Chem. Soc. Perkin Trans. I  15-20 (1987).

 

 2.        Piccirilli, J. A., Benner, S. A. and Rozzell, J. D. The Stereospecificity of Oxaloacetate Decarboxylase: A Stereochemical Imperative? J. Am. Chem. Soc. 109:8084-8085 (1987).

 

 3.        Benner, S. A., Allemann, R. K., Ellington, A. D., Ge, L., Glasfeld, A., Leanz, G. F., Krauch, T., MacPherson, L. J., Piccirilli, J. A. and Weinhold, E.  Natural Selection, Protein Engineering, and the Last Riboorganism:  Rational Model Building in Biochemistry. Cold Spring Harbor Symp. Quant. Biol., 52: 53-63, (1987).

 

4.         Benner, S. A., Glasfeld, A. and Piccirilli, J. A.  Stereospecificity in Enzymology:  Its Place in Evolution.  In Topics in Stereochemistry (E. Eliel  and S. Wilen, eds.; John Wiley  & Sons, NY) 19 pp. 127-207 (1989).

 

 5.        Piccirilli, J. A., Krauch, T., Moroney, S. E. and Benner, S. A.  Enzymatic Incorporation of a New Base Pair  into DNA and RNA Extends the Genetic Alphabet. Nature  343:33-37  (1990).

 

 6.        Piccirilli, J.A., Krauch, T., MacPherson, L.J., and Benner, S.A.  A Direct Route to 3-(_D-Ribofuranosyl)Pyridine Nucleosides.  Helv. Chim. Acta. 74:397-406 (1991).

 

 7.        Herschlag, D., Piccirilli, J.A. and Cech, T.R.  Ribozyme-Catalyzed and Nonenzymatic Reactions of Phosphate Diesters:  Rate Effects upon Substitution of Sulfur for a Nonbridging Phosphoryl Oxygen Atom. Biochemistry, 30:4844-4854 (1991).

 

 8.        Moroney, S.E. and Piccirilli, J.A.  Abortive Products as Initiating  Nucleotides During Transcription by T7 RNA Polymerase. Biochemistry, 30:10343-10349 (1991).

 

 9.        Piccirilli, J.A., Moroney,  S. E. and Benner, S.A.  A C-Nucleoside Base Pairs: A Formycin- Methylpseudouridine Transcription Complex in the Enzymic Polymerization of RNA by T7 RNA Polymerase. Biochemistry, 30:10350-10356 (1991).

 

10.       Piccirilli, J. A.,  McConnell,  Zaug, A. J. Noller,  H. F. and Cech T. R. Aminoacyl Esterase Activity of the Tetrahymena Ribozyme. Science,  256: 1420-1424 (1992).

 

11.       Cech, T. R., Herschlag, D., Piccirilli, J. A., and Pyle, A. M. RNA Catalysis by a Group I Ribozyme: Developing a Model for Transition State Stabilization. J. Biol. Chem., 267:17479-17482, (1992).

 

12.       Piccirilli, J. A., Vyle, J. S., Caruthers, M. H. and Cech, T. R. Metal Ion Catalysis by the Tetrahymena Ribozyme. Nature, 361:85-88 (1993).

 

13.       Sun, S., Tang,  X.-Q., Merchant, A., Anjaneyulu, P. S. R. and Piccirilli, J. A. Efficient Synthesis of 5-(Thioalkyl)uridines via Ring-Opening of a-Ureidomethylene Thiolactones. J. Organic Chem., 61:5708-5709 (1996).

 

14.           Hamm, M. and Piccirilli, J.A.  Incorporation of 2' -Mercaptocytidine into Oligonucleotides via Phosphoramidite Chemistry.  J. Organic Chem., 62:3415-3420 (1997).

 

15.           Sontheimer, E. J., Sun, S. and Piccirilli, J. A. Metal Ion Catalysis During Premessenger RNA Splicing.  Nature, 388:801-804 (1997).

 

16.       Sun, S., Yoshida, A. and Piccirilli, J. A.  Synthesis of 3' Thioribonucleosides and Their Incorporation into Oligoribonucleotides via Phosphoramidite Chemistry. RNA, 3:1352-1363 (1997).

 

17.       Sun, S., Piccirilli, J.A.  Synthesis of 3' -thioribouridine, 3¢ -thioribocytidine, and their phosphoramidites.  Nucleos. Nucleot., 16:1543-1545 (1997).

 

14.           Curley, J. F., Joyce, C. M. and Piccirilli, J. A. Functional Evidence that the 3'-5' Exonuclease of E. Coli DNA Polymerase Employs a Metal Ion in Leaving Group Stabilization. J. Amer. Chem. Soc., 51:12691-12692 (1997).

 

15.           Benner, S. A., Battersby, et al.  Redesigning nucleic acids.  Pure Appl. Chem. 70:263-266 (1998).

 

16.           Brautigam, C.A., Sun, S., Piccirilli, J.A. and Steitz, T.A. Structures of Normal Single-Stranded DNA and Deoxyribo-3'-S-phosphorothiolates Bound to the 3'-5' Exonucleolytic Active Site of DNA Polymerase I from Escherichia coli. Biochemistry, 38:696-704 (1999).

