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Last Name
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Joseph A. Piccirilli

TitleProfessor
InstitutionUniversity of Chicago
DepartmentBiochemistry and Molecular Biology
AddressChicago IL 60637
Email
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    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Hiller DA, Dunican BF, Nallur S, Li NS, Piccirilli JA, Strobel SA. The Positively Charged Active Site of the Bacterial Toxin RelE Causes a Large Shift in the General Base pKa. Biochemistry. 2020 05 05; 59(17):1665-1671. PMID: 32320214.
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    2. Liu D, Geary CW, Chen G, Shao Y, Li M, Mao C, Andersen ES, Piccirilli JA, Rothemund PWK, Weizmann Y. Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures. Nat Chem. 2020 03; 12(3):249-259. PMID: 31959958.
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    3. Ganguly A, Weissman BP, Giese TJ, Li NS, Hoshika S, Rao S, Benner SA, Piccirilli JA, York DM. Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme. Nat Chem. 2020 02; 12(2):193-201. PMID: 31959957.
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    4. Koirala D, Lewicka A, Koldobskaya Y, Huang H, Piccirilli JA. Synthetic Antibody Binding to a Preorganized RNA Domain of Hepatitis C Virus Internal Ribosome Entry Site Inhibits Translation. ACS Chem Biol. 2020 01 17; 15(1):205-216. PMID: 31765566.
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    5. Gaines CS, Piccirilli JA, York DM. The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design. RNA. 2020 02; 26(2):111-125. PMID: 31776179.
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    6. Li NS, Liang W, Piccirilli JA, Tang WJ. Reinvestigating the synthesis and efficacy of small benzimidazole derivatives as presequence protease enhancers. Eur J Med Chem. 2019 Dec 15; 184:111746. PMID: 31610373.
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    7. 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. Nat Commun. 2019 08 09; 10(1):3629. PMID: 31399592.
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    8. Bevilacqua PC, Harris ME, Piccirilli JA, Gaines C, Ganguly A, Kostenbader K, Ekesan S, York DM. An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes. ACS Chem Biol. 2019 06 21; 14(6):1068-1076. PMID: 31095369.
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    9. Wilson TJ, Liu Y, Li NS, Dai Q, Piccirilli JA, Lilley DMJ. Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes. J Am Chem Soc. 2019 05 15; 141(19):7865-7875. PMID: 31017785.
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    10. 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, Benner SA. Hachimoji DNA and RNA: A genetic system with eight building blocks. Science. 2019 02 22; 363(6429):884-887. PMID: 30792304.
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    11. 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. Nat Commun. 2018 10 31; 9(1):4542. PMID: 30382099.
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    12. Lu J, Koo SC, Weissman BP, Harris ME, Li NS, Piccirilli JA. Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State. Biochemistry. 2018 06 26; 57(25):3465-3472. PMID: 29733591.
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    13. 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 Res. 2018 03 16; 46(5):2624-2635. PMID: 29309709.
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    14. Li NS, Lu J, Piccirilli JA. Synthesis of 5'-Thio-3'-O-ribonucleoside Phosphoramidites. J Org Chem. 2017 12 01; 82(23):12003-12013. PMID: 29049877.
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    15. Harris ME, York DM, Piccirilli JA, Anderson VE. Kinetic Isotope Effect Analysis of RNA 2'-O-Transphosphorylation. Methods Enzymol. 2017; 596:433-457. PMID: 28911780.
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    16. DasGupta S, Suslov NB, Piccirilli JA. Structural Basis for Substrate Helix Remodeling and Cleavage Loop Activation in the Varkud Satellite Ribozyme. J Am Chem Soc. 2017 07 19; 139(28):9591-9597. PMID: 28625058.
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    17. Liu D, Shao Y, Chen G, Tse-Dinh YC, Piccirilli JA, Weizmann Y. Synthesizing topological structures containing RNA. Nat Commun. 2017 03 31; 8:14936. PMID: 28361879.
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    18. Sundaram KM, Zhang Y, Mitra AK, Kouadio JK, Gwin K, Kossiakoff AA, Roman BB, Lengyel E, Piccirilli JA. Prolactin Receptor-Mediated Internalization of Imaging Agents Detects Epithelial Ovarian Cancer with Enhanced Sensitivity and Specificity. Cancer Res. 2017 04 01; 77(7):1684-1696. PMID: 28202518.
