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Joseph A. Piccirilli

Professor
jpicciri@uchicago.edu
Biosciences Graduate Program Association
Publications

  1. Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. J Am Chem Soc. 2023 02 08; 145(5):2830-2839. View in: PubMed

  2. Demethylation of dimethyl phosphonate esters with sodium ethanethiolate: Improved synthesis of 5'-methylene substituted 2',5'-deoxyribonucleotides. Nucleosides Nucleotides Nucleic Acids. 2023 Jan 11; 1-9. View in: PubMed

  3. Structural Basis for Fluorescence Activation by Pepper RNA. ACS Chem Biol. 2022 07 15; 17(7):1866-1875. View in: PubMed

  4. Sub-3-? cryo-EM structure of RNA enabled by engineered homomeric self-assembly. Nat Methods. 2022 05; 19(5):576-585. View in: PubMed

  5. Structural basis for substrate binding and catalysis by a self-alkylating ribozyme. Nat Chem Biol. 2022 04; 18(4):376-384. View in: PubMed

  6. Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution. Sci Adv. 2021 Sep 24; 7(39):eabf4459. View in: PubMed

  7. Synthesis of Oligoribonucleotides Containing a 2'-Amino-5'-S-phosphorothiolate Linkage. J Org Chem. 2021 10 01; 86(19):13231-13244. View in: PubMed

  8. The SARS-CoV-2 Programmed -1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 ? Using Chaperone-Assisted RNA Crystallography. ACS Chem Biol. 2021 08 20; 16(8):1469-1481. View in: PubMed

  9. The hammerhead self-cleaving motif as a precursor to complex endonucleolytic ribozymes. RNA. 2021 09; 27(9):1017-1024. View in: PubMed

  10. The Varkud Satellite Ribozyme: A Thirty-Year Journey through Biochemistry, Crystallography, and Computation. Acc Chem Res. 2021 06 01; 54(11):2591-2602. View in: PubMed

  11. 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. View in: PubMed

  12. Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures. Nat Chem. 2020 03; 12(3):249-259. View in: PubMed

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. Hachimoji DNA and RNA: A genetic system with eight building blocks. Science. 2019 02 22; 363(6429):884-887. View in: PubMed

  22. 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

  23. Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State. Biochemistry. 2018 06 26; 57(25):3465-3472. View in: PubMed

  24. 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

  25. Synthesis of 5'-Thio-3'-O-ribonucleoside Phosphoramidites. J Org Chem. 2017 12 01; 82(23):12003-12013. View in: PubMed

  26. Kinetic Isotope Effect Analysis of RNA 2'-O-Transphosphorylation. Methods Enzymol. 2017; 596:433-457. View in: PubMed

  27. 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

  28. Synthesizing topological structures containing RNA. Nat Commun. 2017 03 31; 8:14936. View in: PubMed

  29. 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

  30. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA. 2017 05; 23(5):655-672. View in: PubMed

  31. 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

  32. Efficient Synthetic Approach to Linear Dasatinib-DNA Conjugates by Click Chemistry. Bioconjug Chem. 2016 Oct 19; 27(10):2575-2579. View in: PubMed

  33. 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

  34. Reverse transcriptases lend a hand in splicing catalysis. Nat Struct Mol Biol. 2016 06 07; 23(6):507-9. View in: PubMed

  35. Drug conjugated nanoparticles activated by cancer cell specific mRNA. Oncotarget. 2016 Jun 21; 7(25):38243-38256. View in: PubMed

  36. 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

  37. 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

  38. 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

  39. Crystal structure of the Varkud satellite ribozyme. Nat Chem Biol. 2015 Nov; 11(11):840-6. View in: PubMed

  40. Enzyme transition states from theory and experiment. Biochim Biophys Acta. 2015 Nov; 1854(11):1727-8. View in: PubMed

  41. 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

  42. 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

  43. Spinach RNA aptamer detects lead(II) with high selectivity. Chem Commun (Camb). 2015 May 28; 51(43):9034-7. View in: PubMed

  44. 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

  45. Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism. Biochim Biophys Acta. 2015 Nov; 1854(11):1801-8. View in: PubMed

  46. Heavy atom labeled nucleotides for measurement of kinetic isotope effects. Biochim Biophys Acta. 2015 Nov; 1854(11):1737-45. View in: PubMed

  47. 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

  48. Synthesis of 2'-O-photocaged ribonucleoside phosphoramidites. Nucleosides Nucleotides Nucleic Acids. 2015; 34(2):114-29. View in: PubMed

  49. Origins of life: RNA made in its own mirror image. Nature. 2014 Nov 20; 515(7527):347-8. View in: PubMed

  50. Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by a? T cells. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):E4648-57. View in: PubMed

  51. 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

  52. A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Nat Chem Biol. 2014 Aug; 10(8):686-91. View in: PubMed

  53. 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

  54. 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

  55. RNA catalyses nuclear pre-mRNA splicing. Nature. 2013 Nov 14; 503(7475):229-34. View in: PubMed

  56. 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

  57. 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

  58. Highly stereocontrolled total synthesis of ?-D-mannosyl phosphomycoketide: a natural product from Mycobacterium tuberculosis. J Org Chem. 2013 Jun 21; 78(12):5970-86. View in: PubMed

  59. Chemical origins of life: Prebiotic RNA unstuck. Nat Chem. 2013 May; 5(5):360-2. View in: PubMed

  60. 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

  61. 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

  62. Recognition of guanosine by dissimilar tRNA methyltransferases. RNA. 2012 Sep; 18(9):1687-701. View in: PubMed

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

  64. 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

  65. 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

  66. 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

  67. 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

  68. 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

  69. 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

  70. 2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA. Chem Biol. 2011 Aug 26; 18(8):949-54. View in: PubMed

