Publications [Google Scholar]

218.	PDC: a highly compact file format to store protein 3D coordinates Chengxin Zhang, Anna Marie Pyle Database 2023 () : baad018
217.	A compact regulatory RNA element in human Hsp70 mRNA Wenshuai Wang, Fei Liu, Anna Marie Pyle bioRxiv 2023 () : 2023.02.22.529618
216.	RSCanner: rapid assessment and visualization of RNA structure content Gandhar Mahadeshwar, Rafael Araujo Tavares, Han Wan, Zion Perry, Anna Marie Pyle Bioinformatics 2023 () : btad111
215.	Synthesis, deprotection, and purification of diphosphorylated RNA oligonucleotides. Sarah J Fergione, Olga Fedorova, Anna Marie Pyle ChemRxiv 2023 () :
214.	rMSA: a sequence search and alignment algorithm to improve RNA structure modeling Chengxin Zhang, Yang Zhang, Anna Marie Pyle J Mol Biol 2022 () : 167904
213.	A rapid RIG-I signaling relay mediates efficient antiviral response Daniel T Thoresen, Drew Galls, Benjamin Götte, Wenshuai Wang, Anna M Pyle Mol Cell 2022 () : in press
212.	Structures of a mobile intron retroelement poised to attack its structured DNA target Kevin Chung, Ling Xu, Pengxin Chai, Junhui Peng, Swapnil C Devarkar, Anna Marie Pyle Science 2022 (378) : 627-634
211.	The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands Wenshuai Wang, Anna Marie Pyle Mol Cell 2022 (82) : 4131-4144.e6
210.	A unified approach to sequential and non-sequential structure alignment of proteins, RNAs and DNAs Chengxin Zhang, Anna Marie Pyle iScience 2022 (25) : 105218
209.	US-align: Universal Structure Alignments of Proteins, Nucleic Acids, and Macromolecular Complexes Chengxin Zhang, Morgan Shine, Anna Marie Pyle, Yang Zhang Nat Methods 2022 (19) : 1109–1115
208.	Direct tracking of reverse-transcriptase speed and template sensitivity: implications for sequencing and analysis of long RNA molecules Li-Tao Guo, Sara Olson, Shivali Patel, Brenton R Graveley and Anna Marie Pyle Nucleic Acids Res 2022 (50) : 6980-6989
207.	Monitoring functional RNA binding of RNA-dependent ATPase enzymes such as SF2 helicases using RNA dependent ATPase assays: A RIG-I case study Rong Guo, Anna Marie Pyle Methods Enzymol 2022 (673) : 39-52
206.	A molecular beacon assay for monitoring RNA splicing Qusay Q Omran, Olga Fedorova, Tianshuo Liu, Anna M Pyle Nucleic Acids Res 2022 (50) : e74
205.	The In Vivo and In Vitro Architecture of the Hepatitis C Virus RNA Genome Uncovers Functional RNA Secondary and Tertiary Structures Han Wan, Rebecca L Adams, Brett D Lindenbach, Anna Marie Pyle J Virol 2022 (96) : e0194621
204.	AMIGOS III: Pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids Morgan Shine, Chengxin Zhang, Anna Marie Pyle Bioinformatics 2022 (38) : 2937-2939
203.	CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures Chengxin Zhang, Anna Marie Pyle Acta Crystallogr D 2022 (78) : 466-471
202.	De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report S Gandhi, J Klein, A Robertson, MA Pena-Hernandez, MJ Lin, P Roychoudhury, P Lu, J Fournier, D Ferguson, SAM Bakhash, MC Muenker, A Srivathsan, EA Wunder Jr, N Kerantzas, W Wang, AM Pyle, CB Wilen, O Ogbuagu, AL Greninger, A Iwasaki, WL Schulz, AI Ko Nat Commun 2022 (13) : 1-8
201.	Noncoding RNAs: biology and applications - a Keystone Symposia report J Cable et al. Ann N Y Acad Sci 2021 (1506) : 118-141
200.	Discovery of highly reactive self-splicing group II introns within the mitochondrial genomes of human pathogenic fungi Tianshuo Liu, Anna Marie Pyle Nucleic Acids Res 2021 (49) : 12422-12432
