Joseph A Piccirilli

Joseph A Piccirilli

UNVERIFIED PROFILE

Are you Joseph A Piccirilli?   Register this Author

Register author
Joseph A Piccirilli

Joseph A Piccirilli

Publications by authors named "Joseph A Piccirilli"

Are you Joseph A Piccirilli?   Register this Author

100Publications

2300Reads

39Profile Views

Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures.

Nat Chem 2020 Mar 20;12(3):249-259. Epub 2020 Jan 20.

Department of Chemistry, University of Chicago, Chicago, IL, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41557-019-0406-7DOI Listing
March 2020

The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design.

RNA 2020 Feb 27;26(2):111-125. Epub 2019 Nov 27.

Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1261/rna.071894.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6961537PMC
February 2020

Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme.

Nat Chem 2020 Feb 20;12(2):193-201. Epub 2020 Jan 20.

Laboratory for Biomolecular Simulation Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41557-019-0391-xDOI Listing
February 2020

Synthetic Antibody Binding to a Preorganized RNA Domain of Hepatitis C Virus Internal Ribosome Entry Site Inhibits Translation.

ACS Chem Biol 2020 Jan 10;15(1):205-216. Epub 2019 Dec 10.

Department of Biochemistry and Molecular Biology , The University of Chicago , Chicago , Illinois 60637 , United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acschembio.9b00785DOI Listing
January 2020

Reinvestigating the synthesis and efficacy of small benzimidazole derivatives as presequence protease enhancers.

Eur J Med Chem 2019 Dec 1;184:111746. Epub 2019 Oct 1.

Ben May Cancer Research Institute, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ejmech.2019.111746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874713PMC
December 2019

Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme.

ACS Catal 2019 Dec 27;9(12):10612-10617. Epub 2019 Oct 27.

Laboratory for Biomolecular Simulation Research, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854-8087, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acscatal.9b02035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6902279PMC
December 2019

An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes.

ACS Chem Biol 2019 06 7;14(6):1068-1076. Epub 2019 Jun 7.

Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854-8087 , United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acschembio.9b00202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6661149PMC
June 2019

Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes.

J Am Chem Soc 2019 May 2;141(19):7865-7875. Epub 2019 May 2.

Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex , The University of Dundee , Dow Street , Dundee DD1 5EH , U.K.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jacs.9b02141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6523996PMC
May 2019

Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State.

Biochemistry 2018 06 17;57(25):3465-3472. Epub 2018 May 17.

Department of Biochemistry and Molecular Biology and Department of Chemistry , University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.biochem.8b00031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6693346PMC
June 2018

Kinetic Isotope Effect Analysis of RNA 2'-O-Transphosphorylation.

Methods Enzymol 2017 5;596:433-457. Epub 2017 Sep 5.

Case Western Reserve University School of Medicine, Cleveland, OH, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/bs.mie.2017.07.017DOI Listing
May 2018

Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography.

Nucleic Acids Res 2018 03;46(5):2624-2635

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkx1292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861428PMC
March 2018

Synthesis of 5'-Thio-3'-O-ribonucleoside Phosphoramidites.

J Org Chem 2017 12 31;82(23):12003-12013. Epub 2017 Oct 31.

Department of Biochemistry & Molecular Biology and Department of Chemistry, University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.joc.7b01484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6557410PMC
December 2017

Structural Basis for Substrate Helix Remodeling and Cleavage Loop Activation in the Varkud Satellite Ribozyme.

J Am Chem Soc 2017 07 3;139(28):9591-9597. Epub 2017 Jul 3.

Department of Chemistry, and ‡Department of Biochemistry and Molecular Biology, The University of Chicago , Chicago, Illinois 60637, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jacs.7b03655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5929484PMC
July 2017

Synthesizing topological structures containing RNA.

Nat Commun 2017 03 31;8:14936. Epub 2017 Mar 31.

Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms14936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381007PMC
March 2017

Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment.

J Mol Biol 2016 10 2;428(20):4100-4114. Epub 2016 Sep 2.

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmb.2016.08.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5178103PMC
October 2016

Efficient Synthetic Approach to Linear Dasatinib-DNA Conjugates by Click Chemistry.

Bioconjug Chem 2016 Oct 6;27(10):2575-2579. Epub 2016 Oct 6.

Department of Biochemistry & Molecular Biology and ‡Department of Chemistry, University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.bioconjchem.6b00557DOI Listing
October 2016

Reverse transcriptases lend a hand in splicing catalysis.

