Joseph A. Piccirilli - Publications

Affiliations: 
Chemistry University of Chicago, Chicago, IL 
Area:
chemistry and biochemistryof nucleic acids
Website:
http://chemistry.uchicago.edu/faculty/faculty/person/member/joseph-a-piccirilli.html

156 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Li NS, Liang W, Piccirilli JA, Tang WJ. Reinvestigating the synthesis and efficacy of small benzimidazole derivatives as presequence protease enhancers. European Journal of Medicinal Chemistry. 184: 111746. PMID 31610373 DOI: 10.1016/j.ejmech.2019.111746  0.76
2019 Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AM, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA. A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nature Communications. 10: 3629. PMID 31399592 DOI: 10.1038/s41467-019-11585-z  1
2019 Bevilacqua PC, Harris ME, Piccirilli JA, Gaines C, Ganguly A, Kostenbader K, Ekesan Ş, York DM. An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes. Acs Chemical Biology. PMID 31095369 DOI: 10.1021/acschembio.9b00202  0.36
2019 Wilson TJ, Liu Y, Li NS, Dai Q, Piccirilli JA, Lilley DMJ. Comparison of the structures and mechanisms of the pistol and hammerhead ribozymes. Journal of the American Chemical Society. PMID 31017785 DOI: 10.1021/jacs.9b02141  0.76
2019 Hoshika S, Leal NA, Kim MJ, Kim MS, Karalkar NB, Kim HJ, Bates AM, Watkins NE, SantaLucia HA, Meyer AJ, DasGupta S, Piccirilli JA, Ellington AD, SantaLucia J, Georgiadis MM, et al. Hachimoji DNA and RNA: A genetic system with eight building blocks. Science (New York, N.Y.). 363: 884-887. PMID 30792304 DOI: 10.1126/science.aat0971  0.84
2018 Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA. Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif. Nature Communications. 9: 4542. PMID 30382099 DOI: 10.1038/s41467-018-06942-3  0.36
2018 Lu J, Koo SC, Weissman B, Harris ME, Li NS, Piccirilli JA. Evidence that nucleophile deprotonation exceeds bond formation in the HDV ribozyme transition state. Biochemistry. PMID 29733591 DOI: 10.1021/acs.biochem.8b00031  0.76
2018 Koirala D, Shelke SA, Dupont M, Ruiz S, DasGupta S, Bailey LJ, Benner SA, Piccirilli JA. Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography. Nucleic Acids Research. PMID 29309709 DOI: 10.1093/nar/gkx1292  0.84
2017 Li NS, Lu J, Piccirilli JA. Synthesis of 5´-Thio-3´-O-Ribonucleoside Phosphoramidites. The Journal of Organic Chemistry. PMID 29049877 DOI: 10.1021/acs.joc.7b01484  0.76
2017 Harris ME, York DM, Piccirilli JA, Anderson VE. Kinetic Isotope Effect Analysis of RNA 2'-O-Transphosphorylation. Methods in Enzymology. 596: 433-457. PMID 28911780 DOI: 10.1016/bs.mie.2017.07.017  0.36
2017 DasGupta S, Suslov NB, Piccirilli JA. Structural basis for substrate helix remodeling and cleavage loop activation in the Varkud satellite ribozyme. Journal of the American Chemical Society. PMID 28625058 DOI: 10.1021/jacs.7b03655  0.56
2017 Sundaram KM, Zhang Y, Mitra AK, Kouadio JK, Gwin K, Roman BR, Kossiakoff AA, Lengyel E, Piccirilli J. Prolactin receptor-mediated internalization of imaging agents detects epithelial ovarian cancer with enhanced sensitivity and specificity. Cancer Research. PMID 28202518 DOI: 10.1158/0008-5472.CAN-16-1454  0.32
2017 Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki J, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Feng D, ... ... Piccirilli JA, et al. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. Rna (New York, N.Y.). PMID 28138060 DOI: 10.1261/rna.060368.116  0.76
2016 Biondi E, Lane JD, Das D, Dasgupta S, Piccirilli JA, Hoshika S, Bradley KM, Krantz BA, Benner SA. Laboratory evolution of artificially expanded DNA gives redesignable aptamers that target the toxic form of anthrax protective antigen. Nucleic Acids Research. PMID 27701076 DOI: 10.1093/nar/gkw890  0.84
2016 Li NS, Gossai N, Naumann JA, Gordon PM, Piccirilli JA. Efficient Synthetic Approach to Linear Dasatinib-DNA Conjugates by Click Chemistry. Bioconjugate Chemistry. PMID 27690393 DOI: 10.1021/acs.bioconjchem.6b00557  0.76
2016 Shao Y, Huang H, Qin D, Li NS, Koide A, Staley JP, Koide S, Kossiakoff AA, Piccirilli JA. Specific Recognition of a Single-stranded RNA Sequence by a Synthetic Antibody Fragment. Journal of Molecular Biology. PMID 27593161 DOI: 10.1016/j.jmb.2016.08.029  1
2016 Piccirilli JA, Staley JP. Reverse transcriptases lend a hand in splicing catalysis. Nature Structural & Molecular Biology. 23: 507-509. PMID 27273636 DOI: 10.1038/nsmb.3242  0.52