  71. The mechanism of peptidyl transfer catalysis by the ribosome. Annu Rev Biochem. 2011; 80:527-55. View in: PubMed

  72. 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

  73. 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

  74. 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

  75. 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

  76. The 2.5 ? 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

  77. 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

  78. 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

  79. Separation of RNA phosphorothioate oligonucleotides by HPLC. Methods Enzymol. 2009; 468:289-309. View in: PubMed

  80. 2'-amino-modified ribonucleotides as probes for local interactions within RNA. Methods Enzymol. 2009; 468:107-25. View in: PubMed

  81. Sin resolvase catalytic activity and oligomerization state are tightly coupled. J Mol Biol. 2010 Nov 19; 404(1):16-33. View in: PubMed

  82. 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

  83. 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

  84. 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

  85. 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

  86. Crystal structure of the catalytic core of an RNA-polymerase ribozyme. Science. 2009 Nov 27; 326(5957):1271-5. View in: PubMed

  87. 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

  88. 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

  89. Identification of catalytic metal ion ligands in ribozymes. Methods. 2009 Oct; 49(2):148-66. View in: PubMed

  90. Efficient chemical synthesis of AppDNA by adenylation of immobilized DNA-5'-monophosphate. Org Lett. 2009 Mar 05; 11(5):1067-70. View in: PubMed

  91. Synthesis of 2'-C-beta-methyl-2'-deoxyguanosine. J Org Chem. 2009 Mar 06; 74(5):2227-30. View in: PubMed

  92. 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

  93. 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

  94. Functional identification of ligands for a catalytic metal ion in group I introns. Biochemistry. 2008 Jul 01; 47(26):6883-94. View in: PubMed

  95. 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

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

  97. 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

  98. 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

  99. 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

  100. 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

  101. 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

  102. Modulation of individual steps in group I intron catalysis by a peripheral metal ion. RNA. 2007 Oct; 13(10):1656-67. View in: PubMed

  103. 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

  104. 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

  105. 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

  106. 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

  107. A second divalent metal ion in the group II intron reaction center. Chem Biol. 2007 Jun; 14(6):607-12. View in: PubMed

  108. The mechanism of RNA strand scission: an experimental measure of the Br?nsted coefficient, beta nuc. Angew Chem Int Ed Engl. 2007; 46(20):3714-7. View in: PubMed

  109. 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

  110. 'Turning on' riboswitches to their antibacterial potential. Nat Chem Biol. 2007 Jan; 3(1):16-7. View in: PubMed

  111. A systematic, ligation-based approach to study RNA modifications. RNA. 2006 Nov; 12(11):2025-33. View in: PubMed

  112. Efficient synthesis of 2'-C-beta-methylguanosine. J Org Chem. 2006 May 12; 71(10):4018-20. View in: PubMed

  113. 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

  114. General acid catalysis by the hepatitis delta virus ribozyme. Nat Chem Biol. 2005 Jun; 1(1):45-52. View in: PubMed

  115. Synthesis of 2'-C-difluoromethylribonucleosides and their enzymatic incorporation into oligonucleotides. J Org Chem. 2005 Sep 30; 70(20):7902-10. View in: PubMed

  116. Nucleotide analogues to investigate RNA structure and function. Curr Opin Chem Biol. 2005 Dec; 9(6):585-93. View in: PubMed

  117. Improved synthesis of 2'-amino-2'-deoxyguanosine and its phosphoramidite. Bioorg Med Chem. 2006 Feb 01; 14(3):705-13. View in: PubMed

  118. Functional identification of catalytic metal ion binding sites within RNA. PLoS Biol. 2005 Sep; 3(9):e277. View in: PubMed

  119. 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

  120. 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

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

  122. 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

  123. 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

  124. 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

  125. 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

  126. Synthesis of 2'-C-beta-fluoromethyluridine. Org Lett. 2003 Mar 20; 5(6):807-10. View in: PubMed

  127. 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

  128. 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

  129. 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

  130. 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

  131. Incorporation of 2'-Deoxy-2'-mercaptocytidine into Oligonucleotides via Phosphoramidite Chemistry. J Org Chem. 1997 May 16; 62(10):3415-3420. View in: PubMed

  132. 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

  133. 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

  134. Redesigning nucleic acids. Pure Appl Chem. 1998 Feb; 70(2):263-6. View in: PubMed

  135. Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. Biochemistry. 2001 May 01; 40(17):5161-71. View in: PubMed

  136. 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

  137. 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

  138. 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

  139. 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

  140. 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

  141. 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

  142. 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

  143. 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

  144. 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

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

  146. 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

  147. Synthesis of 3'-thioribonucleosides and their incorporation into oligoribonucleotides via phosphoramidite chemistry. RNA. 1997 Nov; 3(11):1352-63. View in: PubMed

  148. Metal ion catalysis during splicing of premessenger RNA. Nature. 1997 Aug 21; 388(6644):801-5. View in: PubMed

  149. Metal ion catalysis in the Tetrahymena ribozyme reaction. Nature. 1993 Jan 07; 361(6407):85-8. View in: PubMed

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

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  152. 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

  153. 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

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

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  156. Aminoacyl esterase activity of the Tetrahymena ribozyme. Science. 1992 Jun 05; 256(5062):1420-4. View in: PubMed

  157. 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
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