Nat Struct Mol Biol 2016 06;23(6):507-9

Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb.3242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6548540PMC
June 2016

Drug conjugated nanoparticles activated by cancer cell specific mRNA.

Oncotarget 2016 Jun;7(25):38243-38256

Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Minnesota, Minneapolis, MN, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.18632/oncotarget.9430DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5122386PMC
June 2016

Molecular Analysis of Lipid-Reactive Vδ1 γδ T Cells Identified by CD1c Tetramers.

J Immunol 2016 Feb 11;196(4):1933-42. Epub 2016 Jan 11.

Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637; Committee on Immunology, University of Chicago, Chicago, IL 60637;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4049/jimmunol.1502202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744554PMC
February 2016

An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.

RNA 2016 Jan 13;22(1):32-48. Epub 2015 Nov 13.

Department of Biochemistry, Stanford University, Stanford, California 94305, USA Department of Chemical Engineering, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, USA Department of Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, USA Department of Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1261/rna.053710.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691833PMC
January 2016

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 23;1854(11):1795-800. Epub 2015 Mar 23.

Department of Biochemistry, Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, United States. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbapap.2015.02.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4743498PMC
November 2015

Heavy atom labeled nucleotides for measurement of kinetic isotope effects.

Biochim Biophys Acta 2015 Nov 27;1854(11):1737-45. Epub 2015 Mar 27.

Department of Chemistry, University of Chicago, Chicago, IL, USA; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbapap.2015.03.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4584197PMC
November 2015

Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism.

Biochim Biophys Acta 2015 Nov 30;1854(11):1801-8. Epub 2015 Apr 30.

Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, United States; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbapap.2015.04.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4604014PMC
November 2015

Enzyme transition states from theory and experiment.

Biochim Biophys Acta 2015 Nov 22;1854(11):1727-8. Epub 2015 Aug 22.

Effect of Zn(2+) binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbapap.2015.08.006DOI Listing
November 2015

Crystal structure of the Varkud satellite ribozyme.

Nat Chem Biol 2015 Nov 28;11(11):840-6. Epub 2015 Sep 28.

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nchembio.1929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618023PMC
November 2015

Determination of hepatitis delta virus ribozyme N(-1) nucleobase and functional group specificity using internal competition kinetics.

Anal Biochem 2015 Aug 1;483:12-20. Epub 2015 May 1.

Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ab.2015.04.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461535PMC
August 2015

A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair.

Angew Chem Int Ed Engl 2015 Aug 16;54(34):9853-6. Epub 2015 Jul 16.

Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA).

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/anie.201504731DOI Listing
August 2015

Synthesis of 2'-O-photocaged ribonucleoside phosphoramidites.

Nucleosides Nucleotides Nucleic Acids 2015 ;34(2):114-29

a Department of Biochemistry & Molecular Biology and Department of Chemistry , University of Chicago , Chicago , Illinois , United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/15257770.2014.965256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461471PMC
July 2015

Transition State Features in the Hepatitis Delta Virus Ribozyme Reaction Revealed by Atomic Perturbations.

J Am Chem Soc 2015 Jul 14;137(28):8973-82. Epub 2015 Jul 14.

§Department of Biochemistry and Center for Proteomics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jacs.5b01189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758122PMC
July 2015

Spinach RNA aptamer detects lead(II) with high selectivity.

Chem Commun (Camb) 2015 May;51(43):9034-7

Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/c5cc01526jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755583PMC
May 2015

Origins of life: RNA made in its own mirror image.

Nature 2014 Nov 29;515(7527):347-8. Epub 2014 Oct 29.

1] Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA. [2] Department of Chemistry, University of Chicago.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature13935DOI Listing
November 2014

Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by αβ T cells.

Proc Natl Acad Sci U S A 2014 Oct 8;111(43):E4648-57. Epub 2014 Oct 8.

Departments of Biochemistry and Molecular Biology and Committee on Immunology, University of Chicago, Chicago, IL 60637;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1408549111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4217448PMC
October 2014

A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.

Nat Chem Biol 2014 Aug 22;10(8):686-91. Epub 2014 Jun 22.

1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nchembio.1561DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104137PMC
August 2014

Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation.

Curr Opin Chem Biol 2014 Aug 12;21:96-102. Epub 2014 Jul 12.

Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cbpa.2014.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149925PMC
August 2014

Evidence for a group II intron-like catalytic triplex in the spliceosome.

Nat Struct Mol Biol 2014 May 20;21(5):464-471. Epub 2014 Apr 20.

Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago IL.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb.2815DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257784PMC
May 2014

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 31;79(8):3647-52. Epub 2014 Mar 31.

Department of Biochemistry & Molecular Biology, ‡Department of Chemistry, and §Department of Molecular Genetics & Cell Biology, University of Chicago , Chicago, Illinois 60637, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jo4028374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4203407PMC
April 2014

RNA catalyses nuclear pre-mRNA splicing.

Nature 2013 Nov 6;503(7475):229-34. Epub 2013 Nov 6.

1] Graduate Program in Cell and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA [2] Department of Molecular Genetics and Cell Biology, Cummings Life Sciences Center, 920 East 58th Street, The University of Chicago, Chicago, Illinois 60637, USA [3].

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature12734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666680PMC
November 2013

Arginine as a general acid catalyst in serine recombinase-mediated DNA cleavage.

J Biol Chem 2013 Oct 22;288(40):29206-14. Epub 2013 Aug 22.

From the Department of Biochemistry and Molecular Biology and.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/jbc.M113.508028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3790019PMC
October 2013

Highly stereocontrolled total synthesis of β-D-mannosyl phosphomycoketide: a natural product from Mycobacterium tuberculosis.

J Org Chem 2013 Jun 11;78(12):5970-86. Epub 2013 Jun 11.

Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jo4006602DOI Listing
June 2013

Chemical origins of life: Prebiotic RNA unstuck.

Nat Chem 2013 May;5(5):360-2

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nchem.1636DOI Listing
May 2013

Automated solid-phase synthesis of RNA oligonucleotides containing a nonbridging phosphorodithioate linkage via phosphorothioamidites.

J Org Chem 2012 Nov 25;77(21):9889-92. Epub 2012 Oct 25.

Department of Biochemistry & Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jo301834pDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500914PMC
November 2012

General acid-base catalysis mediated by nucleobases in the hairpin ribozyme.

J Am Chem Soc 2012 Oct 25;134(40):16717-24. Epub 2012 Sep 25.

Cancer Research UK, Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ja3067429DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707309PMC
October 2012

Efficient synthesis of 2'-C-α-aminomethyl-2'-deoxynucleosides.

Chem Commun (Camb) 2012 Sep 26;48(70):8754-6. Epub 2012 Jul 26.

Department of Biochemistry & Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/c2cc34556kDOI Listing
September 2012

Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding.

RNA 2012 Jun 26;18(6):1123-41. Epub 2012 Apr 26.

The Pritzker School of Medicine, The University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1261/rna.028738.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3358636PMC
June 2012

Characterization of the reaction path and transition states for RNA transphosphorylation models from theory and experiment.

Angew Chem Int Ed Engl 2012 Jan 11;51(3):647-51. Epub 2011 Nov 11.

BioMaPS Institute for Quantitative Biology, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/anie.201104147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448066PMC
January 2012

Synthesis, properties, and applications of oligonucleotides containing an RNA dinucleotide phosphorothiolate linkage.

Acc Chem Res 2011 Dec 1;44(12):1257-69. Epub 2011 Sep 1.

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ar200131tDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243799PMC
December 2011

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 3;76(21):8718-25. Epub 2011 Oct 3.

Department of Biochemistry & Molecular Biology, The University of Chicago, 929 East 57th Street, MC 1028, Chicago, Illinois 60637, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jo201364xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707316PMC
November 2011

Crystal structure of an RNA polymerase ribozyme in complex with an antibody fragment.

Philos Trans R Soc Lond B Biol Sci 2011 Oct;366(1580):2918-28

Department of Biochemistry and Molecular Biology, The University of Chicago, Gordon Center for Integrative Science, Room W406, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1098/rstb.2011.0144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158925PMC
October 2011

Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design.

Proc Natl Acad Sci U S A 2011 May 25;108(19):7751-6. Epub 2011 Apr 25.

Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://www.pnas.org/cgi/doi/10.1073/pnas.1102294108
Publisher Site
http://dx.doi.org/10.1073/pnas.1102294108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093456PMC
May 2011

The ribotoxin restrictocin recognizes its RNA substrate by selective engagement of active site residues.

Biochemistry 2011 Apr 18;50(14):3004-13. Epub 2011 Mar 18.

