A. Pyle

发表

RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP

I. Tinoco, C. Bustamante, Wei Cheng, 2006, Nature.

Remarkable morphological variability of a common RNA folding motif: the GNRA tetraloop-receptor interaction.

A. Pyle, D. L. Abramovitz, 1997, Journal of molecular biology.

The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks.

S. Butcher, A. Pyle, 2011, Accounts of chemical research.

Inverted repeat Alu elements in the human lincRNA-p21 adopt a conserved secondary structure that regulates RNA function

A. Pyle, Isabel Chillón, 2016, Nucleic acids research.

Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium

Ruth R. Montgomery, T. Horvath, A. Iwasaki, 2020, bioRxiv.

Shape-selective targeting of DNA by phenanthrenequinone diiminerhodium(III) photocleaving agents

J. Barton, A. Pyle, E. Long, 1989 .

Spring-Loaded Mechanism of DNA Unwinding by Hepatitis C Virus NS3 Helicase

Taekjip Ha, Sua Myong, T. Ha, 2007, Science.

The Linker Region of NS3 Plays a Critical Role in the Replication and Infectivity of Hepatitis C Virus

Andrew S. Kohlway, B. Lindenbach, A. Pyle, 2014, Journal of Virology.

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

A. Pyle, M. Marcia, K. Rajashankar, 2013, Acta crystallographica. Section D, Biological crystallography.

How to Drive Your Helicase in a Straight Line

A. Pyle, 2009, Cell.

Principles of ion recognition in RNA: insights from the group II intron structures

A. Pyle, M. Marcia, 2014, RNA.

A new way to see RNA

Elisabeth L. Humphris, A. Pyle, Kevin Keating, 2011, Quarterly Reviews of Biophysics.

A single active-site region for a group II intron

S. Hamill, A. Pyle, A. D. Lencastre, 2005, Nature Structural &Molecular Biology.

Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling

N. Janjić, A. Pyle, A. Gelinas, 2017, Nature Communications.

Probing microstructures in double-helical DNA with chiral metal complexes: recognition of changes in base-pair propeller twisting in solution

J. Barton, A. Pyle, T. Morii, 1990 .

Covariation analysis with improved parameters reveals conservation in lncRNA structures

A. Pyle, Srinivas Somarowthu, R. C. Tavares, 2018, bioRxiv.

Sensitive detection of structural features and rearrangements in long, structured RNA molecules.

R. L. Adams, A. Pyle, Nicholas C. Huston, 2019, Methods in enzymology.

Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms

A. Pyle, C. Wilen, Nicholas C. Huston, 2021, Molecular Cell.

Comprehensive in-vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms

A. Pyle, C. Wilen, Nicholas C. Huston, 2020, bioRxiv.

An evolving arsenal: viral RNA detection by RIG-I-like receptors

A. Pyle, Megan E. Fitzgerald, D. Rawling, 2014, Current Opinion in Microbiology.

Intratumoral delivery of RIG-I agonist SLR14 induces robust antitumor responses

A. Iwasaki, Y. Kong, A. Pyle, 2019, The Journal of experimental medicine.

The Lanthanides and Their Interrelations with Biosystems

H. Sigel, A. Pyle, R. Sigel, 2003 .

Parts, assembly and operation of the RIG-I family of motors.

A. Pyle, D. Rawling, David C. Rawling, 2014, Current opinion in structural biology.

Structural Insights into RNA Recognition by RIGI

Andrew S. Kohlway, B. Lindenbach, A. Pyle, 2022 .

DNA photocleavage by phenanthrenequinone diimine complexes of rhodium(III): shape-selective recognition and reaction

J. Barton, A. Pyle, E. Long, 1992 .

Mixed-ligand complexes of ruthenium(II): factors governing binding to DNA

N. Turro, J. Barton, A. Pyle, 1989 .

Stopped-flow fluorescence spectroscopy of a group II intron ribozyme reveals that domain 1 is an independent folding unit with a requirement for specific Mg2+ ions in the tertiary structure.

A. Pyle, P. Qin, 1997, Biochemistry.

Monitoring functional RNA binding of RNA-dependent ATPase enzymes such as SF2 helicases using RNA dependent ATPase assays: A RIG-I case study.