199.	Insights into the structure and RNA-binding specificity of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) Kuohan Li, Jie Zheng, Melissa Wirawan, Nguyen Mai Trinh, Olga Fedorova, Patrick R Griffin, Anna M Pyle, Dahai Luo Nucleic Acids Res 2021 (49) : 9978-9991
198.	The molecular mechanism of RIG-I activation and signaling Daniel Thoresen, Wenshuai Wang, Drew Galls, Rong Guo, Ling Xu, Anna Marie Pyle Immunological Reviews 2021 (304) : 154-168
197.	Evolving a RIG-I antagonist: a modified DNA aptamer mimics viral RNA Xiaoming Ren, Amy D. Gelinas, Melissa Linehan, Akiko Iwasaki, Wenshuai Wang, Nebojsa Janjic, Anna Marie Pyle Journal of Molecular Biology 2021 (433) : 167227
196.	Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. NG Ravindra et al. PLoS Biol 2021 (19) : e3001143
195.	Comprehensive in-vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms Nicholas C Huston, Han Wan, Madison S. Strine, Rafael CA Tavares, Craig Wilen, Anna Marie Pyle Mol Cell. 2021 (81) : 584-598.e5
194.	The global and local distribution of RNA structure throughout the SARS-CoV-2 genome Rafael de Cesaris Araujo Tavares, Gandhar Mahadeshwar, Nicholas C. Huston and Anna Marie Pyle J Virology 2021 (95) : e02190-20
193.	A stem-loop RNA RIG-I agonist protects against acute and chronic SARS-CoV-2 infection in mice T Mao, B Israelow, C Lucas, CBF Vogels, ML Gomez-Calvo, O Fedorova, MI Breban, BL Menasche, H Dong, M Linehan, Yale SARS-CoV-2 Genome Surveillance Initiative, CB Wilen, ML Landry, ND Grubaugh, AM Pyle, A Iwasaki J Exp Med 2021 (219) : e20211818
192.	Structural optimization of polymeric carriers to enhance the immunostimulatory activity of molecularly defined RIG-I agonists Max E Jacobson, Kyle W Becker, Christian R Palmer, Lucinda E Pastora, R Brock Fletcher, Kathryn A Collins, Olga Fedorova, Craig L Duvall, Anna M Pyle, John T Wilson ACS Cent Sci. 2020 (6) : 2008-2022
191.	Visualizing group II intron dynamics between the first and second steps of splicing Jacopo Manigrasso, Isabel Chillon, Vito Genna, Pietro Vidossich, Srinivas Somarowthu, Anna Marie Pyle, Marco De Vivo, Marco Marcia Nat Commun. 2020 (11) : 2837
190.	Sequencing and Structure Probing of Long RNAs Using MarathonRT: A Next-Generation Reverse Transcriptase Li-Tao Guo, Rebecca L Adams, Han Wan, Nicholas C Huston, Olga Potapova, Sara Olson, Christian M Gallardo, Brenton R Graveley, Bruce E Torbett, Anna Marie Pyle J Mol Biol. 2020 (432) : 3338-3352
189.	Small-Molecule antagonists of the RIG-I Innate Immune Receptor David C. Rawling, G. Erik Jagdmann Jr., Olga Potapova and Anna Marie Pyle ACS Chem Biol. 2020 (15) : 311-317
188.	RIG-I recognition of RNA targets: The influence of terminal base-pair sequence and overhangs on affinity and signaling Xiaoming Ren, Melissa M. Linehan, Akiko Awasaki and Anna Marie Pyle Cell Reports 2019 (29) : 3807-3815
187.	RNA Binding Activates RIG-I by Releasing an Autorepressed Signaling Domain Thayne Dickey, Bo Song and Anna Marie Pyle Science Adv. 2019 (5) : eaax3641
186.	Intratumoral delivery of RIG-I agonist SLR14 induces robust antitumor responses Xiaodong Jiang, Viswanathan Muthusamy, Olga Fedorova, Daniel J. Kim, Marcus Bosenberg, Anna Marie Pyle, and Akiko Iwasaki J Exp Med. 2019 (216) : 2954-2868
185.	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 Michael C. Van Zandt, G. Erik Jagdmann, Darren L. Whitehouse, Min Ji, Jennifer Savoy, Olga Potapova, Alexandra Cousido-Siah, Andre Mitschler, Eduardo I. Howard, Anna Marie Pyle, Alberto D. Podjarny J Med Chem. 2019 (62) : 8164-8177