2016 Gossai NP, Naumann JA, Li NS, Zamora EA, Gordon DJ, Piccirilli JA, Gordon PM. Drug conjugated nanoparticles activated by cancer cell specific mRNA. Oncotarget. PMID 27203672 DOI: 10.18632/oncotarget.9430  1
2016 Zhang S, Gu H, Chen H, Strong E, Ollie EW, Kellerman D, Liang D, Miyagi M, Anderson VE, Piccirilli JA, York DM, Harris ME. Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn(2.) Chemical Communications (Cambridge, England). PMID 26859380 DOI: 10.1039/c5cc10212j  1
2016 Roy S, Ly D, Castro CD, Li NS, Hawk AJ, Altman JD, Meredith SC, Piccirilli JA, Moody DB, Adams EJ. Molecular Analysis of Lipid-Reactive Vδ1 γδ T Cells Identified by CD1c Tetramers. Journal of Immunology (Baltimore, Md. : 1950). PMID 26755823 DOI: 10.4049/jimmunol.1502202  1
2015 Sengupta RN, van Schie SN, Giambaşu G, Dai Q, Yesselman JD, York D, Piccirilli JA, Herschlag D. An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions. Rna (New York, N.Y.). PMID 26567314 DOI: 10.1261/rna.053710.115  1
2015 Suslov NB, DasGupta S, Huang H, Fuller JR, Lilley DM, Rice PA, Piccirilli JA. Crystal structure of the Varkud satellite ribozyme. Nature Chemical Biology. 11: 840-6. PMID 26414446 DOI: 10.1038/nchembio.1929  1
2015 Harris ME, Piccirilli JA, York DM. Enzyme transition states from theory and experiment. Biochimica Et Biophysica Acta. 1854: 1727-8. PMID 26302659 DOI: 10.1016/j.bbapap.2015.08.006  0.36
2015 Hernandez AR, Shao Y, Hoshika S, Yang Z, Shelke SA, Herrou J, Kim HJ, Kim MJ, Piccirilli JA, Benner SA. A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair. Angewandte Chemie (International Ed. in English). PMID 26223188 DOI: 10.1002/anie.201504731  1
2015 Koo SC, Lu J, Li NS, Leung E, Das SR, Harris ME, Piccirilli JA. Transition State Features in the Hepatitis Delta Virus (HDV) Ribozyme Reaction Revealed by Atomic Perturbations. Journal of the American Chemical Society. PMID 26125657 DOI: 10.1021/jacs.5b01189  1
2015 DasGupta S, Shelke SA, Li NS, Piccirilli JA. Spinach RNA aptamer detects lead(ii) with high selectivity. Chemical Communications (Cambridge, England). 51: 9034-7. PMID 25940073 DOI: 10.1039/c5cc01526j  1
2015 Kellerman DL, Simmons KS, Pedraza M, Piccirilli JA, York DM, Harris ME. Determination of hepatitis delta virus ribozyme N(-1) nucleobase and functional group specificity using internal competition kinetics. Analytical Biochemistry. 483: 12-20. PMID 25937290 DOI: 10.1016/j.ab.2015.04.024  1
2015 Harris ME, Piccirilli JA, York DM. Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism. Biochimica Et Biophysica Acta. PMID 25936517 DOI: 10.1016/j.bbapap.2015.04.022  1
2015 Weissman BP, Li NS, York D, Harris M, Piccirilli JA. Heavy atom labeled nucleotides for measurement of kinetic isotope effects. Biochimica Et Biophysica Acta. PMID 25828952 DOI: 10.1016/j.bbapap.2015.03.007  1
2015 Chen H, Piccirilli JA, Harris ME, York DM. Effect of Zn(2+) binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects. Biochimica Et Biophysica Acta. PMID 25812974 DOI: 10.1016/j.bbapap.2015.02.022  1
2015 Lu J, Koo SC, Li NS, Piccirilli JA. Synthesis of 2'-O-photocaged ribonucleoside phosphoramidites. Nucleosides, Nucleotides & Nucleic Acids. 34: 114-29. PMID 25621705 DOI: 10.1080/15257770.2014.965256  1
2015 Anderson VE, Piccirilli JA, Fitzpatrick PF, Marlier JF, Hengge AC, Byers LD, Wong KY, York DM, Harris ME. Enzyme transition states from theory and experiment Biochimica Et Biophysica Acta - Proteins and Proteomics. DOI: 10.1016/j.bbapap.2015.08.006  1
2014 Shelke SA, Piccirilli JA. Origins of life: RNA made in its own mirror image. Nature. 515: 347-8. PMID 25363771 DOI: 10.1038/nature13935  1
2014 Roy S, Ly D, Li NS, Altman JD, Piccirilli JA, Moody DB, Adams EJ. Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by αβ T cells. Proceedings of the National Academy of Sciences of the United States of America. 111: E4648-57. PMID 25298532 DOI: 10.1073/pnas.1408549111  1
2014 Kellerman DL, York DM, Piccirilli JA, Harris ME. Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation. Current Opinion in Chemical Biology. 21: 96-102. PMID 25023967 DOI: 10.1016/j.cbpa.2014.06.010  1
2014 Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA. A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Nature Chemical Biology. 10: 686-91. PMID 24952597 DOI: 10.1038/nchembio.1561  1
2014 Fica SM, Mefford MA, Piccirilli JA, Staley JP. Evidence for a group II intron-like catalytic triplex in the spliceosome. Nature Structural & Molecular Biology. 21: 464-71. PMID 24747940 DOI: 10.1038/nsmb.2815  1