A. Pyle, R. Guo, 2022, Methods in enzymology.

A stem-loop RNA RIG-I agonist protects against acute and chronic SARS-CoV-2 infection in mice

A. Iwasaki, A. Pyle, C. Wilen, 2021, The Journal of experimental medicine.

A stem-loop RNA RIG-I agonist confers prophylactic and therapeutic protection against acute and chronic SARS-CoV-2 infection in mice

A. Iwasaki, A. Pyle, C. Wilen, 2021, bioRxiv.

Branch-point attack in group II introns is a highly reversible transesterification, providing a potential proofreading mechanism for 5'-splice site selection.

A. Pyle, K. Chin, Anna Marie Pyle, 1995, RNA.

AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids

A. Pyle, Chengxin Zhang, Morgan Shine, 2022, Bioinformatics.

Visualizing group II intron dynamics between the first and second steps of splicing

A. Pyle, Isabel Chillón, M. Marcia, 2020, Nature Communications.

NS3 from HCV strain JFH-1 is an unusually robust helicase that is primed to bind and unwind viral RNA

R. L. Adams, A. Pyle, Xiaoming Ren, 2017 .

Inside an intron invasion

A. Pyle, 1996, Nature.

The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands

A. Pyle, A. Marie Pyle, Wenshuai Wang, 2022, Molecular cell.

Synthesis and characterization of physical, electronic, and photochemical aspects of 9,10-phenanthrenequinonediimine complexes of ruthenium(II) and rhodium(III)

J. Barton, A. Pyle, M. Chiang, 1990 .

The C Terminus of Hepatitis C Virus NS4A Encodes an Electrostatic Switch That Regulates NS5A Hyperphosphorylation and Viral Replication

C. Rice, F. Penin, B. Lindenbach, 2007, Journal of Virology.

Double-stranded RNA-dependent ATPase DRH-3

A. Pyle, C. Matranga, 2010, The Journal of Biological Chemistry.

Probing Nucleic Acids with Transition Metal Complexes

J. Barton, A. Pyle, 1991 .

A structural analysis of the group II intron active site and implications for the spliceosome.

P. Perlman, A. Pyle, Kevin Keating, 2010, RNA.

The Serine Protease Domain of Hepatitis C Viral NS3 Activates RNA Helicase Activity by Promoting the Binding of RNA Substrate*

V. Serebrov, A. Pyle, R. Beran, 2007, Journal of Biological Chemistry.

Sequence specificity of a group II intron ribozyme: multiple mechanisms for promoting unusually high discrimination against mismatched targets.

A. Pyle, P. Qin, W. Michels, 1998, Biochemistry.

17 Group II Introns: Ribozymes That Splice RNA and Invade DNA

A. Lambowitz, A. Pyle, 2006 .

Editorial overviewNucleic acids

J. Widom, A. Pyle, 2006 .

A group II intron inserted into a bacterial heat-shock operon shows autocatalytic activity and unusual thermostability.

C. Adamidi, A. Pyle, O. Fedorova, 2003, Biochemistry.

The Thermodynamic Basis for Viral RNA Detection by the RIG-I Innate Immune Sensor

A. Pyle, O. Fedorova, S. Ding, 2012, The Journal of Biological Chemistry.

Temperature-dependent innate defense against the common cold virus limits viral replication at warm temperature in mouse airway cells

Hongyu Zhao, J. Storer, P. Turner, 2015, Proceedings of the National Academy of Sciences.

Synthesis and spectroscopic characterization of the purple tris(phenanthrenequinone diimine)ruthenium(II) ion

J. Barton, A. Pyle, 1987 .

Metal ions in the structure and function of RNA

A. Pyle, Anna Pyle, 2002, JBIC Journal of Biological Inorganic Chemistry.

Site-specific labeling of RNA with fluorophores and other structural probes.

A. Pyle, P. Qin, 1999, Methods.

Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts with substrate 2'-hydroxyl groups.

A. Pyle, E. Griffin, W. Michels, 1995, Chemistry & biology.

Group II Intron Self-Splicing.

A. Pyle, 2016, Annual review of biophysics.

An ultraprocessive, accurate reverse transcriptase encoded by a metazoan group II intron

A. Pyle, Fei Liu, Chen Zhao, 2018, RNA: A publication of the RNA Society.

Visualizing Group II Intron Catalysis through the Stages of Splicing

A. Pyle, M. Marcia, 2012, Cell.

Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function

Barry Honig, Anna Marie Pyle, Kim A. Sharp, 1999, Nature Structural Biology.

The brace for a growing scaffold: Mss116 protein promotes RNA folding by stabilizing an early assembly intermediate.

A. Pyle, O. Fedorova, 2012, Journal of molecular biology.

Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides.

