Updated: October, 2009
2009
Lu J., Li N-S., Koo S.C., Piccirilli J.A. Synthesis of Pyridine, Pyrimidine and Pyridinone C-Nucleoside Phosphoramidites for Probing Cytosine Function in RNA. J Org Chem. Epub ahead of print (2009).
Forconi M., Sengupta R.N., Liu M.C., Sartorelli A.C., Piccirilli J.A., Herschlag D. Structure and function converge to identify a hydrogen bond in a group I ribozyme active site. Angew Chem Int Ed Engl. 48:7171-5 (2009).
Frederiksen J.K., Piccirilli JA. Identification of catalytic metal ion ligands in ribozymes. Methods, 49:148-66 (2009).
Dai, Q., Saikia, M., Li, N-S., Pan, T., and Piccirilli, J.A. Efficient chemical synthesis of AppDNA by adenylation of immobilized DNA-5-monophosphate. Org. Lett., 11:1067-1070 (2009).
Li, N-S., Lu, J., and Piccirilli, J.A.
Synthesis of 2-C--methyl-2deoxyguanosine. J. Org. Chem., 74:2227-2230
(2009).
2008
Plantinga, M.J., Korennykh, A.V., Piccirilli,
J.A., and Correll, C.C. Electrostatic interactions guide the active
site face of a structure-specific ribonuclease to its RNA substrate.
Biochemistry, 47:8912-18 (2008).
Forconi, M., Lee, J., Lee, J., Piccirilli,
J.A., and Herschlag, D. Functional identification of ligands for a
catalytic metal ion in Group I introns. Biochemistry, 47:6883-94
(2008).
Hougland, J.L., Sengupta, R.N., Qing, D.,
Deb, S.K., and Piccirilli, J.A. The 2-hydroxyl group of the guanosine
nucleophile donates a functionally important hydrogen bond in the
Tetrahymena ribozyme reaction. Biochemistry, 47:7684-94 (2008).
Lu, J., Li, N-S., Sengupta, R., and
Piccirilli, J.A. Synthesis and biochemical application of
2'-O-methyl-3'-thioguanosine as a probe to explore group I intron
catalysis Bioorganic & Medicinal Chemistry, 16:5754-60 (2008).
Das, R., Kudaravalli, M., Jonikas, M.,
Laederach, A., Fong, R., Schwans, J. P., Baker, D., Piccirilli, J. A.,
Altman, R. B., and Herschlag, D. (2008) Structural inference of native
and partially folded RNA by high-throughput contact mapping. Proc Natl
Acad Sci U S A 105:4144-9 (2008).
Dai, Q., Frederiksen, J. K., Anderson, V. E.,
Harris, M. E., and Piccirilli, J. A. Efficient synthesis of
[2'-18O]uridine and its incorporation into oligonucleotides: a new tool
for mechanistic study of nucleotidyl transfer reactions by isotope
effect analysis. J Org Chem 73:309-11 (2008).
Ye, J-D., Tereshko, V., Frederiksen, J.K.,
Koide, A., Fellouse, F.A., Sidhu, S.S., Koide, S., Kossiakoff, A.A.,
and Piccirilli, J.A. Synthetic antibodies for specific recognition and
crystallization of structured RNA. Proc Natl Acad Sci U S A 105:82-87
(2008).
2007
Korennykh, A. V., Plantinga, M. J., Correll,
C. C., and Piccirilli, J. A. Linkage between Substrate Recognition and
Catalysis during Cleavage of Sarcin/Ricin Loop RNA by Restrictocin.
Biochemistry, 46: 12744-12756 (2007).
Dai, Q.,
Fong, R., Saikia, M., Stephenson, D., Yu, Y. T., Pan, T., and
Piccirilli, J. A. Identification of recognition residues for
ligation-based detection and quantitation of pseudouridine and
N6-methyladenosine. Nucleic Acids Res., 35:6322-6329 (2007).
Ye, J. D.,
Li, N. S., Dai, Q., and Piccirilli, J. A. The mechanism of RNA strand
scission: an experimental measure of the Bronsted coefficient, beta
nuc. Angew Chem Int Ed Engl 46:3714-7 (2007).
Korennykh, A. V., Correll, C.
C., and Piccirilli, J. A. (2007) Evidence for the importance of
electrostatics in the function of two distinct families of ribosome
inactivating toxins. RNA 13:1391-1396 (2007).
Forconi, M., Piccirilli, J. A., and Herschlag, D. Modulation of
individual steps in group I intron catalysis by a peripheral metal ion.