2014 Li NS, Tuttle N, Staley JP, Piccirilli JA. Synthesis and incorporation of the phosphoramidite derivative of 2'-O-photocaged 3'-s-thioguanosine into oligoribonucleotides: substrate for probing the mechanism of RNA catalysis. The Journal of Organic Chemistry. 79: 3647-52. PMID 24635216 DOI: 10.1021/jo4028374  1
2013 Fica SM, Tuttle N, Novak T, Li NS, Lu J, Koodathingal P, Dai Q, Staley JP, Piccirilli JA. RNA catalyses nuclear pre-mRNA splicing. Nature. 503: 229-34. PMID 24196718 DOI: 10.1038/nature12734  1
2013 Keenholtz RA, Mouw KW, Boocock MR, Li NS, Piccirilli JA, Rice PA. Arginine as a general acid catalyst in serine recombinase-mediated DNA cleavage. The Journal of Biological Chemistry. 288: 29206-14. PMID 23970547 DOI: 10.1074/jbc.M113.508028  1
2013 Gu H, Zhang S, Wong KY, Radak BK, Dissanayake T, Kellerman DL, Dai Q, Miyagi M, Anderson VE, York DM, Piccirilli JA, Harris ME. Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation. Proceedings of the National Academy of Sciences of the United States of America. 110: 13002-7. PMID 23878223 DOI: 10.1073/pnas.1215086110  1
2013 Li NS, Scharf L, Adams EJ, Piccirilli JA. Highly stereocontrolled total synthesis of β-D-mannosyl phosphomycoketide: a natural product from Mycobacterium tuberculosis. The Journal of Organic Chemistry. 78: 5970-86. PMID 23724960 DOI: 10.1021/jo4006602  1
2013 Hernández AR, Piccirilli JA. Chemical origins of life: Prebiotic RNA unstuck. Nature Chemistry. 5: 360-2. PMID 23609081 DOI: 10.1038/nchem.1636  1
2013 Li NS, Piccirilli JA. Synthesis of stereopure acyclic 1,5-dimethylalkane chirons: Building blocks of highly methyl-branched natural products Tetrahedron. 69: 9633-9641. DOI: 10.1016/j.tet.2013.09.020  1
2012 Li NS, Frederiksen JK, Piccirilli JA. Automated solid-phase synthesis of RNA oligonucleotides containing a nonbridging phosphorodithioate linkage via phosphorothioamidites. The Journal of Organic Chemistry. 77: 9889-92. PMID 23050987 DOI: 10.1021/jo301834p  1
2012 Kath-Schorr S, Wilson TJ, Li NS, Lu J, Piccirilli JA, Lilley DM. General acid-base catalysis mediated by nucleobases in the hairpin ribozyme. Journal of the American Chemical Society. 134: 16717-24. PMID 22958171 DOI: 10.1021/ja3067429  1
2012 Sakaguchi R, Giessing A, Dai Q, Lahoud G, Liutkeviciute Z, Klimasauskas S, Piccirilli J, Kirpekar F, Hou YM. Recognition of guanosine by dissimilar tRNA methyltransferases Rna. 18: 1687-1701. PMID 22847817 DOI: 10.1261/rna.032029.111  1
2012 Li NS, Piccirilli JA. Efficient synthesis of 2'-C-α-aminomethyl-2'-deoxynucleosides. Chemical Communications (Cambridge, England). 48: 8754-6. PMID 22836807 DOI: 10.1039/c2cc34556k  1
2012 Frederiksen JK, Li NS, Das R, Herschlag D, Piccirilli JA. Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding. Rna (New York, N.Y.). 18: 1123-41. PMID 22539523 DOI: 10.1261/rna.028738.111  1
2012 Wong KY, Gu H, Zhang S, Piccirilli JA, Harris ME, York DM. Characterization of the reaction path and transition states for RNA transphosphorylation models from theory and experiment. Angewandte Chemie (International Ed. in English). 51: 647-51. PMID 22076983 DOI: 10.1002/anie.201104147  1
2012 Sengupta RN, Herschlag D, Piccirilli JA. Thermodynamic evidence for negative charge stabilization by a catalytic metal ion within an RNA active site. Acs Chemical Biology. 7: 294-9. PMID 22029738 DOI: 10.1021/cb200202q  1
2011 Dai Q, Sengupta R, Deb SK, Piccirilli JA. Synthesis of 2'-N-methylamino-2'-deoxyguanosine and 2'-N,N-dimethylamino-2'-deoxyguanosine and their incorporation into RNA by phosphoramidite chemistry. The Journal of Organic Chemistry. 76: 8718-25. PMID 21942326 DOI: 10.1021/jo201364x  1
2011 Piccirilli JA, Koldobskaya Y. Crystal structure of an RNA polymerase ribozyme in complex with an antibody fragment. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 366: 2918-28. PMID 21930583 DOI: 10.1098/rstb.2011.0144  1
2011 Li NS, Frederiksen JK, Piccirilli JA. Synthesis, properties, and applications of oligonucleotides containing an RNA dinucleotide phosphorothiolate linkage. Accounts of Chemical Research. 44: 1257-69. PMID 21882874 DOI: 10.1021/ar200131t  1
2011 Forconi M, Schwans JP, Porecha RH, Sengupta RN, Piccirilli JA, Herschlag D. 2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA. Chemistry & Biology. 18: 949-54. PMID 21867910 DOI: 10.1016/j.chembiol.2011.07.014  1