 

17.           Tang, X.-Q., Liao, X. and Piccirilli, J.A.  2'-C-Branched Ribonucleosides: Synthesis of the Phosphoramidite Derivatives of 2'-C-ß-Methylcytidine and Their Incorporation into Oligonucleotides.  J. Org. Chem., 64:747-754 (1999).

 

18.           Yoshida, A., Sun, S. and Piccirilli, J. A. A New Metal Ion Interaction in the Tetrahymena Ribozyme Reaction Revealed by Double Sulfur Substitution. Nature Structural Biology, 6:318-321 (1999).

 

19.           Piccirilli, J.A.  Do Enzymes Obey the Baldwin Rules?  A Mechanistic Imperative in Enzymatic Cyclization Reactions?  Chemistry and Biology,  6:R59-R64, (1999).

 

20.           Hamm, M.L. and Piccirilli, J.A. The Synthesis and Characterization of Oligonucleotides Containing 2'-S, 3'-O-Cyclic Phosphorothiolate Termini.  J. Organic Chem., 64:5700-5704, (1999).

 

21.           Sontheimer, E.J., Gordon, P.M. and Piccirilli, J.A.  Metal Ion Catalysis During Group II Intron Self Splicing: Parallels with the Spliceosome.  Genes and Development, 13:1729-1741 (1999).

 

22.           Shan, S., Yoshida, A., Sun, S., Piccirilli, J.A. and Herschlag, D.  Three metal Ions at the active site of the Tetrahymena group I ribozyme.  Proc. Natl. Acad. Sci. USA 96:12299-12304 (1999).

 

23.           Yoshida, A. Shan, S., Herschlag, D. and Piccirilli, J.A. The Role of the Cleavage Site 2'-Hydroxyl in the Tetrahymena Group I Ribozyme Reaction. Chem. Biol., 7:85-96 (2000).

 

24.           Warnecke, J.M., Sontheimer, E.J., Piccirilli, J.A. and Hartmann, R.K.  Active Site Constraints in the Hydrolysis Reaction Catalyzed by Bacterial RNase P: Analysis of Precursor tRNAs with a Single 3'-S-Phosporothiolate Internucleotide Linkage.  Nucleic Acids Res. 28:720-727 (2000).

 

25.           Gordon, P.M., Sontheimer, E.J. and Piccirilli, J.A.  Metal Ion Catalysis During the Exon-Ligation Step of Nuclear pre-mRNA splicing: Extending the Parallels Between the Spliceosome and Group II Introns.  RNA, 6:199-205. (2000).

 

26.           Hamm, M.L., Schwans, J. P. and Piccirilli, J.A. The Hammerhead Ribozyme Catalyzes the Deglycosylation of 2'-Mercaptocytidine.  J. Am. Chem. Soc., 122:4223-4224 (2000).

 

27.           Earnshaw, D.J., Hamm, M.L., Piccirilli, J.A., Karpeisky, A., Beigelman, L., Ross, B.S., Manoharan, M., and Gait, M.J.  Investigation of the proposed interdomain ribose zipper in hairpin ribozyme cleavage using 2¢-modified nucleosides.  Biochemistry 39:6410-6421 (2000).

 

28.           Gordon, P.M., Sontheimer, E.J., and Piccirilli, J.A. Kinetic characterization of the second step of group II intron splicing: Role of metal ions and the cleavage site 2'-OH in catalysis. Biochemistry, 39:12939-52 (2000).

 

29.           Hamm, M.L., Nikolic, D., van Breemen, R.B., and Piccirilli, J.A.  Unconventional origin of metal ion rescue in the hammerhead ribozyme reaction: Mn2+ -assisted redox conversion if 2¢-mercaptocytidine to cytidine.  J. Am. Chem. Soc. 122:12069-12078, (2000).

 

30.           Li, N.S., Tang, X.Q., and Piccirilli, J.A.  2¢-C-branched ribonucleosides. 2. Synthesis of 2¢-C-b-trifluoromethyl pyrimidine ribonucleosides.  Org. Lett. 3:1025-1028 (2001).

 

31.           Shan, S-O., Kravchuk, A.V., Piccirilli, J.A., and Herschlag, D.A.  Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. Biochemistry , 40:5161-5171 (2001).

 

32.           Dai, Q., Piccirilli, J.A., Zheng, C., and Li, S-J.  Crystal Structure of 3¢, 5¢-di-O-acetyl-2¢-C-a-acetyloxymethyl-2,2¢-anhydro-1-(b-D-arabino furanosyl) uracil, C₁₆H₁₈N₂O₉.  Z. Kristallogr. NCS, 216:343-34 (2001).

 

33.           Laio, X., Anjaneyulu, P.S., Curley, J.F., Hsu, M., Boehringer, M., Caruthers, M. H., and Piccirilli, J. A.  The Tetrahymena  Ribozyme Cleaves a 5'-Methylene Phosphonate Monoester ~102-Fold Faster than a Normal Phosphate Diester:  Implications for Enzyme Catalysis of Phosphoryl Transfer Reactions. Biochemistry, 40:10911-10926 (2001).