184.	Sensitive detection of structural features and rearrangements in long, structured RNA molecules Rebecca L. Adams, Nicholas C. Huston, Rafael C. Tavares and Anna Marie Pyle Methods Enzymol. 2019 (623) : 249-289
183.	Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures Rafael CA Tavares, Anna Marie Pyle , Srinivas Somarowthu J Mol Biol. 2019 (431) : 1592-1603
182.	RIG-I selectively discriminates against 5’-monophosphate RNA Xiaoming Ren, Melissa M. Linehan, Akiko Iwasaki and Anna Marie Pyle Cell Rep. 2019 (26) : 2019-2027
181.	Small molecules that target group II introns are potent antifungal agents Olga Fedorova, G. Erik Jagdmann, Rebecca L. Adams, Lin Yuan, Michael C. Van Zandt and Anna Marie Pyle Nat Chem Biol 2018 (14) : 1073-1078
180.	Therapeutically active RIG-I agonist induces immunogenic tumor cell killing in breast cancers David L. Elion, Max E. Jacobson, Donna J. Hicks, Bushra Rahman, Violeta Sanchez, Paula L. Gonzalez-Ericsson, Olga Fedorova, Anna M. Pyle, John T. Wilson and Rebecca S. Cook Cancer Research 2018 (78) : 6183-6195
179.	Regional Differences in Airway Epithelial Cells Reveal Tradeoff between Defense against Oxidative Stress and Defense against Rhinovirus Vila T. Mihaylova, Yong Kong, Olga Fedorova, Lokesh Sharma, Charles S. Dela Cruz, Anna M. Pyle, Akiko Iwasaki, Ellen F. Foxman Cell Rep. 2018 (24) : 3000-3007
178.	microRNA-122 amplifies hepatitis C virus translation by shaping the structure of the internal ribosomal entry site Philipp Schult, Hanna Roth, Rebecca L. Adams, Caroline Mas, Lionel Imbert, Christian Orlik, Alessia Ruggieri, Anna Marie Pyle and Volker Lohmann Nat Commun. 2018 (9) : 2613
177.	A minimal RNA ligand for potent RIG-I activation in living mice Melissa M. Linehan, Thayne H. Dickey, Emanuela S. Molinari, Megan E. Fitzgerald, Olga Potapova, Akiko Iwasaki and Anna Marie Pyle Sci Adv. 2018 (4) : e1701854
176.	Environmentally triggerable retinoic acid-inducible gene I agonists using synthetic polymer overhangs Christian R Palmer, Max E Jacobson, Olga Fedorova, Anna Marie Pyle and John T. Wilson Bioconjug. Chem. 2018 (29) : 742-747
175.	An ultra-processive, accurate reverse transcriptase encoded by a metazoan group II intron Chen Zhao, Fei Liu and Anna Marie Pyle RNA 2018 (24) : 183-195
174.	NS3 from HCV strain JFH-1 is an unusually robust helicase that is primed to bind and unwind viral RNA Ting Zhou, Xiaoming Ren, Rebecca L. Adams and Anna Marie Pyle J Virol. 2018 (92) : e01253-17
173.	The SMAD3 transcription factor binds complex RNA structures with high affinity Thayne Dickey and Anna Marie Pyle Nucleic Acids Res. 2017 (45) : 11980-11988
172.	Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling Xiaoming Ren, Amy D. Gelinas, Ira von Carlowitz, Nebojsa Janjic and Anna Marie Pyle Nat Commun. 2017 (8) : 810
171.	The group II intron maturase: a reverse transcriptase and splicing factor go hand in hand Chen Zhao and Anna Marie Pyle Curr Opin Struct Biol. 2017 (47) : 30-39
170.	Functional RNA structures throughout the Hepatitis C Virus genome Rebecca L. Adams, Nathan Pirakitikulr and Anna Marie Pyle Curr Opin Virol. 2017 (24) : 79-86
169.	Structural insights into the mechanism of group II intron splicing Chen Zhao and Anna Marie Pyle Trends Biochem Sci. 2017 (42) : 470-482
168.	Selective RNA targeting and regulated signaling by RIG-I is controlled by coordination of RNA and ATP binding Megan E. Fitzgerald, David C. Rawling, Olga Potapova, Xiaoming Ren and Anna Marie Pyle Nucleic Acids Res. 2017 (45) : 1442-1454