2011 Leung EK, Suslov N, Tuttle N, Sengupta R, Piccirilli JA. The mechanism of peptidyl transfer catalysis by the ribosome. Annual Review of Biochemistry. 80: 527-55. PMID 21548786 DOI: 10.1146/annurev-biochem-082108-165150  1
2011 Forconi M, Porecha RH, Piccirilli JA, Herschlag D. Tightening of active site interactions en route to the transition state revealed by single-atom substitution in the guanosine-binding site of the Tetrahymena group I ribozyme. Journal of the American Chemical Society. 133: 7791-800. PMID 21539364 DOI: 10.1021/ja111316y  1
2011 Gilbreth RN, Truong K, Madu I, Koide A, Wojcik JB, Li NS, Piccirilli JA, Chen Y, Koide S. Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design. Proceedings of the National Academy of Sciences of the United States of America. 108: 7751-6. PMID 21518904 DOI: 10.1073/pnas.1102294108  1
2011 Plantinga MJ, Korennykh AV, Piccirilli JA, Correll CC. The ribotoxin restrictocin recognizes its RNA substrate by selective engagement of active site residues. Biochemistry. 50: 3004-13. PMID 21417210 DOI: 10.1021/bi1018336  1
2011 Ramu H, Vázquez-Laslop N, Klepacki D, Dai Q, Piccirilli J, Micura R, Mankin AS. Nascent peptide in the ribosome exit tunnel affects functional properties of the A-site of the peptidyl transferase center. Molecular Cell. 41: 321-30. PMID 21292164 DOI: 10.1016/j.molcel.2010.12.031  1
2011 Koldobskaya Y, Duguid EM, Shechner DM, Suslov NB, Ye J, Sidhu SS, Bartel DP, Koide S, Kossiakoff AA, Piccirilli JA. A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination. Nature Structural & Molecular Biology. 18: 100-6. PMID 21151117 DOI: 10.1038/nsmb.1945  1
2011 Li NS, Frederiksen JK, Koo SC, Lu J, Wilson TJ, Lilley DM, Piccirilli JA. A general and efficient approach for the construction of RNA oligonucleotides containing a 5'-phosphorothiolate linkage. Nucleic Acids Research. 39: e31. PMID 21148150 DOI: 10.1093/nar/gkq1265  1
2010 Scharf L, Li NS, Hawk AJ, Garzón D, Zhang T, Fox LM, Kazen AR, Shah S, Haddadian EJ, Gumperz JE, Saghatelian A, Faraldo-Gómez JD, Meredith SC, Piccirilli JA, Adams EJ. The 2.5 Ã… structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation. Immunity. 33: 853-62. PMID 21167756 DOI: 10.1016/j.immuni.2010.11.026  1
2010 Mouw KW, Steiner AM, Ghirlando R, Li NS, Rowland SJ, Boocock MR, Stark WM, Piccirilli JA, Rice PA. Sin resolvase catalytic activity and oligomerization state are tightly coupled. Journal of Molecular Biology. 404: 16-33. PMID 20868695 DOI: 10.1016/j.jmb.2010.08.057  1
2010 Koodathingal P, Novak T, Piccirilli JA, Staley JP. The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5' splice site cleavage during pre-mRNA splicing. Molecular Cell. 39: 385-95. PMID 20705241 DOI: 10.1016/j.molcel.2010.07.014  1
2010 Harris ME, Dai Q, Gu H, Kellerman DL, Piccirilli JA, Anderson VE. Kinetic isotope effects for RNA cleavage by 2'-O- transphosphorylation: nucleophilic activation by specific base. Journal of the American Chemical Society. 132: 11613-21. PMID 20669950 DOI: 10.1021/ja103550e  1
2010 Wilson TJ, Li NS, Lu J, Frederiksen JK, Piccirilli JA, Lilley DM. Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme. Proceedings of the National Academy of Sciences of the United States of America. 107: 11751-6. PMID 20547881 DOI: 10.1073/pnas.1004255107  1
2010 Forconi M, Sengupta RN, Piccirilli JA, Herschlag D. A rearrangement of the guanosine-binding site establishes an extended network of functional interactions in the Tetrahymena group I ribozyme active site. Biochemistry. 49: 2753-62. PMID 20175542 DOI: 10.1021/bi902200n  1
2010 Li NS, Lu J, Piccirilli JA. Synthesis of 2′-C-branched nucleosides Organic Preparations and Procedures International. 42: 191-283. DOI: 10.1080/00304948.2010.483657  1
2010 Lu J, Li NS, Koo SC, Piccirilli JA. Efficient synthesis of N4-methyl-and N4- hydroxycytidine phosphoramidites Synthesis. 2708-2712. DOI: 10.1055/s-0030-1258170  1
2009 Frederiksen JK, Piccirilli JA. Separation of RNA phosphorothioate oligonucleotides by HPLC. Methods in Enzymology. 468: 289-309. PMID 20946775 DOI: 10.1016/S0076-6879(09)68014-9  1
2009 Hougland JL, Piccirilli JA. 2'-amino-modified ribonucleotides as probes for local interactions within RNA. Methods in Enzymology. 468: 107-25. PMID 20946767 DOI: 10.1016/S0076-6879(09)68006-X  1
2009 Shechner DM, Grant RA, Bagby SC, Koldobskaya Y, Piccirilli JA, Bartel DP. Crystal structure of the catalytic core of an RNA-polymerase ribozyme. Science (New York, N.Y.). 326: 1271-5. PMID 19965478 DOI: 10.1126/science.1174676  1