 

34.           Gordon, P.M. and Piccirilli, J.A.  Metal ion coordination by the AGC triad in domain 5 contributes to group II intron catalysis. Nat. Struct. Biol. 8:893-98 (2001).

 

35.           Kuo, L.Y. and Piccirilli, J.A.  Leaving Group Stabilization by Metal Ion Coordination and Hydrogen Bond Donation is an Evolutionarily Conserved Feature of Group I Introns.  Biochim Biophys Acta, 1522(3):158-66 (2001).

 

36.           Szewczak, A. A., Kosek, A.B., Piccirilli, J.A., and Strobel, S.A.  Identification of an active site ligand for a group I ribozyme catalytic metal ion.  Biochemistry  41(8):2516-25 (2002).

 

37.           Dai, Q., and Piccirilli, J. A.  Synthesis of 2'-C-b-Fluoromethyluridine.  Org. Lett. 5:807-810 (2003).

 

38.           Li, N-S. and Piccirilli, J. A.  Synthesis of the Phosphoramidite Derivative of 2¢ Deoxy-2¢-C-b-methylcytidine.  J. Org. Chem. 68:6799-6802 (2003)

 

43.           Schwans, J. P., Cortez, C. N., Olvera, J.M., and Piccirilli, J.A.  2'-Mercaptonucleotide Interference Reveals Regions of close Packing Within Folded RNA Molecules. J. Amer. Chem. Soc., 125:10012-10018 (2003)

 

44.           Gordon, P. M., Fong, R., Deb, S.K., Li, N-S, Schwans, JP., Ye, J-D, and Piccirilli, J.A.  New Strategies for Exploring RNA's 2'-OH expose the importance of solvent during group II intron catalysis. Chem. & Biol. 11:237-246 (2004).

 

45.           Schwans, J.P., Li, N-S., and Piccirilli, J.A.  A Packing Density Metric for Exploring the Interior of Folded RNA Molecules. Angew. Chem. Int. Ed. 43:3033-3037 (2004).

 

46.           Li, N-S. and Piccirilli, J. A.  Synthesis of the Phosphoramidite Derivatives of 2¢ Deoxy-2¢-C-a-methylcytidine and 2'-Deoxy-2'-C-a-hydroxymethylcytidine:  Analogues for Chemical Dissection of RNA's 2¢-Hydroxyl Group.  J. Org. Chem. 69:4751-4759 (2004).

 

47.           Dai, Q. and Piccirilli, J.A.  Efficient Synthesis of 2',3'-Dideoxy-2'-Amino-3'-Thiouridine. Org. Lett. 6:2169-2172 (2004).

 

48.           Hougland, J. L., Deb, S,K., Maric, D, and Piccirilli, J.A.  An atomic mutation cycle for exploring RNA's 2¢-hydroxyl group.  J. Am. Chem. Soc., 126:13578-13579 (2004).

 

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

 

50.           Hougland, J. L., Kravchuk, A.V., Herschlag, D., and Piccirilli, J.A.  Functional identification of catalytic metal ion binding sites within RNA.  PLoS Biol.,3:1536-1548 (2005).

 

51.           Ye, J-D., Liao, X., and Piccirilli, J. A.  Synthesis of 2'-C-difluoromethyl-ribonucleosides and their enzymatic incorporation into oligonucleotides.  J. Org. Chem.,70:7902-7910 (2005).

 

52.           Li, N-S. and Piccirilli, J.A.  Synthesis of 2'-Deoxy-2'-C-a-methylpurine nucleosides.  Synthesis, 17: 2865-2870 (2005).

 

53.           Dai, Q., Deb, S.K., Hougland, J.L. and Piccirilli, J.A.  Improved synthesis of 2'-amino-2'-deoxyguanosine and its phosphoramidite.  Biorg. & Med. Chem., 14:705-713 (2006).

 

54.           Korennykh, A.V., Piccirilli, J.A., and Correll, C.C.  The electrostatic character of the ribosome surface enables extraordinarily rapid target location by ribotoxins.  Nat. Struct. & Mol. Biol., 13:3436-3446 (2006).

 

55.           Li, N-S. and Piccirilli, J.A.  Efficient Synthesis of 2'-C-b-methylguanosine. J. Org. Chem. 71:4018-4020 (2006).

 

56.           Saikia, M., Dai, Q., Decatur, W.A., Fournier, M.J., Piccirilli, J.A., and Pan, T.  A systematic, ligation-based approach to study RNA modifications.  RNA 12:1-9 (2006).

 

57.           Li, N-S. and Piccirilli, J.A.  Synthesis of 2´-C-a-(Hydroxyalkyl) and 2´-C-a-Alkylcytidine Phosphoramidites: Analogues for Probing Solvent Interactions with RNA. J. Org. Chem., 72:1198-1210 (2007).

 

Ye, J-D., Li, N-S., Dai, Q., and Piccirilli, J.A.  The Mechanism of RNA Strand Scission: an experimental measure of b_nuc. Angew. Chem. Int. Ed., in press (2007).