167.	Opportunities and challenges in RNA structural modeling and design Tamar Schlick and Anna Marie Pyle Biophys J. 2017 (Epub ahead of print) :
166.	Visualizing the secondary and tertiary architectural domains of lncRNA RepA Fei Liu, Srinivas Somarowthu and Anna Marie Pyle Nat Chem Biol 2017 (13) : 282-289
165.	Inverted repeat Alu elements in the human lincRNA-p21 adopt a conserved secondary structure that regulates RNA function Isabel Chillon and Anna Marie Pyle Nucleic Acids Res. 2016 (44) : 9462-9471
164.	Group II intron self-splicing Anna Marie Pyle Annu Rev Biophys. 2016 (45) : 183-205
163.	Transcriptome analysis of human cumulus cells reveals hypoxia as the main determinant of follicular senescence Emanuela Molinari, Bar Haim, Anna Marie Pyle and Pasquale Patrizio Mol Hum Reprod. 2016 (22) : 866-876
162.	Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution Chen Zhao and Anna Marie Pyle Nat Struct Mol Biol. 2016 (23) : 558-565
161.	Editorial overview: Nucleic acids and their protein complexes David M. Lilley and Anna Marie Pyle Curr Opin Struct Biol. 2016 (36) : vii-viii
160.	The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures Nathan Pirakitikulr, Andrew Kohlway, Brett D. Lindenbach and Anna Marie Pyle Mol Cell 2016 (62) : 111-120
159.	Challenges in RNA structural modeling and design Anna Marie Pyle and Tamar Schlick J Mol Biol. 2016 (428) : 733-735
158.	Crystal structure of group II intron domain 1 reveals a template for RNA assembly Chen Zhao, K.R. Rajashankar, Marco Marcia and Anna Marie Pyle Nature Chemical Biology 2015 (11) : 967-972
157.	Establishing the role of ATP for the function of the RIG-I innate immune sensor David Rawling, Megan Fitzgerald and Anna Marie Pyle Elife 2015 (4) : E09391
156.	Native Purification and Analysis of Long RNAs Isabel Chillón Gazquez, Marco Marcia, Michal Legiewicz, Fei Liu, Srinivas Somarowthu and Anna Marie Pyle Methods in Enzymology 2015 (558) : 3-37
155.	HOTAIR forms an intricate and modular secondary structure Srinivas Somarowthu, Michal Legiewicz, Isabel Chillón Gazquez, Marco Marcia, Fei Liu and Anna Marie Pyle Mol Cell 2015 (58) : 353-361
154.	Rediscovering RNA Anna Marie Pyle RNA 2015 (21) : 714-715
153.	Temperature-dependent innate defense against the common cold virus limits viral replication at warm temperature in mouse airway cells Ellen F. Foxman, James A. Storer, Megan E. Fitzgerald, Bethany R. Wasik, Lin Hou, Hongyu Zhao, Paul E. Turner, Anna Marie Pyle and Akiko Iwasaki Proc. Natl. Acad. Sci. USA 2015 (112) : 827-832
152.	Looking at LncRNAs with the Ribozyme Toolkit Anna Marie Pyle Mol Cell 2014 (56) : 13-17
151.	The RIG-I ATPase core has evolved a functional requirement for alosteric stabilization by the pincer domain David Rawling, Andrew Kohlway, Dahai Luo, Steve C. Ding and Anna Marie Pyle Nucleic Acids Res. 2014 (42) : 11601-11611
150.	The linker region of NS3 plays a critical role in the replication and infectivity of hepatitis C virus Andrew Kohlway, Nathan Pirakitikulr, Steve C. Ding, Feng Yang, Dahai Luo, Brett D. Lindenbach and Anna Marie Pyle J Virol. 2014 (18) : 10970-10974
149.	An evolving arsenal: viral RNA detection by RIG-I-like receptors Megan Fitzgerald, David C. Rawling, Adriana Vela and Anna Marie Pyle Curr Opin Microbiol. 2014 (20) : 76-81
148.	Parts, assembly and operation of the RIG-I family of motors David C. Rawling and Anna Marie Pyle Curr Opin Struct Biol. 2014 (25) : 25-33