2009 Lu J, Li NS, Koo SC, Piccirilli JA. Synthesis of pyridine, pyrimidine and pyridinone C-nucleoside phosphoramidites for probing cytosine function in RNA. The Journal of Organic Chemistry. 74: 8021-30. PMID 19791761 DOI: 10.1021/jo9016919  1
2009 Forconi M, Sengupta RN, Liu MC, Sartorelli AC, Piccirilli JA, Herschlag D. Structure and function converge to identify a hydrogen bond in a group I ribozyme active site. Angewandte Chemie (International Ed. in English). 48: 7171-5. PMID 19708048 DOI: 10.1002/anie.200903006  1
2009 Frederiksen JK, Piccirilli JA. Identification of catalytic metal ion ligands in ribozymes. Methods (San Diego, Calif.). 49: 148-66. PMID 19651216 DOI: 10.1016/j.ymeth.2009.07.005  1
2009 Dai Q, Saikia M, Li NS, Pan T, Piccirilli JA. Efficient chemical synthesis of AppDNA by adenylation of immobilized DNA-5'-monophosphate. Organic Letters. 11: 1067-70. PMID 19191584 DOI: 10.1021/ol802815g  1
2009 Li NS, Lu J, Piccirilli JA. Synthesis of 2'-C-beta-methyl-2'-deoxyguanosine. The Journal of Organic Chemistry. 74: 2227-30. PMID 19173609 DOI: 10.1021/jo802666k  1
2008 Plantinga MJ, Korennykh AV, Piccirilli JA, Correll CC. Electrostatic interactions guide the active site face of a structure-specific ribonuclease to its RNA substrate. Biochemistry. 47: 8912-8. PMID 18672906 DOI: 10.1021/bi800592g  1
2008 Hougland JL, Sengupta RN, Dai Q, Deb SK, Piccirilli JA. The 2'-hydroxyl group of the guanosine nucleophile donates a functionally important hydrogen bond in the tetrahymena ribozyme reaction. Biochemistry. 47: 7684-94. PMID 18572927 DOI: 10.1021/bi8000648  1
2008 Forconi M, Lee J, Lee JK, Piccirilli JA, Herschlag D. Functional identification of ligands for a catalytic metal ion in group I introns. Biochemistry. 47: 6883-94. PMID 18517225 DOI: 10.1021/bi800519a  1
2008 Lu J, Li NS, Sengupta RN, Piccirilli JA. 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. PMID 18397828 DOI: 10.1016/j.bmc.2008.03.061  1
2008 Piccirilli JA. Biochemistry. Toward understanding self-splicing. Science (New York, N.Y.). 320: 56-7. PMID 18388278 DOI: 10.1126/science.1156721  1
2008 Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D. Structural inference of native and partially folded RNA by high-throughput contact mapping. Proceedings of the National Academy of Sciences of the United States of America. 105: 4144-9. PMID 18322008 DOI: 10.1073/pnas.0709032105  1
2008 Ye JD, Tereshko V, Frederiksen JK, Koide A, Fellouse FA, Sidhu SS, Koide S, Kossiakoff AA, Piccirilli JA. Synthetic antibodies for specific recognition and crystallization of structured RNA. Proceedings of the National Academy of Sciences of the United States of America. 105: 82-7. PMID 18162543 DOI: 10.1073/pnas.0709082105  1
2008 Dai Q, Frederiksen JK, Anderson VE, Harris ME, Piccirilli JA. 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. The Journal of Organic Chemistry. 73: 309-11. PMID 18052189 DOI: 10.1021/jo701727h  1
2007 Korennykh AV, Plantinga MJ, Correll CC, Piccirilli JA. Linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop RNA by restrictocin. Biochemistry. 46: 12744-56. PMID 17929942 DOI: 10.1021/bi700931y  1
2007 Dai Q, Fong R, Saikia M, Stephenson D, Yu YT, Pan T, Piccirilli JA. Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine. Nucleic Acids Research. 35: 6322-9. PMID 17881375 DOI: 10.1093/nar/gkm657  1
2007 Forconi M, Piccirilli JA, Herschlag D. Modulation of individual steps in group I intron catalysis by a peripheral metal ion. Rna (New York, N.Y.). 13: 1656-67. PMID 17720880 DOI: 10.1261/rna.632007  1
2007 Ye JD, Barth CD, Anjaneyulu PS, Tuschl T, Piccirilli JA. Reactions of phosphate and phosphorothiolate diesters with nucleophiles: comparison of transition state structures. Organic & Biomolecular Chemistry. 5: 2491-7. PMID 17637971 DOI: 10.1039/b707205h  1
2007 Dai Q, Lea CR, Lu J, Piccirilli JA. Syntheses of (2')3'-15N-amino-(2')3'-deoxyguanosine and determination of their pKa values by 15N NMR spectroscopy. Organic Letters. 9: 3057-60. PMID 17629287 DOI: 10.1021/ol071129h  1
2007 Li NS, Lu J, Piccirilli JA. Efficient synthesis of methyl 3,5-di-O-benzyl-alpha-D-ribofuranoside and application to the synthesis of 2'-C-beta-alkoxymethyluridines. Organic Letters. 9: 3009-12. PMID 17629285 DOI: 10.1021/ol071075b  1
2007 Korennykh AV, Correll CC, Piccirilli JA. Evidence for the importance of electrostatics in the function of two distinct families of ribosome inactivating toxins. Rna (New York, N.Y.). 13: 1391-6. PMID 17626843 DOI: 10.1261/rna.619707  1
