Joseph A. Piccirilli

Biosciences Graduate Program Association
Publications
  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 May 05; 59(17):1665-1671. View in: PubMed

  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 Mar; 12(3):249-259. View in: PubMed

  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. View in: PubMed

  4. Ganguly A, Weissman BP, Piccirilli JA, York DM. Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme. ACS Catal. 2019 Dec 06; 9(12):10612-10617. View in: PubMed

  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. View in: PubMed

  6. 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. View in: PubMed

  7. 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. View in: PubMed

  8. 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. View in: PubMed

  9. 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. View in: PubMed

  10. 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. View in: PubMed

  11. 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. View in: PubMed

  12. 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. View in: PubMed

  13. 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. View in: PubMed

  14. 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. View in: PubMed

  15. Li NS, Lu J, Piccirilli JA. Synthesis of 5'-Thio-3'-O-ribonucleoside Phosphoramidites. J Org Chem. 2017 12 01; 82(23):12003-12013. View in: PubMed

  16. Harris ME, York DM, Piccirilli JA, Anderson VE. Kinetic Isotope Effect Analysis of RNA 2'-O-Transphosphorylation. Methods Enzymol. 2017; 596:433-457. View in: PubMed

  17. 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. View in: PubMed

  18. 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. View in: PubMed

  19. 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. View in: PubMed

  20. 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. View in: PubMed

  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. View in: PubMed

  22. 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. View in: PubMed

  23. 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. View in: PubMed

  24. Piccirilli JA, Staley JP. Reverse transcriptases lend a hand in splicing catalysis. Nat Struct Mol Biol. 2016 06 07; 23(6):507-9. View in: PubMed

  25. 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. View in: PubMed

  26. 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. View in: PubMed

  27. 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. View in: PubMed

  28. 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. View in: PubMed

  29. 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. View in: PubMed

  30. Harris ME, Piccirilli JA, York DM. Enzyme transition states from theory and experiment. Biochim Biophys Acta. 2015 Nov; 1854(11):1727-8. View in: PubMed

  31. 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. View in: PubMed

  32. 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. View in: PubMed

  33. 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. View in: PubMed

  34. 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. View in: PubMed

  35. 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. View in: PubMed

  36. 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. View in: PubMed

  37. 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. View in: PubMed

  38. Lu J, Koo SC, Li NS, Piccirilli JA. Synthesis of 2'-O-photocaged ribonucleoside phosphoramidites. Nucleosides Nucleotides Nucleic Acids. 2015; 34(2):114-29. View in: PubMed

  39. Shelke SA, Piccirilli JA. Origins of life: RNA made in its own mirror image. Nature. 2014 Nov 20; 515(7527):347-8. View in: PubMed

  40. 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. View in: PubMed

  41. 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. View in: PubMed

  42. 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. View in: PubMed

  43. 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. View in: PubMed

  44. 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. View in: PubMed

  45. 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. View in: PubMed

  46. 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. View in: PubMed

  47. 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. View in: PubMed

  48. 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. View in: PubMed

  49. Hernández AR, Piccirilli JA. Chemical origins of life: Prebiotic RNA unstuck. Nat Chem. 2013 May; 5(5):360-2. View in: PubMed

  50. 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. View in: PubMed

  51. 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. View in: PubMed

  52. 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. View in: PubMed

  53. Li NS, Piccirilli JA. Efficient synthesis of 2'-C-a-aminomethyl-2'-deoxynucleosides. Chem Commun (Camb). 2012 Sep 11; 48(70):8754-6. View in: PubMed

  54. 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. View in: PubMed

  55. 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. View in: PubMed

  56. 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. View in: PubMed

  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. View in: PubMed

  58. 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. View in: PubMed

  59. 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. View in: PubMed

  60. 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. View in: PubMed

  61. 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. View in: PubMed

  62. 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. View in: PubMed

  63. 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. View in: PubMed

  64. 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. View in: PubMed

  65. 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. View in: PubMed

  66. 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. View in: PubMed

  67. 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. View in: PubMed

  68. 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. View in: PubMed

  69. Frederiksen JK, Piccirilli JA. Separation of RNA phosphorothioate oligonucleotides by HPLC. Methods Enzymol. 2009; 468:289-309. View in: PubMed

  70. Hougland JL, Piccirilli JA. 2'-amino-modified ribonucleotides as probes for local interactions within RNA. Methods Enzymol. 2009; 468:107-25. View in: PubMed