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    19. Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Lach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B, Xiao Y, Xu X, Zhang D, Zok T, Westhof E. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA. 2017 05; 23(5):655-672. PMID: 28138060.
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    20. Li NS, Gossai NP, Naumann JA, Gordon PM, Piccirilli JA. Efficient Synthetic Approach to Linear Dasatinib-DNA Conjugates by Click Chemistry. Bioconjug Chem. 2016 Oct 19; 27(10):2575-2579. PMID: 27690393.
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    21. 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 Res. 2016 Nov 16; 44(20):9565-9577. PMID: 27701076.
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    22. 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. J Mol Biol. 2016 10 09; 428(20):4100-4114. PMID: 27593161.
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    23. Gossai NP, Naumann JA, Li NS, Zamora EA, Gordon DJ, Piccirilli JA, Gordon PM. Drug conjugated nanoparticles activated by cancer cell specific mRNA. Oncotarget. 2016 Jun 21; 7(25):38243-38256. PMID: 27203672.
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    24. Piccirilli JA, Staley JP. Reverse transcriptases lend a hand in splicing catalysis. Nat Struct Mol Biol. 2016 06 07; 23(6):507-9. PMID: 27273636.
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    25. 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+). Chem Commun (Camb). 2016 Mar 25; 52(24):4462-5. PMID: 26859380.
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    26. 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 Vd1 ?d T Cells Identified by CD1c Tetramers. J Immunol. 2016 Feb 15; 196(4):1933-42. PMID: 26755823.
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    27. Sengupta RN, Van Schie SN, Giambasu 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. 2016 Jan; 22(1):32-48. PMID: 26567314.
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    28. Suslov NB, DasGupta S, Huang H, Fuller JR, Lilley DM, Rice PA, Piccirilli JA. Crystal structure of the Varkud satellite ribozyme. Nat Chem Biol. 2015 Nov; 11(11):840-6. PMID: 26414446.
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    29. Harris ME, Piccirilli JA, York DM. Enzyme transition states from theory and experiment. Biochim Biophys Acta. 2015 Nov; 1854(11):1727-8. PMID: 26302659.
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    30. 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. Angew Chem Int Ed Engl. 2015 Aug 17; 54(34):9853-6. PMID: 26223188.
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    31. Koo SC, Lu J, Li NS, Leung E, Das SR, Harris ME, Piccirilli JA. Transition State Features in the Hepatitis Delta Virus Ribozyme Reaction Revealed by Atomic Perturbations. J Am Chem Soc. 2015 Jul 22; 137(28):8973-82. PMID: 26125657.
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    32. DasGupta S, Shelke SA, Li NS, Piccirilli JA. Spinach RNA aptamer detects lead(II) with high selectivity. Chem Commun (Camb). 2015 May 28; 51(43):9034-7. PMID: 25940073.
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    33. 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. Anal Biochem. 2015 Aug 15; 483:12-20. PMID: 25937290.
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    34. Harris ME, Piccirilli JA, York DM. Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism. Biochim Biophys Acta. 2015 Nov; 1854(11):1801-8. PMID: 25936517.
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    35. Weissman BP, Li NS, York D, Harris M, Piccirilli JA. Heavy atom labeled nucleotides for measurement of kinetic isotope effects. Biochim Biophys Acta. 2015 Nov; 1854(11):1737-45. PMID: 25828952.
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    36. Chen H, Piccirilli JA, Harris ME, York DM. Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects. Biochim Biophys Acta. 2015 Nov; 1854(11):1795-800. PMID: 25812974.
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    37. Lu J, Koo SC, Li NS, Piccirilli JA. Synthesis of 2'-O-photocaged ribonucleoside phosphoramidites. Nucleosides Nucleotides Nucleic Acids. 2015; 34(2):114-29. PMID: 25621705.
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    38. Shelke SA, Piccirilli JA. Origins of life: RNA made in its own mirror image. Nature. 2014 Nov 20; 515(7527):347-8. PMID: 25363771.
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    39. 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 aß T cells. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):E4648-57. PMID: 25298532.
