Joseph Piccirilli to Nucleic Acid Conformation
This is a "connection" page, showing publications Joseph Piccirilli has written about Nucleic Acid Conformation.
Connection Strength
4.358
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Linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop RNA by restrictocin. Biochemistry. 2007 Nov 06; 46(44):12744-56.
Score: 0.236
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General acid catalysis by the hepatitis delta virus ribozyme. Nat Chem Biol. 2005 Jun; 1(1):45-52.
Score: 0.199
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RNA-Puzzles Round V: blind predictions of 23 RNA structures. Nat Methods. 2025 Feb; 22(2):399-411.
Score: 0.194
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Unraveling RNA Conformation Dynamics in Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-like Episode Syndrome with Solid-State Nanopores. ACS Nano. 2024 07 02; 18(26):17240-17250.
Score: 0.188
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Structural Basis for Fluorescence Activation by Pepper RNA. ACS Chem Biol. 2022 07 15; 17(7):1866-1875.
Score: 0.163
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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: 0.159
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The SARS-CoV-2 Programmed -1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 Å Using Chaperone-Assisted RNA Crystallography. ACS Chem Biol. 2021 08 20; 16(8):1469-1481.
Score: 0.153
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The hammerhead self-cleaving motif as a precursor to complex endonucleolytic ribozymes. RNA. 2021 09; 27(9):1017-1024.
Score: 0.152
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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.
Score: 0.137
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A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nat Commun. 2019 08 09; 10(1):3629.
Score: 0.134
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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: 0.123
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Synthesizing topological structures containing RNA. Nat Commun. 2017 03 31; 8:14936.
Score: 0.114
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Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment. J Mol Biol. 2016 10 09; 428(20):4100-4114.
Score: 0.109
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Crystal structure of the Varkud satellite ribozyme. Nat Chem Biol. 2015 Nov; 11(11):840-6.
Score: 0.102
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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.
Score: 0.101
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Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism. Biochim Biophys Acta. 2015 Nov; 1854(11):1801-8.
Score: 0.100
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A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Nat Chem Biol. 2014 Aug; 10(8):686-91.
Score: 0.094
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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.
Score: 0.088
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Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding. RNA. 2012 Jun; 18(6):1123-41.
Score: 0.081
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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: 0.078
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Synthesis, properties, and applications of oligonucleotides containing an RNA dinucleotide phosphorothiolate linkage. Acc Chem Res. 2011 Dec 20; 44(12):1257-69.
Score: 0.077
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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: 0.073
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Biochemistry. Toward understanding self-splicing. Science. 2008 Apr 04; 320(5872):56-7.
Score: 0.061
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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.
Score: 0.061
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Synthetic antibodies for specific recognition and crystallization of structured RNA. Proc Natl Acad Sci U S A. 2008 Jan 08; 105(1):82-7.
Score: 0.060
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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.
Score: 0.060
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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.
Score: 0.056
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A universal Fab targeting a conserved U1A-RNA epitope for RNA structure determination by cryo-EM. Nucleic Acids Res. 2026 May 20; 54(10).
Score: 0.054
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Nucleotide analogues to investigate RNA structure and function. Curr Opin Chem Biol. 2005 Dec; 9(6):585-93.
Score: 0.051
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Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers. Proteins. 2026 Jan; 94(1):51-78.
Score: 0.051
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Mechanistic studies of small molecule ligands selective to RNA single G bulges. Nucleic Acids Res. 2025 Jun 20; 53(12).
Score: 0.050
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An atomic mutation cycle for exploring RNA's 2'-hydroxyl group. J Am Chem Soc. 2004 Oct 27; 126(42):13578-9.
Score: 0.048
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Post-transcriptional methylation of mitochondrial-tRNA differentially contributes to mitochondrial pathology. Nat Commun. 2024 10 18; 15(1):9008.
Score: 0.048
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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 08 27; 121(35):e2410206121.
Score: 0.047
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A packing-density metric for exploring the interior of folded RNA molecules. Angew Chem Int Ed Engl. 2004 Jun 07; 43(23):3033-7.
Score: 0.047
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2'-mercaptonucleotide interference reveals regions of close packing within folded RNA molecules. J Am Chem Soc. 2003 Aug 20; 125(33):10012-8.
Score: 0.044
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Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis. Biochemistry. 2023 07 04; 62(13):2079-2092.
Score: 0.044
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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: 0.043
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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: 0.036
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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: 0.035
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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.
Score: 0.035
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Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures. Nat Chem. 2020 03; 12(3):249-259.
Score: 0.035
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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: 0.033
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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: 0.033
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Hachimoji DNA and RNA: A genetic system with eight building blocks. Science. 2019 02 22; 363(6429):884-887.
Score: 0.032
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Synthesis of 3'-thioribonucleosides and their incorporation into oligoribonucleotides via phosphoramidite chemistry. RNA. 1997 Nov; 3(11):1352-63.
Score: 0.030
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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: 0.028
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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.
Score: 0.027
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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: 0.026
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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: 0.025
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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: 0.025
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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.
Score: 0.025
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Evidence for a group II intron-like catalytic triplex in the spliceosome. Nat Struct Mol Biol. 2014 May; 21(5):464-471.
Score: 0.023
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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: 0.023
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Recognition of guanosine by dissimilar tRNA methyltransferases. RNA. 2012 Sep; 18(9):1687-701.
Score: 0.021
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Aminoacyl esterase activity of the Tetrahymena ribozyme. Science. 1992 Jun 05; 256(5062):1420-4.
Score: 0.020
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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: 0.019
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The ribotoxin restrictocin recognizes its RNA substrate by selective engagement of active site residues. Biochemistry. 2011 Apr 12; 50(14):3004-13.
Score: 0.019
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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: 0.018
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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: 0.017
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Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature. 1990 Jan 04; 343(6253):33-7.
Score: 0.017
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Crystal structure of the catalytic core of an RNA-polymerase ribozyme. Science. 2009 Nov 27; 326(5957):1271-5.
Score: 0.017
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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: 0.016
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Electrostatic interactions guide the active site face of a structure-specific ribonuclease to its RNA substrate. Biochemistry. 2008 Aug 26; 47(34):8912-8.
Score: 0.016
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The electrostatic character of the ribosomal surface enables extraordinarily rapid target location by ribotoxins. Nat Struct Mol Biol. 2006 May; 13(5):436-43.
Score: 0.013
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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: 0.009
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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: 0.005