Emil Alexov, Barry Honig, Anna Marie Pyle, 2007, Journal of molecular biology.

An alternative route for the folding of large RNAs: apparent two-state folding by a group II intron ribozyme.

L. J. Su, M. Brenowitz, A. Pyle, 2003, Journal of molecular biology.

Branch-site selection in a group II intron mediated by active recognition of the adenine amino group and steric exclusion of non-adenine functionalities.

L. Beigelman, A. Pyle, A. Khodadadi, 1997, Journal of molecular biology.

Three essential and conserved regions of the group II intron are proximal to the 5'-splice site.

A. Pyle, Alexandre de Lencastre, A. de Lencastre, 2007, RNA.

A tertiary interaction that links active-site domains to the 5′ splice site of a group II intron

A. Pyle, M. Boudvillain, A. D. Lencastre, 2000, Nature.

RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).

Helen M Berman, David C Richardson, Anna Marie Pyle, 2008, RNA.

High resolution footprinting of EcoRI and distamycin with Rh(phi)2(bpy)3+, a new photofootprinting reagent.

J. Barton, A. Pyle, T. Morii, 1989, Nucleic acids research.

Ribozyme recognition of RNA by tertiary interactions with specific ribose 2′-OH groups

T. Cech, A. Pyle, 1991, Nature.

Anna Marie Pyle, A. Pyle, Megan E. Fitzgerald, 2014, Nucleic acids research.

Duplex RNA activated ATPases (DRAs)

Andrew S. Kohlway, A. Pyle, D. Luo, 2013, RNA biology.

Molecular Mechanics of RNA Translocases

A. Pyle, S. Ding, 2012, Methods in Enzymology.

mda-5: An interferon-inducible putative RNA helicase with double-stranded RNA-dependent ATPase activity and melanoma growth-suppressive properties

Paul B. Fisher, Anna Marie Pyle, Eckhard Jankowsky, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Visualizing the secondary and tertiary architectural domains of lncRNA RepA.

Anna Marie Pyle, A. Pyle, Fei Liu, 2017, Nature chemical biology.

HOTAIR forms an intricate and modular secondary structure.

Anna Marie Pyle, Marco Marcia, A. Pyle, 2015, Molecular cell.

Noncoding RNAs: biology and applications—a Keystone Symposia report

Howard Y. Chang, Allison M. Porman, Lydia M. Contreras, 2021, Annals of the New York Academy of Sciences.

Noncoding RNAs: A story of networks and long-distance relationships.

A. Pyle, M. Ostankovitch, 2013, Journal of molecular biology.

Translocation and unwinding mechanisms of RNA and DNA helicases.

A. Pyle, 2008, Annual review of biophysics.

US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes

A. Pyle, Chengxin Zhang, Yang Zhang, 2022, Nature Methods.

Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes

Ruth R. Montgomery, Ryan D. Chow, T. Horvath, 2021, PLoS biology.

The group II intron maturase: a reverse transcriptase and splicing factor go hand in hand.

A. Pyle, Chen Zhao, 2017, Current opinion in structural biology.

The RIG-I ATPase core has evolved a functional requirement for allosteric stabilization by the Pincer domain

Andrew S. Kohlway, A. Pyle, D. Luo, 2014, Nucleic acids research.

Therapeutically Active RIG-I Agonist Induces Immunogenic Tumor Cell Killing in Breast Cancers.

A. Pyle, John T. Wilson, Max E. Jacobson, 2018, Cancer research.

Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures.

Anna Marie Pyle, A. Pyle, Srinivas Somarowthu, 2019, Journal of molecular biology.

Looking at LncRNAs with the ribozyme toolkit.

A. Pyle, 2014, Molecular cell.

Insights into the structure and RNA-binding specificity of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3)

P. Griffin, A. Pyle, D. Luo, 2021, Nucleic acids research.

Structural insights into the role of Dicer-related helicase 3 in RNAi in Caenorhabditis elegans

P. Griffin, A. Pyle, D. Luo, 2021, bioRxiv.

Structural Insights into RNA Recognition by RIG-I

Andrew S. Kohlway, B. Lindenbach, A. Pyle, 2011, Cell.

Visualizing ATP-dependent RNA translocation by the NS3 helicase from HCV.

Todd C Appleby, J. R. Somoza, Xiaohong Liu, 2011, Journal of molecular biology.