147.	Principles of ion recognition in RNA: insights from the group II intron structures Marco Marcia and Anna Marie Pyle RNA 2014 (20) : 516-27
146.	Dicer-related helicase 3 (DRH-3) forms an obligate dimer for recognizing 22G-RNA Megan Fitzgerald, Adriana Vela and Anna Marie Pyle Nucleic Acids Res. 2014 (42) : 19-30
145.	Coordinating the party: assembly factors and ribogenesis Anna Marie Pyle Mol Cell 2013 (52) : 469-470
144.	Visualizing the ai5γ group IIB intron Srinivas Somarowthu, Michal Legiewicz, Kevin S. Keating and Anna Marie Pyle Nucleic Acids Res. 2013 (42) : 1947-58
143.	Solving nucleic acid structures by molecular replacement: examples from group II intron studies Marco Marcia, Elisabeth Humphris-Narayaan, Kevin S. Keating, Srinivas Somarowthu, K. Rajashankar and Anna Marie Pyle Acta Crystallogr D 2013 (69) : 2174-2185
142.	Hepatitis C virus RNA replication and virus particle assembly require specific dimerization of the NS4A protein transmembrane domain Andrew Kohlway, Nathan Pirakitikulr, Francisco N. Barrera, Olga Potapova, Donald M. Engelman, Anna Marie Pyle and Brett D. Lindenbach J Virol. 2014 (88) : 628-42
141.	Non-coding RNAs: A Story of Networks and Long Distance Relationships M. Ostankovitch and Anna Marie Pyle J Mol Biol. 2013 (425) : 3577-3581
140.	Defining the functional determinants for RNA surveillance by RIG-I Andrew Kohlway, Dahai Luo, David C. Rawling, Steve C. Ding and Anna Marie Pyle EMBO Rep. 2013 (14) : 772-779
139.	Predicted group II intron lineages E and F comprise catalytically active ribozymes Vivian Nagy, Nathan Parakitikulr, Katherine I. Zhou, Isabel Chillon, Jerome Luo and Anna Marie Pyle RNA 2013 (19) : 1266-1278
138.	Now on display: a gallery of group II intron structures at different stages of catalysis Marco Marcia, Srinivas Somarowthu and Anna Marie Pyle Mob DNA 2013 (4) : 14
137.	Duplex RNA activated ATPases (DRAs): Platforms for RNA sensing signaling and processing Dahai Luo, Andrew Kohlway and Anna Marie Pyle RNA Biol. 2013 (10) : 111-120
136.	Visualizing group II intron catalysis through the stages of splicing Marco Marcia and Anna Marie Pyle Cell 2012 (151) : 497-507
135.	The thermodynamic basis for viral RNA detection by the RIG-I innate immune sensor Adriana Vela, Olga Fedorova, Steve O. Ding and Anna Marie Pyle J Biol Chem. 2012 (287) : 42564-42573
134.	Visualizing the determinants of viral RNA recognition by innate immune sensor RIG-I Dahai Luo, Andrew Kohlway, Adriana Vela and Anna Marie Pyle Structure 2012 (20) : 1983-1988
133.	RCrane: semi-automated RNA model building Kevin S. Keating and Anna Marie Pyle Acta Crystallogr D 2012 (68) : 985-995
132.	Molecular mechanics of RNA translocases Steve C. Ding and Anna Marie Pyle Methods Enzymol. 2012 (511) : 131-147
131.	The brace for a growing scaffold: Mss116 protein promotes RNA folding by stabilizing an early assembly intermediate Olga Fedorova and Anna Marie Pyle J Mol Biol. 2012 (422) : 347-365
130.	Crystal structure of a group II intron in the pre-catalytic state RT Chan, AR Robart, KR Rajashankar, Anna Marie Pyle and Navtej Toor Nat Struct Mol Biol. 2012 (19) : 555-557
129.	Discrete RNA libraries from pseudo-torsional space Elisabeth Humphris-Narayanan and Anna Marie Pyle, J Mol Biol. 2012 (421) : 6-26
128.	Structural insights into RNA recognition by RIG-I Dahai Luo, Steve C. Ding, Adriana Vela, Andrew Kohlway, Brett D. Lindenbach and Anna Marie Pyle Cell 2011 (147) : 409-422
127.	The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks Samuel E. Butcher, Anna Marie Pyle Acc Chem Res. 2011 (44) : 1302-1311