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi1018336DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071035PMC
April 2011

A general and efficient approach for the construction of RNA oligonucleotides containing a 5'-phosphorothiolate linkage.

Nucleic Acids Res 2011 Mar 9;39(5):e31. Epub 2010 Dec 9.

Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th Street, Room W406, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkq1265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061073PMC
March 2011

2'-amino-modified ribonucleotides as probes for local interactions within RNA.

Methods Enzymol 2009 17;468:107-25. Epub 2009 Nov 17.

Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/S0076-6879(09)68006-XDOI Listing
January 2011

Separation of RNA phosphorothioate oligonucleotides by HPLC.

Methods Enzymol 2009 17;468:289-309. Epub 2009 Nov 17.

The Pritzker School of Medicine, University of Chicago, Chicago, Illinois, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/S0076-6879(09)68014-9DOI Listing
January 2011

Sin resolvase catalytic activity and oligomerization state are tightly coupled.

J Mol Biol 2010 Nov 22;404(1):16-33. Epub 2010 Sep 22.

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmb.2010.08.057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2976518PMC
November 2010

Kinetic isotope effects for RNA cleavage by 2'-O- transphosphorylation: nucleophilic activation by specific base.

J Am Chem Soc 2010 Aug;132(33):11613-21

RNA Center and Departmet of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44118, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ja103550eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946848PMC
August 2010

The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5' splice site cleavage during pre-mRNA splicing.

Mol Cell 2010 Aug;39(3):385-95

Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2010.07.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3722364PMC
August 2010

Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme.

Proc Natl Acad Sci U S A 2010 Jun 14;107(26):11751-6. Epub 2010 Jun 14.

Cancer Research United Kingdom Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1004255107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2900685PMC
June 2010

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

Department of Biochemistry, Beckman Center, B400, Stanford University, Stanford, CA 94305-5307, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/anie.200903006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862986PMC
January 2010

Synthesis of pyridine, pyrimidine and pyridinone C-nucleoside phosphoramidites for probing cytosine function in RNA.

J Org Chem 2009 Nov;74(21):8021-30

Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jo9016919DOI Listing
November 2009

Crystal structure of the catalytic core of an RNA-polymerase ribozyme.

Science 2009 Nov;326(5957):1271-5

Whitehead Institute for Biomedical Research and Howard Hughes Medical Institute, 9 Cambridge Center, Cambridge, MA 02142, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1174676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978776PMC
November 2009

Identification of catalytic metal ion ligands in ribozymes.

Methods 2009 Oct 3;49(2):148-66. Epub 2009 Aug 3.

The Pritzker School of Medicine, The University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymeth.2009.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3470912PMC
October 2009

Synthesis of 2'-C-beta-methyl-2'-deoxyguanosine.

J Org Chem 2009 Mar;74(5):2227-30

Howard Hughes Medical Institute, Department of Biochemistry & Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jo802666kDOI Listing
March 2009

Efficient chemical synthesis of AppDNA by adenylation of immobilized DNA-5'-monophosphate.

Org Lett 2009 Mar;11(5):1067-70

Department of Biochemistry & Molecular Biology, The University of Chicago, 929 East 57th Street, MC 1028, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ol802815gDOI Listing
March 2009

Electrostatic interactions guide the active site face of a structure-specific ribonuclease to its RNA substrate.

Biochemistry 2008 Aug 2;47(34):8912-8. Epub 2008 Aug 2.

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi800592gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2646754PMC
August 2008

Functional identification of ligands for a catalytic metal ion in group I introns.

Biochemistry 2008 Jul 3;47(26):6883-94. Epub 2008 Jun 3.

Department of Biochemistry and Chemistry, Stanford University, Stanford, California 94305, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi800519aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758101PMC
July 2008

The 2'-hydroxyl group of the guanosine nucleophile donates a functionally important hydrogen bond in the tetrahymena ribozyme reaction.

Biochemistry 2008 Jul 24;47(29):7684-94. Epub 2008 Jun 24.

Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi8000648DOI Listing
July 2008

Synthesis and biochemical application of 2'-O-methyl-3'-thioguanosine as a probe to explore group I intron catalysis.

Bioorg Med Chem 2008 May 27;16(10):5754-60. Epub 2008 Mar 27.

Howard Hughes Medical Institute, Department of Biochemistry & Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmc.2008.03.061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2664738PMC
May 2008

Biochemistry. Toward understanding self-splicing.