RNA 13:1656-1667 (2007).
Li, N.-S.,
and Piccirilli, J. A. Synthesis of 2'-C-alpha-(Hydroxyalkyl) and
2'-C-alpha-Alkylcytidine Phosphoramidites: Analogues for Probing
Solvent Interactions with RNA. J Org Chem 72:1198-1210 .
Gordon, P. M., Fong, R., and
Piccirilli, J. A. A Second Divalent Metal Ion in the Group II Intron
Reaction Center. Chem Biol 14:607-612 (2007).
Li, N.-S., Lu, J., and Piccirilli, J. A. Efficient synthesis of methyl
3,5-di-O-benzyl-alpha-D-ribofuranoside and application to the synthesis
of 2'-C-beta-alkoxymethyluridines. Org. Lett. 9:3009-3012. Org Lett
9:3009-3012 (2007).
Dai, Q., Lea, C. R., Lu, J., and Piccirilli, J. A. Syntheses of
(2')3'-15N-Amino-(2')3'-deoxyguanosine and Determination of Their pKa
Values by 15N NMR Spectroscopy. Org Lett 9:3057-3060 (2007).
Ye, J.-D., Barth, C. D., Anjaneyulu,
P. S. R., Tuschl, T., and Piccirilli, J. A. Reactions of phosphate and
phosphorothiolate diesters with nucleophiles: comparison of transition
state structures. Org & Bio Chemistry 5:2491-2497 (2007).
Li, N-S. and Piccirilli, J.A. Synthesis of
2´-C--(Hydroxyalkyl) and 2´-C--Alkylcytidine Phosphoramidites:
Analogues for Probing Solvent Interactions with RNA. J. Org. Chem.,
72:1198-1210 (2007).
2006
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).
Li, N-S. and Piccirilli, J.A. Efficient Synthesis of 2'-C--methylguanosine. J. Org. Chem. 71:4018-4020 (2006).
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., 13:3436-446
(2006).
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).
2005
Das, S. R., and Piccirilli, J.A. General acid
catalysis by the hepatitis delta virus ribozyme. Nat. Chem. Biol.,
1:45-52 (2005)
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).
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).
Li, N-S. and Piccirilli, J.A. Synthesis of 2'-Deoxy-2'-C--methylpurine nucleosides. Synthesis, 17: 2865-2870 (2005).
2004
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).
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).
Li, N-S. and Piccirilli, J. A.
Synthesis of the Phosphoramidite Derivatives of 2
Deoxy-2-C--methylcytidine and 2'-Deoxy-2'-C--hydroxymethylcytidine:
Analogues for Chemical Dissection of RNA's 2-Hydroxyl Group. J. Org.
Chem. 69:4751-4759 (2004).
Dai, Q. and Piccirilli, J.A.
Efficient Synthesis of 2',3'-Dideoxy-2'-Amino-3'-Thiouridine. Org.
Lett. 6:2169-2172 (2004).
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).
2003
Dai, Q., and Piccirilli, J. A. Synthesis of 2'-C--Fluoromethyluridine. Org. Lett. 5:807-810 (2003).
Li, N-S. and Piccirilli, J. A. Synthesis of the Phosphoramidite
Derivative of 2 Deoxy-2-C--methylcytidine. J. Org. Chem. 68:6799-6802
(2003).
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).
2002
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 41:2516-25 (2002).
2001
Li, N.S., Tang, X.Q., and Piccirilli,
J.A. 2-C-branched ribonucleosides. 2. Synthesis of
2-C--trifluoromethyl pyrimidine ribonucleosides. Org. Lett.
3:1025-1028 (2001).
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).
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).
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).
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).
2000
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).
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).
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)
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).
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).
1999
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).
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).
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).
Piccirilli, J.A. Do Enzymes Obey the Baldwin Rules? A Mechanistic
Imperative in Enzymatic Cyclization Reactions? Chemistry and Biology,
6:R59-R64, (1999).
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).
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).
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).
1997
Hamm, M. and Piccirilli, J.A.
Incorporation of 2' -Mercaptocytidine into Oligonucleotides via
Phosphoramidite Chemistry. J. Organic Chem., 62:3415-3420 (1997).
Sontheimer, E. J., Sun, S. and Piccirilli, J. A. Metal Ion Catalysis
During Premessenger RNA Splicing. Nature, 388:801-804 (1997).
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).
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).
1996
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 alpha-Ureidomethylene
Thiolactones. J. Organic Chem., 61:5708-5709 (1996).
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