126.	RNA helicases and remodeling proteins Anna Marie Pyle Curr Opin Chem Biol. 2011 (15) : 636-642
125.	A new way to see RNA Kevin S, Keating, Elisabeth L. Humphris and Anna Marie Pyle Q Rev Biophys. 2011 (44) : 433-466
124.	The ever-growing complexity of nucleic acids: from small DNA and RNA motifs to large molecular assemblies and machines Anna Marie Pyle and Zippora Shakked Curr Opin Struct Biol. 2011 (21) : 293-295
123.	Mechanism of Mss116 ATPase Reveals Functional Diversity of DEAD-Box Proteins Wenxiang. Cao, Maria M. Cowman, Steve Ding, Arnon Henn, Elizabeth R. Middleton, Michael J. Bradley, Elizabeth Rhoades, David D. Hackney, Anna Marie Pyle and Enrique M. De La Cruz J Mol Biol. 2011 (409) : 399-414
122.	Unmasking the active helicase conformation of NS3 from Hepatitis C virus Steve C. Ding, Andrew S. Kohlway and Anna Marie Pyle J Virol. 2011 (85) : 4343-4353
121.	Visualizing ATP-dependent RNA translocation by the NS3 helicase from HCV TC Appleby, R Anderson, Olga Fedorova, Anna Marie Pyle, X Liu, KM Brendza, JR Somoza J Mol Biol. 2011 (405) : 1139-1153
120.	The acidic domain of hepatitis C virus NS4A contributes to RNA replication and virus particle assembly Tung Phan, Andrew Kohlway, Peniel Dimberu, Anna Marie Pyle and Brett D. Lindenbach J Virol. 2011 (85) : 1193-1204
119.	Single-molecule analysis of Mss116-mediated group II intron folding Krishanthi S. Karunatilaka, Amanda Solem, Anna Marie Pyle and David Rueda Nature 2010 (467) : 935-939
118.	Touching RNA Anna Marie Pyle The Scientist 2010 (24) : 34-39
117.	Dual roles for the Mss116 cofactor during splicing of the ai5γ group II intron Nora Zingler, Amanda Solem and Anna Marie Pyle Nucl. Acids Res. 2010 (38) : 6602-6609
116.	Double stranded RNA-dependent ATPase DRH-3: insight into its role in RNA silencing in Caenorhabditis elegans Christian Matranga and Anna Marie Pyle J Biol Chem. 2010 (285) : 25363-25371
115.	The tertiary structure of Group II introns: implications for Biological Function and Evolution Anna Marie Pyle Crit Rev Biochem Mol Biol. 2010 (45) : 215-232
114.	Semiautomated model building for RNA crystallography by using a directed rotameric approach Kevin S. Keating and Anna M. Pyle PNAS 2010 (107) : 8177-8182
113.	Protein facilitated folding of group II intron ribozymes Olga Fedorova, Amanda Solem and Anna Marie Pyle J Mol Biol. 2010 (397) : 799-813
112.	The 2’-OH group at the group II intron terminus acts as a proton shuttle to permit reverse splicing Michael Roitzsch, Olga Fedorova and Anna Marie Pyle Nat Chem Biol. 2010 (6) : 218-224
111.	The NPH-II helicase displays efficient DNA-RNA helicase activity and a pronounced purine sequence bias Sean Taylor, Amanda Solem, Jane Kawaoka and Anna Marie Pyle J Biol Chem. 2010 (285) : 11692-11703
110.	Tertiary architecture of the Oceanobacillus iheynesis group II intron Navtej Toor, Kevin S. Keating, Olga Fedorova, K. Rajashankar, Jimin Wang and Anna Marie Pyle RNA 2010 (16) : 57-69
109.	A structural analysis of the group II intron active site and implications for the spliceosome Kevin S. Keating, Navtej Toor, Philip S. Perlman and Anna Marie Pyle RNA 2010 (16) : 1-9
108.	How to drive your helicase in a straight line Anna Marie Pyle Cell 2009 (139) : 458-459
107.	Structural insights into RNA splicing Navtej Toor, Kevin S. Keating and Anna Marie Pyle Curr Opin Struct Biol. 2009 (19) : 260-266