Establishing a Mechanistic Basis for the Large Kinetic Steps of the NS3 Helicase*

V. Serebrov, A. Pyle, R. Beran, 2009, Journal of Biological Chemistry.

Backbone tracking by the SF2 helicase NPH-II

A. Pyle, E. Jankowsky, J. Kawaoka, 2004, Nature Structural &Molecular Biology.

NS3 from Hepatitis C Virus Strain JFH-1 Is an Unusually Robust Helicase That Is Primed To Bind and Unwind Viral RNA

R. L. Adams, A. Pyle, Xiaoming Ren, 2017, Journal of Virology.

Unmasking the Active Helicase Conformation of Nonstructural Protein 3 from Hepatitis C Virus

Andrew S. Kohlway, A. Pyle, S. Ding, 2011, Journal of Virology.

The NPH-II Helicase Displays Efficient DNA·RNA Helicase Activity and a Pronounced Purine Sequence Bias*

A. Pyle, S. D. Taylor, Amanda C Solem, 2010, The Journal of Biological Chemistry.

Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase

V. Serebrov, A. Pyle, 2004, Nature.

The DEAH‐box protein PRP22 is an ATPase that mediates ATP‐dependent mRNA release from the spliceosome and unwinds RNA duplexes

A. Pyle, E. Jankowsky, J. Abelson, 1998, The EMBO journal.

RNA folding.

A. Pyle, J. Green, 1995, Current opinion in structural biology.

An ultraprocessive, accurate reverse transcriptase encoded by a metazoan group II intron

A. Pyle, Fei Liu, Chen Zhao, 2018, RNA.

Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure.

Anna Marie Pyle, Kevin S Keating, A. Pyle, 2007, Journal of molecular biology.

RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space.

Anna Marie Pyle, A. Pyle, C. M. Duarte, 2003, Nucleic acids research.

Active disruption of an RNA-protein interaction by a DExH/D RNA helicase.

A. Pyle, S. Shuman, C. H. Gross, 2001, Science.

The molecular mechanism of RIG‐I activation and signaling

A. Pyle, L. Xu, Daniel T. Thoresen, 2021, Immunological reviews.

The In Vivo and In Vitro Architecture of the Hepatitis C Virus RNA Genome Uncovers Functional RNA Secondary and Tertiary Structures

B. Lindenbach, R. L. Adams, A. Pyle, 2022, Journal of virology.

The Global and Local Distribution of RNA Structure throughout the SARS-CoV-2 Genome

Anna Marie Pyle, A. Pyle, Nicholas C. Huston, 2020, Journal of Virology.

The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures.

Andrew S. Kohlway, B. Lindenbach, A. Pyle, 2016, Molecular cell.

Stepping through an RNA structure: A novel approach to conformational analysis.

A. Pyle, C. M. Duarte, C M Duarte, 1998, Journal of molecular biology.

De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report

A. Iwasaki, B. Lindenbach, A. Ko, 2022, Nature Communications.

Defining the functional determinants for RNA surveillance by RIG-I

Andrew S. Kohlway, A. Pyle, D. Luo, 2013, EMBO reports.

microRNA-122 amplifies hepatitis C virus translation by shaping the structure of the internal ribosomal entry site

R. L. Adams, A. Pyle, C. Mas, 2018, Nature Communications.

Discovery of highly reactive self-splicing group II introns within the mitochondrial genomes of human pathogenic fungi

A. Pyle, Tianshuo Liu, 2021, Nucleic acids research.

Functional RNA structures throughout the Hepatitis C Virus genome.

R. L. Adams, A. Pyle, N. Pirakitikulr, 2017, Current opinion in virology.

Author Correction: Visualizing group II intron dynamics between the first and second steps of splicing

A. Pyle, Isabel Chillón, M. Marcia, 2022, Nature communications.

Hepatitis C Virus RNA Replication and Virus Particle Assembly Require Specific Dimerization of the NS4A Protein Transmembrane Domain

Andrew S. Kohlway, D. Engelman, B. Lindenbach, 2013, Journal of Virology.

RNA binding activates RIG-I by releasing an autorepressed signaling domain

A. Pyle, T. Dickey, B. Song, 2019, Science Advances.

Establishing the role of ATP for the function of the RIG-I innate immune sensor

A. Pyle, Megan E. Fitzgerald, D. Rawling, 2015, eLife.

Sequencing and structure probing of long RNAs using MarathonRT: a next-generation reverse transcriptase.

B. Graveley, B. Torbett, R. L. Adams, 2020, Journal of molecular biology.

Transcriptome analysis of human cumulus cells reveals hypoxia as the main determinant of follicular senescence.