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    40. Kellerman DL, York DM, Piccirilli JA, Harris ME. Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation. Curr Opin Chem Biol. 2014 Aug; 21:96-102. PMID: 25023967.
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    41. 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. Nat Chem Biol. 2014 Aug; 10(8):686-91. PMID: 24952597.
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    42. Fica SM, Mefford MA, Piccirilli JA, Staley JP. Evidence for a group II intron-like catalytic triplex in the spliceosome. Nat Struct Mol Biol. 2014 May; 21(5):464-471. PMID: 24747940.
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    43. 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. J Org Chem. 2014 Apr 18; 79(8):3647-52. PMID: 24635216.
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    44. 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. 2013 Nov 14; 503(7475):229-34. PMID: 24196718.
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    45. Keenholtz RA, Mouw KW, Boocock MR, Li NS, Piccirilli JA, Rice PA. Arginine as a general acid catalyst in serine recombinase-mediated DNA cleavage. J Biol Chem. 2013 Oct 04; 288(40):29206-14. PMID: 23970547.
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    46. 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. Proc Natl Acad Sci U S A. 2013 Aug 06; 110(32):13002-7. PMID: 23878223.
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    47. Li NS, Scharf L, Adams EJ, Piccirilli JA. Highly stereocontrolled total synthesis of ß-D-mannosyl phosphomycoketide: a natural product from Mycobacterium tuberculosis. J Org Chem. 2013 Jun 21; 78(12):5970-86. PMID: 23724960.
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    48. Hernández AR, Piccirilli JA. Chemical origins of life: Prebiotic RNA unstuck. Nat Chem. 2013 May; 5(5):360-2. PMID: 23609081.
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    49. Li NS, Frederiksen JK, Piccirilli JA. Automated solid-phase synthesis of RNA oligonucleotides containing a nonbridging phosphorodithioate linkage via phosphorothioamidites. J Org Chem. 2012 Nov 02; 77(21):9889-92. PMID: 23050987.
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    50. Kath-Schorr S, Wilson TJ, Li NS, Lu J, Piccirilli JA, Lilley DM. General acid-base catalysis mediated by nucleobases in the hairpin ribozyme. J Am Chem Soc. 2012 Oct 10; 134(40):16717-24. PMID: 22958171.
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    51. 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. 2012 Sep; 18(9):1687-701. PMID: 22847817.
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    52. Li NS, Piccirilli JA. Efficient synthesis of 2'-C-a-aminomethyl-2'-deoxynucleosides. Chem Commun (Camb). 2012 Sep 11; 48(70):8754-6. PMID: 22836807.
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    53. 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. 2012 Jun; 18(6):1123-41. PMID: 22539523.
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    54. 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. Angew Chem Int Ed Engl. 2012 Jan 16; 51(3):647-51. PMID: 22076983.
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    55. Sengupta RN, Herschlag D, Piccirilli JA. Thermodynamic evidence for negative charge stabilization by a catalytic metal ion within an RNA active site. ACS Chem Biol. 2012 Feb 17; 7(2):294-9. PMID: 22029738.
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    56. Piccirilli JA, Koldobskaya Y. Crystal structure of an RNA polymerase ribozyme in complex with an antibody fragment. Philos Trans R Soc Lond B Biol Sci. 2011 Oct 27; 366(1580):2918-28. PMID: 21930583.
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    57. 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. J Org Chem. 2011 Nov 04; 76(21):8718-25. PMID: 21942326.
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    58. Li NS, Frederiksen JK, Piccirilli JA. Synthesis, properties, and applications of oligonucleotides containing an RNA dinucleotide phosphorothiolate linkage. Acc Chem Res. 2011 Dec 20; 44(12):1257-69. PMID: 21882874.
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    59. Forconi M, Schwans JP, Porecha RH, Sengupta RN, Piccirilli JA, Herschlag D. 2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA. Chem Biol. 2011 Aug 26; 18(8):949-54. PMID: 21867910.
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    60. 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. J Am Chem Soc. 2011 May 25; 133(20):7791-800. PMID: 21539364.
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    61. 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. Proc Natl Acad Sci U S A. 2011 May 10; 108(19):7751-6. PMID: 21518904.