106.	The linear form of a group II intron catalyzes efficient autocatalytic reverse-splicing, establishing a potential for mobility Michael Roitzsch and Anna Marie Pyle RNA 2009 (15) : 473-482
105.	The NS4A protein from hepatitis C virus promotes RNA-coupled ATP hydrolysis by the NS3 helicase Rudolf K. Beran, Brett D. Lindenbach. and Anna M. Pyle J Virol. 2009 (83) : 3268-3275
104.	Establishing a mechanistic basis for the large kinetic steps of the NS3 helicase Victor Serebrov, Rudolf K. Beran and Anna Marie Pyle J Biol Chem. 2009 (284) : 2512-2521
103.	Structural Basis for Exon Recognition by a Group II Intron Navtej Toor. K. Rajashankar, Kevin S. Keating and Anna M. Pyle Nat Struct Mol Biol. 2008 (15) : 1221-1222
102.	Protein-facilitated ribozyme folding and catalysis Nora Zingler, Amanda Solem and Anna Marie Pyle Nucleic Acids Symp Ser (Oxf). No. 52 2008 (52) : 67-68
101.	The GANC Tetraloop: A novel motif in the Group IIC intron structure Kevin S. Keating, Navtej Toor and Anna Marie Pyle J Mol Biol. 2008 (383) : 475-481
100.	Hepatitis C viral NS3-4A protease activity is enhanced by the NS3 helicase Rudolf K.F. Beran and Anna Marie Pyle J Biol Chem. 2008 (283) : 29929-29937
99.	Group II introns and their protein collaborators Amanda Solem, Nora Zingler, Anna Marie Pyle and Jennifer Li-Pook-Than in Non-Protein Coding RNAs (ed.N.G. Walter et al.), Ch. 8 2008 () :
98.	A conserved element that stabilizes the group II intron active site Olga Fedorova and Anna Marie Pyle RNA 2008 (14) : 1048-1056
97.	Group II Introns: Catalysts for splicing, genomic change and evolution Anna Marie Pyle in Ribozymes and RNA Catalysis (ed. D.M.J. Lilley and F. Eckstein), pp. 201-228. Royal Society of Chemistry, Cambridge 2008 () :
96.	Crystal structure of a self-spliced group II intron Navtej Toor, Kevin S. Keating, Sean D. Taylor and Anna Marie Pyle Science 2008 (320) : 77-82
95.	Translocation and unwinding mechanisms of RNA and DNA helicases Anna Marie Pyle Ann Rev Biophys 2008 (37) : 317-336
94.	RNA backbone consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution) Jane S. Richardson, Bohdan Schneider, L.W. Murray, G.J. Kapral, R.M. Immormino, J.J. Headd, D.C. Richardson, D. Ham, E. Hershkovits, L.D. Williams, Kevin S. Keating, Anna Marie Pyle, D. Micallef, J. Westbrook and H.M. Berman RNA 2008 (14) : 465-481
93.	Three essential and conserved regions of a group II intron are proximal to the 5’-splice site Alexandre de Lencastre and Anna Marie Pyle RNA 2008 (14) : 11-24
92.	A kinetic intermediate that regulates proper folding of a group II intron RNA Christina Waldsich and Anna Marie Pyle J Mol Biol. 2008 (375) : 572-580
91.	The serine protease domain of hepatitis C viral NS3 activates RNA helicase activity by promoting the binding of RNA substrate Rudolf K. Beran, Victor Serebrov and Anna Marie Pyle J Biol Chem. 2007 (282) : 34913-34920
90.	Evaluating and learning from RNA pseudotorsional space: Quantitative validation of a reduced representation for RNA structure Leven M. Wadley, Kevin S. Keating, Chuck M. Duarte and Anna Marie Pyle J Mol Biol. 2007 (372) : 942-957
89.	The C terminus of hepatitis C virus NS4A encodes an electrostatic switch that regulates NS5A hyperphosphorylation and viral replication Brett D. Lindenbach, B.M. Pragai, R. Montserret, Rudolf K. Beran, Anna Marie Pyle, F. Penin, and C.M. Rice J Virol. 2007 (81) : 8905-8918
88.	Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase S. Myong, Michael M. Bruno, Anna Marie Pyle, and T. Ha Science 2007 (317) : 513-516