2007 Gordon PM, Fong R, Piccirilli JA. A second divalent metal ion in the group II intron reaction center. Chemistry & Biology. 14: 607-12. PMID 17584608 DOI: 10.1016/j.chembiol.2007.05.008  1
2007 Ye JD, Li NS, Dai Q, Piccirilli JA. The mechanism of RNA strand scission: an experimental measure of the Brønsted coefficient, beta nuc. Angewandte Chemie (International Ed. in English). 46: 3714-7. PMID 17415726 DOI: 10.1002/anie.200605124  1
2007 Li NS, Piccirilli JA. Synthesis of 2'-C-alpha-(hydroxyalkyl) and 2'-C-alpha-alkylcytidine phosphoramidites: analogues for probing solvent interactions with RNA. The Journal of Organic Chemistry. 72: 1198-210. PMID 17288373 DOI: 10.1021/jo062002t  1
2007 Lea CR, Piccirilli JA. 'Turning on' riboswitches to their antibacterial potential. Nature Chemical Biology. 3: 16-7. PMID 17173021 DOI: 10.1038/nchembio0107-16  1
2006 Saikia M, Dai Q, Decatur WA, Fournier MJ, Piccirilli JA, Pan T. A systematic, ligation-based approach to study RNA modifications. Rna (New York, N.Y.). 12: 2025-33. PMID 16963711 DOI: 10.1261/rna.208906  1
2006 Li NS, Piccirilli JA. Efficient synthesis of 2'-C-beta-methylguanosine. The Journal of Organic Chemistry. 71: 4018-20. PMID 16674089 DOI: 10.1021/jo0602165  1
2006 Korennykh AV, Piccirilli JA, Correll CC. The electrostatic character of the ribosomal surface enables extraordinarily rapid target location by ribotoxins. Nature Structural & Molecular Biology. 13: 436-43. PMID 16604082 DOI: 10.1038/nsmb1082  1
2006 Dai Q, Deb SK, Hougland JL, Piccirilli JA. Improved synthesis of 2'-amino-2'-deoxyguanosine and its phosphoramidite. Bioorganic & Medicinal Chemistry. 14: 705-13. PMID 16202607 DOI: 10.1016/j.bmc.2005.08.050  1
2005 Das SR, Piccirilli JA. General acid catalysis by the hepatitis delta virus ribozyme. Nature Chemical Biology. 1: 45-52. PMID 16407993 DOI: 10.1038/nchembio703  1
2005 Ye JD, Liao X, Piccirilli JA. Synthesis of 2'-C-difluoromethylribonucleosides and their enzymatic incorporation into oligonucleotides. The Journal of Organic Chemistry. 70: 7902-10. PMID 16277309 DOI: 10.1021/jo0507542  1
2005 Das SR, Fong R, Piccirilli JA. Nucleotide analogues to investigate RNA structure and function. Current Opinion in Chemical Biology. 9: 585-93. PMID 16242990 DOI: 10.1016/j.cbpa.2005.10.009  1
2005 Hougland JL, Kravchuk AV, Herschlag D, Piccirilli JA. Functional identification of catalytic metal ion binding sites within RNA. Plos Biology. 3: e277. PMID 16092891 DOI: 10.1371/journal.pbio.0030277  1
2005 Li NS, Piccirilli JA. Synthesis of 2′-deoxy-2′-C-α-methylpurine nucleosides Synthesis. 2865-2870. DOI: 10.1055/s-2005-872204  1
2004 Hougland JL, Deb SK, Maric D, Piccirilli JA. An atomic mutation cycle for exploring RNA's 2'-hydroxyl group. Journal of the American Chemical Society. 126: 13578-9. PMID 15493890 DOI: 10.1021/ja0469129  1
2004 Li NS, Piccirilli JA. Synthesis of the phosphoramidite derivatives of 2'-deoxy-2'-C-alpha-methylcytidine and 2'-deoxy-2'-C-alpha-hydroxymethylcytidine: analogues for chemical dissection of RNA's 2'-hydroxyl group. The Journal of Organic Chemistry. 69: 4751-9. PMID 15230598 DOI: 10.1021/jo0495337  1
2004 Dai Q, Piccirilli JA. Efficient synthesis of 2',3'-dideoxy-2'-amino-3'-thiouridine. Organic Letters. 6: 2169-72. PMID 15200312 DOI: 10.1021/ol049366x  1
2004 Schwans JP, Li NS, Piccirilli JA. A packing-density metric for exploring the interior of folded RNA molecules. Angewandte Chemie (International Ed. in English). 43: 3033-7. PMID 15188472 DOI: 10.1002/anie.200353575  1
2004 Gordon PM, Fong R, Deb SK, Li NS, Schwans JP, Ye JD, Piccirilli JA. New strategies for exploring RNA's 2'-OH expose the importance of solvent during group II intron catalysis. Chemistry & Biology. 11: 237-46. PMID 15123285 DOI: 10.1016/j.chembiol.2004.02.011  1
2003 Li NS, Piccirilli JA. Synthesis of the phosphoramidite derivative of 2'-deoxy-2'-C-beta-methylcytidine. The Journal of Organic Chemistry. 68: 6799-802. PMID 12919052 DOI: 10.1021/jo034263y  1
2003 Schwans JP, Cortez CN, Olvera JM, Piccirilli JA. 2'-mercaptonucleotide interference reveals regions of close packing within folded RNA molecules. Journal of the American Chemical Society. 125: 10012-8. PMID 12914464 DOI: 10.1021/ja035175y  1
2003 Dai Q, Piccirilli JA. Synthesis of 2'-C-beta-fluoromethyluridine. Organic Letters. 5: 807-10. PMID 12633077 DOI: 10.1021/ol027364b  1