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    62. Plantinga MJ, Korennykh AV, Piccirilli JA, Correll CC. The ribotoxin restrictocin recognizes its RNA substrate by selective engagement of active site residues. Biochemistry. 2011 Apr 12; 50(14):3004-13. PMID: 21417210.
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    63. 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. Mol Cell. 2011 Feb 04; 41(3):321-30. PMID: 21292164.
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    64. Leung EK, Suslov N, Tuttle N, Sengupta R, Piccirilli JA. The mechanism of peptidyl transfer catalysis by the ribosome. Annu Rev Biochem. 2011; 80:527-55. PMID: 21548786.
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    65. 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 Å structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation. Immunity. 2010 Dec 14; 33(6):853-62. PMID: 21167756.
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    66. 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. Nat Struct Mol Biol. 2011 Jan; 18(1):100-6. PMID: 21151117.
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    67. 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 Res. 2011 Mar; 39(5):e31. PMID: 21148150.
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    68. 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. J Mol Biol. 2010 Nov 19; 404(1):16-33. PMID: 20868695.
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    69. 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. J Am Chem Soc. 2010 Aug 25; 132(33):11613-21. PMID: 20669950.
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    70. 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. Mol Cell. 2010 Aug 13; 39(3):385-95. PMID: 20705241.
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    71. Wilson TJ, Li NS, Lu J, Frederiksen JK, Piccirilli JA, Lilley DM. Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme. Proc Natl Acad Sci U S A. 2010 Jun 29; 107(26):11751-6. PMID: 20547881.
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    72. 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. 2010 Mar 30; 49(12):2753-62. PMID: 20175542.
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    73. Shechner DM, Grant RA, Bagby SC, Koldobskaya Y, Piccirilli JA, Bartel DP. Crystal structure of the catalytic core of an RNA-polymerase ribozyme. Science. 2009 Nov 27; 326(5957):1271-5. PMID: 19965478.
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    74. Frederiksen JK, Piccirilli JA. Separation of RNA phosphorothioate oligonucleotides by HPLC. Methods Enzymol. 2009; 468:289-309. PMID: 20946775.
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    75. Hougland JL, Piccirilli JA. 2'-amino-modified ribonucleotides as probes for local interactions within RNA. Methods Enzymol. 2009; 468:107-25. PMID: 20946767.
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    76. Lu J, Li NS, Koo SC, Piccirilli JA. Synthesis of pyridine, pyrimidine and pyridinone C-nucleoside phosphoramidites for probing cytosine function in RNA. J Org Chem. 2009 Nov 06; 74(21):8021-30. PMID: 19791761.
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    77. Frederiksen JK, Piccirilli JA. Identification of catalytic metal ion ligands in ribozymes. Methods. 2009 Oct; 49(2):148-66. PMID: 19651216.
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    78. Li NS, Lu J, Piccirilli JA. Synthesis of 2'-C-beta-methyl-2'-deoxyguanosine. J Org Chem. 2009 Mar 06; 74(5):2227-30. PMID: 19173609.
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    79. Dai Q, Saikia M, Li NS, Pan T, Piccirilli JA. Efficient chemical synthesis of AppDNA by adenylation of immobilized DNA-5'-monophosphate. Org Lett. 2009 Mar 05; 11(5):1067-70. PMID: 19191584.
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    80. 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. Angew Chem Int Ed Engl. 2009; 48(39):7171-5. PMID: 19708048.
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    81. 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. 2008 Aug 26; 47(34):8912-8. PMID: 18672906.
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    82. 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. 2008 Jul 22; 47(29):7684-94. PMID: 18572927.
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    83. Forconi M, Lee J, Lee JK, Piccirilli JA, Herschlag D. Functional identification of ligands for a catalytic metal ion in group I introns. Biochemistry. 2008 Jul 01; 47(26):6883-94. PMID: 18517225.
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    84. Piccirilli JA. Biochemistry. Toward understanding self-splicing. Science. 2008 Apr 04; 320(5872):56-7. PMID: 18388278.
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    85. 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. Bioorg Med Chem. 2008 May 15; 16(10):5754-60. PMID: 18397828.
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    86. 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. Proc Natl Acad Sci U S A. 2008 Mar 18; 105(11):4144-9. PMID: 18322008.
