Joseph Piccirilli to RNA, Catalytic
This is a "connection" page, showing publications Joseph Piccirilli has written about RNA, Catalytic.
Connection Strength
11.199
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Structural basis for substrate binding and catalysis by a self-alkylating ribozyme. Nat Chem Biol. 2022 04; 18(4):376-384.
Score: 0.689
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Synthesis of Oligoribonucleotides Containing a 2'-Amino-5'-S-phosphorothiolate Linkage. J Org Chem. 2021 10 01; 86(19):13231-13244.
Score: 0.673
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The hammerhead self-cleaving motif as a precursor to complex endonucleolytic ribozymes. RNA. 2021 09; 27(9):1017-1024.
Score: 0.661
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The Varkud Satellite Ribozyme: A Thirty-Year Journey through Biochemistry, Crystallography, and Computation. Acc Chem Res. 2021 06 01; 54(11):2591-2602.
Score: 0.657
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Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State. Biochemistry. 2018 06 26; 57(25):3465-3472.
Score: 0.534
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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.
Score: 0.503
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Crystal structure of the Varkud satellite ribozyme. Nat Chem Biol. 2015 Nov; 11(11):840-6.
Score: 0.445
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Origins of life: RNA made in its own mirror image. Nature. 2014 Nov 20; 515(7527):347-8.
Score: 0.418
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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.
Score: 0.340
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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.
Score: 0.339
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A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination. Nat Struct Mol Biol. 2011 Jan; 18(1):100-6.
Score: 0.319
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Identification of catalytic metal ion ligands in ribozymes. Methods. 2009 Oct; 49(2):148-66.
Score: 0.291
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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.
Score: 0.269
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Biochemistry. Toward understanding self-splicing. Science. 2008 Apr 04; 320(5872):56-7.
Score: 0.265
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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.
Score: 0.265
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A second divalent metal ion in the group II intron reaction center. Chem Biol. 2007 Jun; 14(6):607-12.
Score: 0.250
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Functional identification of catalytic metal ion binding sites within RNA. PLoS Biol. 2005 Sep; 3(9):e277.
Score: 0.221
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General acid catalysis by the hepatitis delta virus ribozyme. Nat Chem Biol. 2005 Jun; 1(1):45-52.
Score: 0.216
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A potential role for RNA aminoacylation prior to its role in peptide synthesis. Proc Natl Acad Sci U S A. 2024 Aug 27; 121(35):e2410206121.
Score: 0.206
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Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis. Biochemistry. 2023 07 04; 62(13):2079-2092.
Score: 0.190
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Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. J Am Chem Soc. 2023 02 08; 145(5):2830-2839.
Score: 0.185
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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.
Score: 0.172
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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.
Score: 0.168
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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.
Score: 0.158
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The role of the cleavage site 2'-hydroxyl in the Tetrahymena group I ribozyme reaction. Chem Biol. 2000 Feb; 7(2):85-96.
Score: 0.150
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Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme. Nat Chem. 2020 02; 12(2):193-201.
Score: 0.150
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The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design. RNA. 2020 02; 26(2):111-125.
Score: 0.149
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Metal ion catalysis during group II intron self-splicing: parallels with the spliceosome. Genes Dev. 1999 Jul 01; 13(13):1729-41.
Score: 0.144
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Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes. J Am Chem Soc. 2019 05 15; 141(19):7865-7875.
Score: 0.143
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A new metal ion interaction in the Tetrahymena ribozyme reaction revealed by double sulfur substitution. Nat Struct Biol. 1999 Apr; 6(4):318-21.
Score: 0.142
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RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA. 2017 05; 23(5):655-672.
Score: 0.122
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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.
Score: 0.112
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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.
Score: 0.110
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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.
Score: 0.108
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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.
Score: 0.100
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Metal ion catalysis in the Tetrahymena ribozyme reaction. Nature. 1993 Jan 07; 361(6407):85-8.
Score: 0.092
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General acid-base catalysis mediated by nucleobases in the hairpin ribozyme. J Am Chem Soc. 2012 Oct 10; 134(40):16717-24.
Score: 0.090
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Aminoacyl esterase activity of the Tetrahymena ribozyme. Science. 1992 Jun 05; 256(5062):1420-4.
Score: 0.088
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2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA. Chem Biol. 2011 Aug 26; 18(8):949-54.
Score: 0.084
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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.
Score: 0.082
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A general and efficient approach for the construction of RNA oligonucleotides containing a 5'-phosphorothiolate linkage. Nucleic Acids Res. 2011 Mar; 39(5):e31.
Score: 0.080
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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.
Score: 0.077
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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.
Score: 0.076
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Crystal structure of the catalytic core of an RNA-polymerase ribozyme. Science. 2009 Nov 27; 326(5957):1271-5.
Score: 0.074
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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.
Score: 0.070
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Modulation of individual steps in group I intron catalysis by a peripheral metal ion. RNA. 2007 Oct; 13(10):1656-67.
Score: 0.063
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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.
Score: 0.063
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Nucleotide analogues to investigate RNA structure and function. Curr Opin Chem Biol. 2005 Dec; 9(6):585-93.
Score: 0.056
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RNA-Puzzles Round V: blind predictions of 23 RNA structures. Nat Methods. 2025 Feb; 22(2):399-411.
Score: 0.053
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Identification of an active site ligand for a group I ribozyme catalytic metal ion. Biochemistry. 2002 Feb 26; 41(8):2516-25.
Score: 0.043
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Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. Biochemistry. 2001 May 01; 40(17):5161-71.
Score: 0.041
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Investigation of the proposed interdomain ribose zipper in hairpin ribozyme cleavage using 2'-modified nucleosides. Biochemistry. 2000 May 30; 39(21):6410-21.
Score: 0.038
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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.
Score: 0.038
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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.
Score: 0.037
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Origin of life. RNA seeks its maker. Nature. 1995 Aug 17; 376(6541):548-9.
Score: 0.028
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RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization. J Biol Chem. 1992 Sep 05; 267(25):17479-82.
Score: 0.023
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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.
Score: 0.021
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Functional identification of ligands for a catalytic metal ion in group I introns. Biochemistry. 2008 Jul 01; 47(26):6883-94.
Score: 0.017