2002 Szewczak AA, Kosek AB, Piccirilli JA, Strobel SA. Identification of an active site ligand for a group I ribozyme catalytic metal ion. Biochemistry. 41: 2516-25. PMID 11851398 DOI: 10.1021/bi011973u  1
2001 Kuo LY, Piccirilli JA. Leaving group stabilization by metal ion coordination and hydrogen bond donation is an evolutionarily conserved feature of group I introns. Biochimica Et Biophysica Acta. 1522: 158-66. PMID 11779630 DOI: 10.1016/S0167-4781(01)00327-X  1
2001 Gordon PM, Piccirilli JA. Metal ion coordination by the AGC triad in domain 5 contributes to group II intron catalysis. Nature Structural Biology. 8: 893-8. PMID 11573097 DOI: 10.1038/nsb1001-893  1
2001 Liao X, Anjaneyulu PS, Curley JF, Hsu M, Boehringer M, Caruthers MH, Piccirilli JA. The tetrahymena ribozyme cleaves a 5'-methylene phosphonate monoester approximately 10(2)-fold faster than a normal phosphate diester: implications for enzyme catalysis of phosphoryl transfer reactions. Biochemistry. 40: 10911-26. PMID 11551186 DOI: 10.1021/bi010801u  1
2001 Shan S, Kravchuk AV, Piccirilli JA, Herschlag D. Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. Biochemistry. 40: 5161-71. PMID 11318638  1
2001 Li NS, Tang XQ, Piccirilli JA. 2'-C-branched ribonucleosides. 2. Synthesis of 2'-C-beta-trifluoromethyl pyrimidine ribonucleosides. Organic Letters. 3: 1025-8. PMID 11277786 DOI: 10.1021/ol0155687  1
2001 Dai Q, Piccirilli JA, Zheng C, Li SJ. Crystal structure of 3′,5′-di-O-acetyl-2′-C-α-acetyloxymethyl-2,2′- anhydro-1-(β-D-arabinofuranosyl)uracil, C16H18N2O9 Zeitschrift Fur Kristallographie - New Crystal Structures. 216: 343-346.  1
2000 Gordon PM, Sontheimer EJ, Piccirilli JA. 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. PMID 11041859 DOI: 10.1021/bi001089o  1
2000 Earnshaw DJ, Hamm ML, Piccirilli JA, Karpeisky A, Beigelman L, Ross BS, Manoharan M, Gait MJ. Investigation of the proposed interdomain ribose zipper in hairpin ribozyme cleavage using 2'-modified nucleosides. Biochemistry. 39: 6410-21. PMID 10828955 DOI: 10.1021/bi992974d  1
2000 Gordon PM, Sontheimer EJ, Piccirilli JA. Metal ion catalysis during the exon-ligation step of nuclear pre-mRNA splicing: extending the parallels between the spliceosome and group II introns. Rna (New York, N.Y.). 6: 199-205. PMID 10688359 DOI: 10.1017/S1355838200992069  1
2000 Yoshida A, Shan So, Herschlag D, Piccirilli JA. The role of the cleavage site 2'-hydroxyl in the Tetrahymena group I ribozyme reaction. Chemistry & Biology. 7: 85-96. PMID 10662698 DOI: 10.1016/S1074-5521(00)00074-0  1
2000 Warnecke JM, Sontheimer EJ, Piccirilli JA, Hartmann RK. Active site constraints in the hydrolysis reaction catalyzed by bacterial RNase P: analysis of precursor tRNAs with a single 3'-S-phosphorothiolate internucleotide linkage. Nucleic Acids Research. 28: 720-7. PMID 10637323  1
2000 Hamm ML, Schwans JP, Piccirilli JA. The hammerhead ribozyme catalyzes the deglycosylation of 2'- mercaptocytidine [6] Journal of the American Chemical Society. 122: 4223-4224. DOI: 10.1021/ja993027v  1
2000 Hamm ML, Nikolic D, Van Breemen RB, Piccirilli JA. Unconventional origin of metal ion rescue in the hammerhead ribozyme reaction: Mn2+-assisted redox conversion of 2′-mercaptocytidine to cytidine Journal of the American Chemical Society. 122: 12069-12078. DOI: 10.1021/ja000379p  1
1999 Hamm ML, Piccirilli JA. Synthesis and Characterization of Oligonucleotides Containing 2'-S,3'-O-Cyclic Phosphorothiolate Termini. The Journal of Organic Chemistry. 64: 5700-5704. PMID 11674644  0.36
1999 Tang XQ, Liao X, Piccirilli JA. 2'-C-Branched Ribonucleosides: Synthesis of the Phosphoramidite Derivatives of 2'-C-beta-Methylcytidine and Their Incorporation into Oligonucleotides. The Journal of Organic Chemistry. 64: 747-754. PMID 11674142  0.64
1999 Shan So, Yoshida A, Sun S, Piccirilli JA, Herschlag D. Three metal ions at the active site of the Tetrahymena group I ribozyme. Proceedings of the National Academy of Sciences of the United States of America. 96: 12299-304. PMID 10535916 DOI: 10.1073/pnas.96.22.12299  1
1999 Sontheimer EJ, Gordon PM, Piccirilli JA. Metal ion catalysis during group II intron self-splicing: parallels with the spliceosome. Genes & Development. 13: 1729-41. PMID 10398685  1
1999 Yoshida A, Sun S, Piccirilli JA. A new metal ion interaction in the Tetrahymena ribozyme reaction revealed by double sulfur substitution. Nature Structural Biology. 6: 318-21. PMID 10201397 DOI: 10.1038/7551  1