P. Patrizio, A. Pyle, H. Bar, 2016, Molecular human reproduction.

Discovery of N-substituted 3-amino-4-(3-boronopropyl)pyrrolidine-3-carboxylic acids as highly potent third generation inhibitors of human arginase I and II.

A. Pyle, O. Potapova, E. Howard, 2019, Journal of medicinal chemistry.

Now on display: a gallery of group II intron structures at different stages of catalysis

A. Pyle, M. Marcia, Srinivas Somarowthu, 2013, Mobile DNA.

The tertiary structure of group II introns: implications for biological function and evolution

A. Pyle, 2010, Critical reviews in biochemistry and molecular biology.

Tertiary architecture of the Oceanobacillus iheyensis group II intron.

Jimin Wang, A. Pyle, K. Rajashankar, 2009, RNA.

Group II Introns and Their Protein Collaborators

A. Pyle, N. Zingler, Amanda C Solem, 2009 .

for the spliceosome A structural analysis of the group II intron active site and implications

P. Perlman, A. Pyle, Kevin Keating, 2009 .

Protein-facilitated folding of group II intron ribozymes.

Anna Marie Pyle, A. Pyle, Olga Fedorova, 2010, Journal of molecular biology.

The linear form of a group II intron catalyzes efficient autocatalytic reverse splicing, establishing a potential for mobility.

A. Pyle, M. Roitzsch, 2009, RNA.

Folding of group II introns: a model system for large, multidomain RNAs?

A. Pyle, C. Waldsich, O. Fedorova, 2007, Trends in biochemical sciences.

Structural Insights into the Mechanism of Group II Intron Splicing.

A. Pyle, Chen Zhao, 2017, Trends in biochemical sciences.

Two competing pathways for self-splicing by group II introns: a quantitative analysis of in vitro reaction rates and products.

A. Pyle, D. Daniels, D. Daniels, 1996, Journal of molecular biology.

Native Purification and Analysis of Long RNAs.

A. Pyle, M. Legiewicz, Isabel Chillón, 2015, Methods in enzymology.

New tricks from an itinerant intron

A. Pyle, 2000, Nature Structural Biology.

Group II intron splicing in vivo by first-step hydrolysis

P. Perlman, M. Podar, A. Pyle, 1998, Nature.

Structural insights into RNA splicing.

Anna Marie Pyle, Navtej Toor, Kevin S Keating, 2009, Current opinion in structural biology.

Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry.

A. Pyle, R. Sigel, 2007, Chemical reviews.

Robust translocation along a molecular monorail: the NS3 helicase from hepatitis C virus traverses unusually large disruptions in its track.

A. Pyle, E. Jankowsky, Michael M. Bruno, 2006, Journal of molecular biology.

The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding

A. Pyle, P. Pang, P. Planet, 2002, The EMBO journal.

Small Molecule Antagonists of the RIG-I Innate Immune Receptor.

A. Pyle, O. Potapova, G. E. Jagdmann, 2020, ACS chemical biology.

RSCanner: rapid assessment and visualization of RNA structure content

A. Pyle, Han Wan, Rafael C A Tavares, 2023, Bioinform..

Structural Optimization of Polymeric Carriers to Enhance the Immunostimulatory Activity of Molecularly Defined RIG-I Agonists

C. Duvall, A. Pyle, John T. Wilson, 2020, ACS central science.

Ribozymes: a distinct class of metalloenzymes.

A. Pyle, A M Pyle, Anna Marie Pyle, 1993, Science.

The DExH protein NPH-II is a processive and directional motor for unwinding RNA

A. Pyle, S. Shuman, C. H. Gross, 2000, Nature.

Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells

Ruth R. Montgomery, T. Horvath, A. Iwasaki, 2020 .

Crystal Structure of a Self-Spliced Group II Intron

Anna Marie Pyle, Navtej Toor, Kevin S. Keating, 2008, Science.

A DEAD protein that activates intron self-splicing without unwinding RNA.

A. Pyle, N. Zingler, Amanda C Solem, 2006, Molecular cell.

Choosing between DNA and RNA: the polymer specificity of RNA helicase NPH-II

Anna Marie Pyle, A. Pyle, Jane Kawaoka, 2005, Nucleic acids research.

Control of branch‐site choice by a group II intron

P. Perlman, A. Pyle, V. Chu, 2001, The EMBO journal.

Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution

A. Pyle, Chen Zhao, 2016, Nature Structural &Molecular Biology.

The receptor for branch-site docking within a group II intron active site.