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    87. 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. Proc Natl Acad Sci U S A. 2008 Jan 08; 105(1):82-7. PMID: 18162543.
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    88. 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. J Org Chem. 2008 Jan 04; 73(1):309-11. PMID: 18052189.
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    89. Korennykh AV, Plantinga MJ, Correll CC, Piccirilli JA. Linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop RNA by restrictocin. Biochemistry. 2007 Nov 06; 46(44):12744-56. PMID: 17929942.
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    90. 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 Res. 2007; 35(18):6322-9. PMID: 17881375.
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    91. Forconi M, Piccirilli JA, Herschlag D. Modulation of individual steps in group I intron catalysis by a peripheral metal ion. RNA. 2007 Oct; 13(10):1656-67. PMID: 17720880.
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    92. 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. Org Lett. 2007 Aug 02; 9(16):3057-60. PMID: 17629287.
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    93. 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. Org Lett. 2007 Aug 02; 9(16):3009-12. PMID: 17629285.
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    94. Korennykh AV, Correll CC, Piccirilli JA. Evidence for the importance of electrostatics in the function of two distinct families of ribosome inactivating toxins. RNA. 2007 Sep; 13(9):1391-6. PMID: 17626843.
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    95. Ye JD, Barth CD, Anjaneyulu PS, Tuschl T, Piccirilli JA. Reactions of phosphate and phosphorothiolate diesters with nucleophiles: comparison of transition state structures. Org Biomol Chem. 2007 Aug 07; 5(15):2491-7. PMID: 17637971.
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    96. Gordon PM, Fong R, Piccirilli JA. A second divalent metal ion in the group II intron reaction center. Chem Biol. 2007 Jun; 14(6):607-12. PMID: 17584608.
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    97. Li NS, Piccirilli JA. Synthesis of 2'-C-alpha-(hydroxyalkyl) and 2'-C-alpha-alkylcytidine phosphoramidites: analogues for probing solvent interactions with RNA. J Org Chem. 2007 Feb 16; 72(4):1198-210. PMID: 17288373.
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    98. Lea CR, Piccirilli JA. 'Turning on' riboswitches to their antibacterial potential. Nat Chem Biol. 2007 Jan; 3(1):16-7. PMID: 17173021.
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    99. Ye JD, Li NS, Dai Q, Piccirilli JA. The mechanism of RNA strand scission: an experimental measure of the Brønsted coefficient, beta nuc. Angew Chem Int Ed Engl. 2007; 46(20):3714-7. PMID: 17415726.
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    100. Saikia M, Dai Q, Decatur WA, Fournier MJ, Piccirilli JA, Pan T. A systematic, ligation-based approach to study RNA modifications. RNA. 2006 Nov; 12(11):2025-33. PMID: 16963711.
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    101. Li NS, Piccirilli JA. Efficient synthesis of 2'-C-beta-methylguanosine. J Org Chem. 2006 May 12; 71(10):4018-20. PMID: 16674089.
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    102. Korennykh AV, Piccirilli JA, Correll CC. The electrostatic character of the ribosomal surface enables extraordinarily rapid target location by ribotoxins. Nat Struct Mol Biol. 2006 May; 13(5):436-43. PMID: 16604082.
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    103. Das SR, Fong R, Piccirilli JA. Nucleotide analogues to investigate RNA structure and function. Curr Opin Chem Biol. 2005 Dec; 9(6):585-93. PMID: 16242990.
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    104. Dai Q, Deb SK, Hougland JL, Piccirilli JA. Improved synthesis of 2'-amino-2'-deoxyguanosine and its phosphoramidite. Bioorg Med Chem. 2006 Feb 01; 14(3):705-13. PMID: 16202607.
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    105. Ye JD, Liao X, Piccirilli JA. Synthesis of 2'-C-difluoromethylribonucleosides and their enzymatic incorporation into oligonucleotides. J Org Chem. 2005 Sep 30; 70(20):7902-10. PMID: 16277309.
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    106. Hougland JL, Kravchuk AV, Herschlag D, Piccirilli JA. Functional identification of catalytic metal ion binding sites within RNA. PLoS Biol. 2005 Sep; 3(9):e277. PMID: 16092891.