1999 Piccirilli JA. Do enzymes obey the Baldwin rules? A mechanistic imperative in enzymatic cyclization reactions. Chemistry & Biology. 6: R59-64. PMID 10074471 DOI: 10.1016/S1074-5521(99)89001-2  1
1999 Brautigam CA, Sun S, Piccirilli JA, Steitz TA. 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. PMID 9888810 DOI: 10.1021/bi981537g  1
1999 Hamm ML, Piccirilli JA. Synthesis and characterization of oligonucleotides containing 2'-S,3'-O- cyclic phosphorothiolate termini Journal of Organic Chemistry. 64: 5700-5704. DOI: 10.1021/jo9903508  1
1999 Tang XQ, Liao X, Piccirilli JA. 2'-C-branched ribonucleosides: Synthesis of the phosphoramidite derivatives of 2'-C-β-methylcytidine and their incorporation into oligonucleotides Journal of Organic Chemistry. 64: 747-754. DOI: 10.1021/jo981329u  1
1998 Benner SA, Battersby TR, Eschgfaller B, Hutter D, Kodra JT, Lutz S, Arslan T, Baschlin DK, Blattler M, Egli M, Hammer C, Held HA, Horlacher J, Huang Z, Hyrup B, ... ... Piccirilli JA, et al. Redesigning nucleic acids. Pure and Applied Chemistry. Chimie Pure Et AppliquéE. 70: 263-6. PMID 11542721  1
1997 Hamm ML, Piccirilli JA. Incorporation of 2'-Deoxy-2'-mercaptocytidine into Oligonucleotides via Phosphoramidite Chemistry. The Journal of Organic Chemistry. 62: 3415-3420. PMID 11671734 DOI: 10.1021/jo970096o  1
1997 Sun S, Yoshida A, Piccirilli JA. Synthesis of 3'-thioribonucleosides and their incorporation into oligoribonucleotides via phosphoramidite chemistry. Rna (New York, N.Y.). 3: 1352-63. PMID 9409625  1
1997 Sontheimer EJ, Sun S, Piccirilli JA. Metal ion catalysis during splicing of premessenger RNA. Nature. 388: 801-5. PMID 9285595 DOI: 10.1038/42068  1
1997 Piccirilli JA, Hamm ML. Mechanisms of phosphoryl transfer revealed by modified nucleic acids Faseb Journal. 11: A1284.  1
1997 Hamm ML, Piccirilli JA. Incorporation of 2′-Deoxy-2′-mercaptocytidine into Oligonucleotides via Phosphoramidite Chemistry Journal of Organic Chemistry. 62: 3413-3414.  1
1997 Sun S, Piccirilli JA. Synthesis of 3'-thioribouridine, 3'-thioribocytidine, and their phosphoramidites Nucleosides and Nucleotides. 16: 1543-1545.  1
1996 Sun S, Tang XQ, Merchant A, Anjaneyulu PSR, Piccirilli JA. Efficient synthesis of 5-(thioalkyl)uridines via ring opening of α-ureidomethylene thiolactones Journal of Organic Chemistry. 61: 5708-5709. DOI: 10.1021/jo960966m  1
1995 Piccirilli JA. Origin of life. RNA seeks its maker. Nature. 376: 548-9. PMID 7543655 DOI: 10.1038/376548a0  1
1993 Piccirilli JA, Vyle JS, Caruthers MH, Cech TR. Metal ion catalysis in the Tetrahymena ribozyme reaction. Nature. 361: 85-8. PMID 8421499 DOI: 10.1038/361085a0  1
1992 Piccirilli JA, McConnell TS, Zaug AJ, Noller HF, Cech TR. Aminoacyl esterase activity of the Tetrahymena ribozyme. Science (New York, N.Y.). 256: 1420-4. PMID 1604316  1
1992 Cech TR, Herschlag D, Piccirilli JA, Pyle AM. RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization. The Journal of Biological Chemistry. 267: 17479-82. PMID 1381347  1
1991 Herschlag D, Piccirilli JA, Cech TR. Ribozyme-catalyzed and nonenzymatic reactions of phosphate diesters: rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom. Biochemistry. 30: 4844-54. PMID 2036355  1
1991 Piccirilli JA, Moroney SE, Benner SA. A C-nucleotide base pair: methylpseudouridine-directed incorporation of formycin triphosphate into RNA catalyzed by T7 RNA polymerase. Biochemistry. 30: 10350-6. PMID 1718418 DOI: 10.1021/bi00106a037  1
1991 Moroney SE, Piccirilli JA. Abortive products as initiating nucleotides during transcription by T7 RNA polymerase. Biochemistry. 30: 10343-9. PMID 1718417 DOI: 10.1021/bi00106a036  1
1991 Piccirilli JA, Krauch T, MacPherson LJ, Benner SA. A direct route to 3-(D-rubofuranosyl)pyridine nucleosides Helvetica Chimica Acta. 74: 397-406.  1
1990 Piccirilli JA, Krauch T, Moroney SE, Benner SA. Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature. 343: 33-7. PMID 1688644 DOI: 10.1038/343033a0  1
1987 Benner SA, Allemann RK, Ellington AD, Ge L, Glasfeld A, Leanz GF, Krauch T, MacPherson LJ, Moroney S, Piccirilli JA. Natural selection, protein engineering, and the last riboorganism: rational model building in biochemistry. Cold Spring Harbor Symposia On Quantitative Biology. 52: 53-63. PMID 2456885  1
1987 Piccirilli JA, Rozzell JD, Benner SA. The stereospecificity of oxaloacetate decarboxylase: A stereochemical imperative? Journal of the American Chemical Society. 109: 8084-8085.  1
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