Science 2008 Apr;320(5872):56-7

Department of Biochemistry and Molecular Biology and Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1156721DOI Listing
April 2008

Structural inference of native and partially folded RNA by high-throughput contact mapping.

Proc Natl Acad Sci U S A 2008 Mar 5;105(11):4144-9. Epub 2008 Mar 5.

Departments of Biochemistry, Bioengineering, and Genetics, Stanford University, Stanford, CA 94305, USA.

View Article

Download full-text PDF

Source
http://www.pnas.org/cgi/doi/10.1073/pnas.0709032105
Publisher Site
http://dx.doi.org/10.1073/pnas.0709032105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2393762PMC
March 2008

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 4;73(1):309-11. Epub 2007 Dec 4.

Department of Biochemistry & Molecular Biology, Department of Chemistry, and Howard Hughes Medical Institute, The University of Chicago, MC 1028, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jo701727hDOI Listing
January 2008

Synthetic antibodies for specific recognition and crystallization of structured RNA.

Proc Natl Acad Sci U S A 2008 Jan 27;105(1):82-7. Epub 2007 Dec 27.

Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0709082105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2224236PMC
January 2008

Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine.

Nucleic Acids Res 2007 18;35(18):6322-9. Epub 2007 Sep 18.

Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkm657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2094055PMC
November 2007

Linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop RNA by restrictocin.

Biochemistry 2007 Nov 12;46(44):12744-56. Epub 2007 Oct 12.

Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi700931yDOI Listing
November 2007

Modulation of individual steps in group I intron catalysis by a peripheral metal ion.

RNA 2007 Oct 24;13(10):1656-67. Epub 2007 Aug 24.

Department of Biochemistry, Stanford University, Stanford, California 94305, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1261/rna.632007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1986806PMC
October 2007

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

Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/anie.200605124DOI Listing
August 2007

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 13;9(16):3009-12. Epub 2007 Jul 13.

Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ol071075bDOI Listing
August 2007

Syntheses of (2')3'-15N-amino-(2')3'-deoxyguanosine and determination of their pKa values by 15N NMR spectroscopy.

Org Lett 2007 Aug 13;9(16):3057-60. Epub 2007 Jul 13.

Department of Biochemistry & Molecular Biology, The University of Chicago, 929 East 57th Street, MC 1028, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ol071129hDOI Listing
August 2007

Reactions of phosphate and phosphorothiolate diesters with nucleophiles: comparison of transition state structures.

Org Biomol Chem 2007 Aug 29;5(15):2491-7. Epub 2007 Jun 29.

Department of Biochemistry and Molecular Biology, Department of Chemistry, Howard Hughes Medical Institute, The University of Chicago, 929 E 57th St., CIS-W408A, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/b707205hDOI Listing
August 2007

A second divalent metal ion in the group II intron reaction center.

Chem Biol 2007 Jun;14(6):607-12

Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.chembiol.2007.05.008DOI Listing
June 2007

Synthesis of 2'-C-alpha-(hydroxyalkyl) and 2'-C-alpha-alkylcytidine phosphoramidites: analogues for probing solvent interactions with RNA.

J Org Chem 2007 Feb;72(4):1198-210

Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jo062002tDOI Listing
February 2007

'Turning on' riboswitches to their antibacterial potential.

Nat Chem Biol 2007 Jan;3(1):16-7

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nchembio0107-16DOI Listing
January 2007

A systematic, ligation-based approach to study RNA modifications.

RNA 2006 Nov 8;12(11):2025-33. Epub 2006 Sep 8.

Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1261/rna.208906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1624908PMC
November 2006

The electrostatic character of the ribosomal surface enables extraordinarily rapid target location by ribotoxins.

Nat Struct Mol Biol 2006 May 9;13(5):436-43. Epub 2006 Apr 9.

Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb1082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1847776PMC
May 2006

Efficient synthesis of 2'-C-beta-methylguanosine.

J Org Chem 2006 May;71(10):4018-20

Howard Hughes Medical Institute, Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jo0602165DOI Listing
May 2006

General acid catalysis by the hepatitis delta virus ribozyme.

Nat Chem Biol 2005 Jun 3;1(1):45-52. Epub 2005 May 3.

Howard Hughes Medical Institute, Department of Biochemistry & Molecular Biology, University of Chicago, 5841 S. Maryland Avenue, MC1028, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nchembio703DOI Listing
June 2005