S. Hamill, A. Pyle, 2006, Molecular cell.

Catalytic Reaction Mechanisms and Structural Features of Group II Intron Ribozymes

A. Pyle, 1996 .

Building a kinetic framework for group II intron ribozyme activity: quantitation of interdomain binding and reaction rate.

A. Pyle, J. Green, Anna Marie Pyle, 1994, Biochemistry.

RCrane: semi-automated RNA model building

Anna Marie Pyle, Kevin S. Keating, A. Pyle, 2012, Acta crystallographica. Section D, Biological crystallography.

The Acidic Domain of Hepatitis C Virus NS4A Contributes to RNA Replication and Virus Particle Assembly

Andrew S. Kohlway, B. Lindenbach, A. Pyle, 2010, Journal of Virology.

Prediction of functional tertiary interactions and intermolecular interfaces from primary sequence data.

Anna Marie Pyle, Eckhard Jankowsky, A. Pyle, 2005, Journal of experimental zoology. Part B, Molecular and developmental evolution.

Discrete RNA libraries from pseudo-torsional space.

Anna Marie Pyle, Elisabeth Humphris-Narayanan, A. Pyle, 2012, Journal of molecular biology.

The 2′-OH group at the group II intron terminus acts as a proton shuttle

A. Pyle, M. Roitzsch, O. Fedorova, 2009, Nature chemical biology.

RNA helicases and remodeling proteins

A. Pyle, 2011, Current Opinion in Chemical Biology.

Nucleotide analog interference mapping and suppression (NAIM/NAIS): specific applications in studies of RNA tertiary structure, dynamic helicase mechanism, and RNA-protrein interactions

A. Pyle, M. Boudvillain, O. Fedorova, 2005 .

DNA repair: Big engine finds small breaks

Anna Marie Pyle, A. Pyle, 2004, Nature.

RIG-I Recognition of RNA Targets: The Influence of Terminal Base Pair Sequence and Overhangs on Affinity and Signaling.

A. Iwasaki, A. Pyle, Xiaoming Ren, 2019, Cell reports.

Environmentally Triggerable Retinoic Acid-Inducible Gene I Agonists Using Synthetic Polymer Overhangs.

A. Pyle, John T. Wilson, Max E. Jacobson, 2018, Bioconjugate chemistry.

Direct tracking of reverse-transcriptase speed and template sensitivity: implications for sequencing and analysis of long RNA molecules

B. Graveley, A. Pyle, S. Olson, 2022, Nucleic acids research.

Group II intron folding under near-physiological conditions: collapsing to the near-native state.

A. Pyle, C. Waldsich, O. Fedorova, 2007, Journal of molecular biology.

Lanthanide ions as probes for metal ions in the structure and catalytic mechanism of ribozymes.

A. Pyle, R. Sigel, 2003, Metal ions in biological systems.

A compact regulatory RNA element in human Hsp70 mRNA

A. Pyle, Fei Liu, Wenshuai Wang, 2023, bioRxiv.

A molecular beacon assay for monitoring RNA splicing

A. Pyle, O. Fedorova, Tianshuo Liu, 2022, Nucleic acids research.

Structures of a Mobile Intron Retroelement Poised to Attack Its Structured DNA Target

A. Pyle, Junhui Peng, Pengxin Chai, 2022, Science.

Visualizing the solvent‐inaccessible core of a group II intron ribozyme

L. J. Su, A. Pyle, C. M. Duarte, 2001, The EMBO journal.

Guiding ribozyme cleavage through motif recognition: the mechanism of cleavage site selection by a group ii intron ribozyme.

L. J. Su, A. Pyle, P. Qin, 2001, Journal of molecular biology.

Opportunities and Challenges in RNA Structural Modeling and Design.

Tamar Schlick, Anna Marie Pyle, T. Schlick, 2017, Biophysical journal.

RIG-I Selectively Discriminates against 5'-Monophosphate RNA.

A. Iwasaki, A. Pyle, Xiaoming Ren, 2019, Cell reports.

A minimal RNA ligand for potent RIG-I activation in living mice

A. Iwasaki, A. Pyle, O. Potapova, 2017, Science Advances.

Regional Differences in Airway Epithelial Cells Reveal Tradeoff between Defense against Oxidative Stress and Defense against Rhinovirus

A. Iwasaki, Y. Kong, C. D. Dela Cruz, 2018, Cell reports.

A Nanoparticle RIG-I Agonist for Cancer Immunotherapy

A. Pyle, K. Gibson-Corley, Venkata R. Krishnamurthy, 2023, bioRxiv.

RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization.