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    107. Das SR, Piccirilli JA. General acid catalysis by the hepatitis delta virus ribozyme. Nat Chem Biol. 2005 Jun; 1(1):45-52. PMID: 16407993.
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    108. Edwards DC, Metz CE, Nishikawa RM. The hypervolume under the ROC hypersurface of "near-guessing" and "near-perfect" observers in N-class classification tasks. IEEE Trans Med Imaging. 2005 Mar; 24(3):293-9. PMID: 31840007.
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    109. Hougland JL, Deb SK, Maric D, Piccirilli JA. An atomic mutation cycle for exploring RNA's 2'-hydroxyl group. J Am Chem Soc. 2004 Oct 27; 126(42):13578-9. PMID: 15493890.
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    110. 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. J Org Chem. 2004 Jul 09; 69(14):4751-9. PMID: 15230598.
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    111. Dai Q, Piccirilli JA. Efficient synthesis of 2',3'-dideoxy-2'-amino-3'-thiouridine. Org Lett. 2004 Jun 24; 6(13):2169-72. PMID: 15200312.
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    112. Schwans JP, Li NS, Piccirilli JA. A packing-density metric for exploring the interior of folded RNA molecules. Angew Chem Int Ed Engl. 2004 Jun 07; 43(23):3033-7. PMID: 15188472.
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    113. 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. Chem Biol. 2004 Feb; 11(2):237-46. PMID: 15123285.
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    114. Li NS, Piccirilli JA. Synthesis of the phosphoramidite derivative of 2'-deoxy-2'-C-beta-methylcytidine. J Org Chem. 2003 Aug 22; 68(17):6799-802. PMID: 12919052.
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    115. Schwans JP, Cortez CN, Olvera JM, Piccirilli JA. 2'-mercaptonucleotide interference reveals regions of close packing within folded RNA molecules. J Am Chem Soc. 2003 Aug 20; 125(33):10012-8. PMID: 12914464.
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    116. Dai Q, Piccirilli JA. Synthesis of 2'-C-beta-fluoromethyluridine. Org Lett. 2003 Mar 20; 5(6):807-10. PMID: 12633077.
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    117. Szewczak AA, Kosek AB, Piccirilli JA, Strobel SA. Identification of an active site ligand for a group I ribozyme catalytic metal ion. Biochemistry. 2002 Feb 26; 41(8):2516-25. PMID: 11851398.
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    118. Kuo LY, Piccirilli JA. Leaving group stabilization by metal ion coordination and hydrogen bond donation is an evolutionarily conserved feature of group I introns. Biochim Biophys Acta. 2001 Dec 30; 1522(3):158-66. PMID: 11779630.
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    119. Gordon PM, Piccirilli JA. Metal ion coordination by the AGC triad in domain 5 contributes to group II intron catalysis. Nat Struct Biol. 2001 Oct; 8(10):893-8. PMID: 11573097.
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    120. 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. 2001 Sep 18; 40(37):10911-26. PMID: 11551186.
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    121. Shan S, Kravchuk AV, Piccirilli JA, Herschlag D. Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. Biochemistry. 2001 May 01; 40(17):5161-71. PMID: 11318638.
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    122. Li NS, Tang XQ, Piccirilli JA. 2'-C-branched ribonucleosides. 2. Synthesis of 2'-C-beta-trifluoromethyl pyrimidine ribonucleosides. Org Lett. 2001 Apr 05; 3(7):1025-8. PMID: 11277786.
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    123. 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. 2000 Oct 24; 39(42):12939-52. PMID: 11041859.
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    124. 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. 2000 May 30; 39(21):6410-21. PMID: 10828955.
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    125. 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 Res. 2000 Feb 01; 28(3):720-7. PMID: 10637323.
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    126. Yoshida A, Shan So, Herschlag D, Piccirilli JA. The role of the cleavage site 2'-hydroxyl in the Tetrahymena group I ribozyme reaction. Chem Biol. 2000 Feb; 7(2):85-96. PMID: 10662698.
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    127. 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. 2000 Feb; 6(2):199-205. PMID: 10688359.
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    128. Shan So, Yoshida A, Sun S, Piccirilli JA, Herschlag D. Three metal ions at the active site of the Tetrahymena group I ribozyme. Proc Natl Acad Sci U S A. 1999 Oct 26; 96(22):12299-304. PMID: 10535916.