  71. 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. View in: PubMed

  72. 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. View in: PubMed

  73. 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. View in: PubMed

  74. 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. View in: PubMed

  75. 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. View in: PubMed

  76. 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. View in: PubMed

  77. 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. View in: PubMed

  78. 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. View in: PubMed

  79. Frederiksen JK, Piccirilli JA. Identification of catalytic metal ion ligands in ribozymes. Methods. 2009 Oct; 49(2):148-66. View in: PubMed

  80. 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. View in: PubMed

  81. Li NS, Lu J, Piccirilli JA. Synthesis of 2'-C-beta-methyl-2'-deoxyguanosine. J Org Chem. 2009 Mar 06; 74(5):2227-30. View in: PubMed

  82. 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. View in: PubMed

  83. 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. View in: PubMed

  84. 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. View in: PubMed

  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. View in: PubMed

  86. Piccirilli JA. Biochemistry. Toward understanding self-splicing. Science. 2008 Apr 04; 320(5872):56-7. View in: PubMed

  87. 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. View in: PubMed

  88. 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. View in: PubMed

  89. 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. View in: PubMed

  90. 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. View in: PubMed

  91. 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. View in: PubMed

  92. 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. View in: PubMed

  93. 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. View in: PubMed

  94. 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. View in: PubMed

  95. 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. View in: PubMed

  96. 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. View in: PubMed

  97. 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. View in: PubMed

  98. 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. View in: PubMed

  99. 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. View in: PubMed

  100. Lea CR, Piccirilli JA. 'Turning on' riboswitches to their antibacterial potential. Nat Chem Biol. 2007 Jan; 3(1):16-7. View in: PubMed

  101. 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. View in: PubMed

  102. Li NS, Piccirilli JA. Efficient synthesis of 2'-C-beta-methylguanosine. J Org Chem. 2006 May 12; 71(10):4018-20. View in: PubMed

  103. 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. View in: PubMed

  104. Das SR, Piccirilli JA. General acid catalysis by the hepatitis delta virus ribozyme. Nat Chem Biol. 2005 Jun; 1(1):45-52. View in: PubMed

  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. View in: PubMed

  106. Das SR, Fong R, Piccirilli JA. Nucleotide analogues to investigate RNA structure and function. Curr Opin Chem Biol. 2005 Dec; 9(6):585-93. View in: PubMed

  107. 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. View in: PubMed

  108. 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. View in: PubMed

  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. View in: PubMed

  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. View in: PubMed

  111. Dai Q, Piccirilli JA. Efficient synthesis of 2',3'-dideoxy-2'-amino-3'-thiouridine. Org Lett. 2004 Jun 24; 6(13):2169-72. View in: PubMed

  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. View in: PubMed

  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. View in: PubMed

  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. View in: PubMed

  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. View in: PubMed

  116. Dai Q, Piccirilli JA. Synthesis of 2'-C-beta-fluoromethyluridine. Org Lett. 2003 Mar 20; 5(6):807-10. View in: PubMed

  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. View in: PubMed

  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. View in: PubMed

  119. 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. View in: PubMed

  120. 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. View in: PubMed

  121. 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. View in: PubMed

  122. 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. View in: PubMed

  123. 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. View in: PubMed

  124. 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. View in: PubMed

  125. 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. View in: PubMed

  126. 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. View in: PubMed

  127. 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. View in: PubMed

  128. 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. View in: PubMed

  129. 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. View in: PubMed

  130. 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. View in: PubMed

  131. 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. View in: PubMed

  132. 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. View in: PubMed

  133. 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. View in: PubMed

  134. 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. View in: PubMed

  135. Piccirilli JA. Do enzymes obey the Baldwin rules? A mechanistic imperative in enzymatic cyclization reactions. Chem Biol. 1999 Mar; 6(3):R59-64. View in: PubMed

  136. 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. View in: PubMed

  137. 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. View in: PubMed

  138. Sontheimer EJ, Sun S, Piccirilli JA. Metal ion catalysis during splicing of premessenger RNA. Nature. 1997 Aug 21; 388(6644):801-5. View in: PubMed

  139. Piccirilli JA, Vyle JS, Caruthers MH, Cech TR. Metal ion catalysis in the Tetrahymena ribozyme reaction. Nature. 1993 Jan 07; 361(6407):85-8. View in: PubMed

  140. Piccirilli JA. Origin of life. RNA seeks its maker. Nature. 1995 Aug 17; 376(6541):548-9. View in: PubMed

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  142. 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. View in: PubMed

  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. View in: PubMed

  144. Moroney SE, Piccirilli JA. Abortive products as initiating nucleotides during transcription by T7 RNA polymerase. Biochemistry. 1991 Oct 22; 30(42):10343-9. View in: PubMed

  145. 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. View in: PubMed

  146. 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. View in: PubMed

  147. 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. View in: PubMed