T. Cech, D. Herschlag, J. Piccirilli, 1992, The Journal of biological chemistry.

A protocol for capturing RNA-sensing innate immune receptors in multiple conformations by single-particle cryo-EM

A. Pyle, O. Fedorova, Wenshuai Wang, 2023, STAR protocols.

Visualizing the determinants of viral RNA recognition by innate immune sensor RIG-I.

Andrew S. Kohlway, A. Pyle, D. Luo, 2012, Structure.

RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme

T. Cech, A. Pyle, F. L. Murphy, 1992, Nature.

Productive folding to the native state by a group II intron ribozyme.

L. J. Su, M. Brenowitz, A. Pyle, 2002, Journal of molecular biology.

The architectural organization and mechanistic function of group II intron structural elements.

A. Pyle, P. Qin, Anna Marie Pyle, 1998, Current opinion in structural biology.

Replacement of the conserved G.U with a G-C pair at the cleavage site of the Tetrahymena ribozyme decreases binding, reactivity, and fidelity.

D. Turner, S. Strobel, T. Cech, 1994, Biochemistry.

Single-molecule analysis of Mss116-mediated group II intron folding

A. Pyle, D. Rueda, Krishanthi S. Karunatilaka, 2010, Nature.

Group II introns: highly specific endonucleases with modular structures and diverse catalytic functions.

L. J. Su, A. Pyle, O. Fedorova, 2002, Methods.

Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling

N. Janjić, A. Pyle, A. Gelinas, 2017, Nature Communications.

Direct measurement of oligonucleotide substrate binding to wild-type and mutant ribozymes from Tetrahymena.

T. Cech, A. Pyle, J. Mcswiggen, 1990, Proceedings of the National Academy of Sciences of the United States of America.

The NS4A Protein of Hepatitis C Virus Promotes RNA-Coupled ATP Hydrolysis by the NS3 Helicase

B. Lindenbach, A. Pyle, R. Beran, 2009, Journal of Virology.

Hepatitis C Viral NS3-4A Protease Activity Is Enhanced by the NS3 Helicase*S⃞

A. Pyle, R. Beran, 2008, Journal of Biological Chemistry.

Catalytic Role of 2′-Hydroxyl Groups Within a Group II Intron Active Site

A. Pyle, D. L. Abramovitz, R. Friedman, 1996, Science.

Linking the group II intron catalytic domains: tertiary contacts and structural features of domain 3

A. Pyle, O. Fedorova, 2005, The EMBO journal.

Semiautomated model building for RNA crystallography using a directed rotameric approach

Anna Marie Pyle, Kevin S Keating, A. Pyle, 2010, Proceedings of the National Academy of Sciences.

Visualizing group II intron dynamics between the first and second steps of splicing

A. Pyle, Isabel Chillón, M. Marcia, 2020, Nature Communications.

Crystal structure of group II intron domain 1 reveals a template for RNA assembly

A. Pyle, M. Marcia, K. Rajashankar, 2015, Nature chemical biology.

Selective RNA targeting and regulated signaling by RIG-I is controlled by coordination of RNA and ATP binding

Andrew S. Kohlway, A. Pyle, O. Potapova, 2016, Nucleic acids research.

Small molecules that target group II introns are potent antifungal agents

R. L. Adams, A. Pyle, M. V. Van Zandt, 2018, Nature Chemical Biology.

Title. Mechanism of Action of KL-50, a Novel Imidazotetrazine for the Treatment of Drug-Resistant Brain Cancers.

J. Sarkaria, M. Rees, A. Pyle, 2023 .

microRNA-122 amplifies hepatitis C virus translation by shaping the structure of the internal ribosomal entry site

R. L. Adams, A. Pyle, C. Mas, 2018, Nature Communications.

Using DNAzymes to cut, process, and map RNA molecules for structural studies or modification.

A. Pyle, M. Boudvillain, E. Jankowsky, 2000, Methods in enzymology.

MRT-ModSeq – Rapid detection of RNA modifications with MarathonRT

A. Pyle, Han Wan, Rafael C A Tavares, 2023, bioRxiv.

A rapid RIG-I signaling relay mediates efficient antiviral response

A. Pyle, Benjamin Götte, Daniel T. Thoresen, 2022, Molecular cell.

Ribozyme catalysis from the major groove of group II intron domain 5.

A. Karpeisky, L. Beigelman, A. Pyle, 1998, Molecular cell.

Conversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: elucidation of reaction mechanism and structure/function relationships.