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    129. Hamm ML, Piccirilli JA. Synthesis and Characterization of Oligonucleotides Containing 2'-S,3'-O-Cyclic Phosphorothiolate Termini. J Org Chem. 1999 Jul 23; 64(15):5700-5704. PMID: 11674644.
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    130. Sontheimer EJ, Gordon PM, Piccirilli JA. Metal ion catalysis during group II intron self-splicing: parallels with the spliceosome. Genes Dev. 1999 Jul 01; 13(13):1729-41. PMID: 10398685.
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    131. Yoshida A, Sun S, Piccirilli JA. A new metal ion interaction in the Tetrahymena ribozyme reaction revealed by double sulfur substitution. Nat Struct Biol. 1999 Apr; 6(4):318-21. PMID: 10201397.
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    132. Piccirilli JA. Do enzymes obey the Baldwin rules? A mechanistic imperative in enzymatic cyclization reactions. Chem Biol. 1999 Mar; 6(3):R59-64. PMID: 10074471.
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    133. 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. J Org Chem. 1999 Feb 05; 64(3):747-754. PMID: 11674142.
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    134. 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. 1999 Jan 12; 38(2):696-704. PMID: 9888810.
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    135. 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, Jenny TF, Jurczyk SC, Konig M, von Krosigk U, Lutz MJ, MacPherson LJ, Moroney SE, Muller E, Nambiar KP, Piccirilli JA, Switzer CY, Vogel JJ, Richert C, Roughton AL, Schmidt J, Schneider KC, Stackhouse J. Redesigning nucleic acids. Pure Appl Chem. 1998 Feb; 70(2):263-6. PMID: 11542721.
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    136. Sun S, Yoshida A, Piccirilli JA. Synthesis of 3'-thioribonucleosides and their incorporation into oligoribonucleotides via phosphoramidite chemistry. RNA. 1997 Nov; 3(11):1352-63. PMID: 9409625.
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    137. Sontheimer EJ, Sun S, Piccirilli JA. Metal ion catalysis during splicing of premessenger RNA. Nature. 1997 Aug 21; 388(6644):801-5. PMID: 9285595.
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    138. Hamm ML, Piccirilli JA. Incorporation of 2'-Deoxy-2'-mercaptocytidine into Oligonucleotides via Phosphoramidite Chemistry. J Org Chem. 1997 May 16; 62(10):3415-3420. PMID: 11671734.
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    139. Piccirilli JA. Origin of life. RNA seeks its maker. Nature. 1995 Aug 17; 376(6541):548-9. PMID: 7543655.
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    140. Piccirilli JA, Vyle JS, Caruthers MH, Cech TR. Metal ion catalysis in the Tetrahymena ribozyme reaction. Nature. 1993 Jan 07; 361(6407):85-8. PMID: 8421499.
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    141. Cech TR, Herschlag D, Piccirilli JA, Pyle AM. RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization. J Biol Chem. 1992 Sep 05; 267(25):17479-82. PMID: 1381347.
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    142. Piccirilli JA, McConnell TS, Zaug AJ, Noller HF, Cech TR. Aminoacyl esterase activity of the Tetrahymena ribozyme. Science. 1992 Jun 05; 256(5062):1420-4. PMID: 1604316.
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    143. 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. 1991 Oct 22; 30(42):10350-6. PMID: 1718418.
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    144. Moroney SE, Piccirilli JA. Abortive products as initiating nucleotides during transcription by T7 RNA polymerase. Biochemistry. 1991 Oct 22; 30(42):10343-9. PMID: 1718417.
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    145. 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. 1991 May 21; 30(20):4844-54. PMID: 2036355.
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    146. Piccirilli JA, Krauch T, Moroney SE, Benner SA. Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature. 1990 Jan 04; 343(6253):33-7. PMID: 1688644.
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    147. Benner SA, Allemann RK, Ellington AD, Ge L, Glasfeld A, Leanz GF, Krauch T, MacPherson LJ, Moroney S, Piccirilli JA, et al. Natural selection, protein engineering, and the last riboorganism: rational model building in biochemistry. Cold Spring Harb Symp Quant Biol. 1987; 52:53-63. PMID: 2456885.
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