A. Pyle, W. Michels, 1995, Biochemistry.

Structural basis for exon recognition by a group II intron

A. Pyle, K. Rajashankar, Kevin Keating, 2008, Nature Structural &Molecular Biology.

Visualizing the ai5γ group IIB intron

A. Pyle, M. Legiewicz, Srinivas Somarowthu, 2013, Nucleic acids research.

Predicted group II intron lineages E and F comprise catalytically active ribozymes

A. Pyle, Isabel Chillón, N. Pirakitikulr, 2013, RNA.

Crystal structure of a group II intron in the pre-catalytic state

A. Pyle, K. Rajashankar, A. Robart, 2012, Nature Structural &Molecular Biology.

The GANC tetraloop: a novel motif in the group IIC intron structure.

A. Pyle, Kevin Keating, N. Toor, 2008, Journal of molecular biology.

Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif

Dipali G. Sashital, S. Butcher, A. Palmer, 2004, Nature Structural &Molecular Biology.

Domains 2 and 3 interact to form critical elements of the group II intron active site.

A. Pyle, T. Mitros, O. Fedorova, 2003, Journal of molecular biology.

Antagonistic substrate binding by a group II intron ribozyme.

A. Pyle, P. Qin, 1999, Journal of molecular biology.

Mechanism of Mss116 ATPase reveals functional diversity of DEAD-Box proteins.

A. Pyle, W. Cao, E. M. De La Cruz, 2011, Journal of molecular biology.

The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery.

Anna Marie Pyle, A. Pyle, Leven M Wadley, 2004, Nucleic acids research.

The SMAD3 transcription factor binds complex RNA structures with high affinity

A. Pyle, T. Dickey, 2017, Nucleic acids research.

Defining the functional determinants for RNA surveillance by RIG-I

Andrew S. Kohlway, A. Pyle, D. Luo, 2013, EMBO Reports.

Capping by Branching: A New Ribozyme Makes Tiny Lariats

A. Pyle, 2005, Science.

Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq

A. Pyle, C. Wilen, A. N. Sexton, 2023, Nature communications.

The pathway for DNA recognition and RNA integration by a group II intron retrotransposon.

A. Lambowitz, A. Pyle, Y. Aizawa, 2003, Molecular cell.

More than one way to splice an RNA: branching without a bulge and splicing without branching in group II introns.

P. Perlman, M. Podar, A. Pyle, 1998, RNA.

The ever-growing complexity of nucleic acids: from small DNA and RNA motifs to large molecular assemblies and machines.

A. Pyle, Zippi Shakked, 2011, Current opinion in structural biology.

The brace for a growing scaffold: Mss116 protein promotes RNA folding by stabilizing an early assembly intermediate.

A. Pyle, O. Fedorova, 2012, Journal of molecular biology.

The Acidic Domain of Hepatitis C Virus NS4A Contributes to RNA Replication and Virus Particle Assembly

Andrew S. Kohlway, B. Lindenbach, A. Pyle, 2010, Journal of Virology.

The E3 ligase Riplet promotes RIG-I signaling independent of RIG-I oligomerization

A. Pyle, Benjamin Götte, Wenshuai Wang, 2023, Nature communications.

Metal ion binding sites in a group II intron core

A. Pyle, R. Sigel, A. Vaidya, 2000, Nature Structural Biology.

A folding control element for tertiary collapse of a group II intron ribozyme

A. Pyle, C. Waldsich, 2007, Nature Structural &Molecular Biology.

The SMN complex drives structural changes in human snRNAs to enable snRNP assembly

A. Pyle, A. Prusty, Han Wan, 2023, Nature communications.

A compact regulatory RNA element in mouse Hsp70 mRNA

A. Pyle, Fei Liu, Wenshuai Wang, 2023, bioRxiv.

Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells

Ruth R. Montgomery, T. Horvath, A. Iwasaki, 2020 .

PDC: a highly compact file format to store protein 3D coordinates

A. Pyle, Chengxin Zhang, 2023, Database J. Biol. Databases Curation.

De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report

M. C. Muenker, A. Iwasaki, B. Lindenbach, 2021, Nature Communications.

H/D exchange in methane and other saturated hydrocarbons catalyzed by a supported zirconium complex

A. Pyle, Klaus‐Joachim Jens, 1986 .

Structural insights into RNA splicing.

A. Pyle, Kevin Keating, N. Toor, 2009, Current opinion in structural biology.