87.	Tinkering with transcription factor proteins: the role of transcription factor adaptation in developmental evolution Günter P. Wagner and Anna Marie Pyle Novartis Found.Symp. 2007 (284) : 116-125
86.	Folding of group II introns: a model system for large, multidomain RNAs? Anna Marie Pyle, Olga Fedorova and Christina Waldsich Trends Biochem Sci. 2007 (32) : 138-145
85.	Calculation of pK(a)s in RNA: On the structural origins and functional roles of protonated nucleotides Chris L. Tang, Emil Alexov, Anna Marie Pyle and Barry Honig J Mol Biol. 2007 (366) : 1475-1496
84.	Group II intron folding under near-physiological conditions: collapsing to the near-native state Olga Fedorova, Christina Waldsich and Anna Marie Pyle J Mol Biol. 2007 (366) : 1099-1114
83.	Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry Roland K.O. Sigel and Anna Marie Pyle Chemical Reviews 2007 (107) : 97-113
82.	A folding control element for tertiary collapse of a group II intron ribozyme Christina Waldsich and Anna Marie Pyle Nature Structural & Molecular Biology 2007 (14) : 37-44
81.	A DEAD protein that activates intron self-splicing without unwinding RNA Amanda Solem, Nora Zingler and Anna Marie Pyle Mol Cell 2006 (24) : 611-617
80.	The receptor for branch-site docking within a group II intron active site Stephanie Hamill and Anna Marie Pyle Mol Cell 2006 (23) : 831-840
79.	Robust translocation along a molecular monorail: the NS3 helicase from hepatitis C virus traverses unusually large disruptions in its track Rudolf K. Beran, Michael M. Bruno, Heath A. Bowers, Eckhard Jankowsky and Anna Marie Pyle J Mol Biol. 2006 (358) : 974-982
78.	Nucleic acids an Editorial Overview edited by Anna Marie Pyle and Jonathan Widom Curr Opin Struct Biol. 2006 (16) : 267-269
77.	RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP Sophie Dumont, Wei Cheng, Victor Serebrov, Rudolf Beran, Ignacio Tinoco Jr., Anna Marie Pyle and Carlos Bustamante Nature 2006 (439) : 105-108
76.	RNA Structure and Function Anna Marie Pyle in Nucleic Acids in Chemistry and Biology, 3rd edition (ed. G. M. Blackburn et al.), pp. 253-293. The Royal Society of Chemistry, Thomas Graham House, Cambridge, UK 2006 () :
75.	Group II Introns: Ribozymes That Splice RNA and Invade DNA Anna Marie Pyle and Alan M. Lambowitz in The RNA World, 3rd edition (ed. R.F. Gesteland et al.), pp. 469-505. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York 2006 () :
74.	Nucleotide Analog Interference Mapping and Suppression: Specific Applications in Studies of RNA Tertiary Structure, Dynamic Helicase Mechanism and RNA-Protein Interactions Olga Fedorova, Marc Boudvillain, Jane Kawaoka and Anna Marie Pyle in Handbook of RNA Biochemistry (ed. R.K. Hartmann et al.) pp. 259-293. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 2005 () :
73.	An obligate intermediate along the slow folding pathway of a group II intron ribozyme Linhui J. Su, Christina Waldsich and Anna Marie Pyle NAR 2005 (33) : 6674-6687
72.	Linking the group II intron catalytic domains: Tertiary contacts and structural features of domain 3 Olga Fedorova and Anna Marie Pyle EMBO J. 2005 (24) : 3906-3916
71.	Capping by branching: a new ribozyme makes tiny lariats Anna Marie Pyle Science 2005 (309) : 1530-1531
70.	Single active-site region for a group II intron Alexandre DeLencastre, Stephanie Hamill and Anna Marie Pyle Nat Struct Mol Biol. 2005 (12) : 626-627
69.	Choosing between DNA and RNA: the polymer specificity of RNA helicase NPH-II Jane Kawaoka and Anna Marie Pyle Nucl. Acids Res. 2005 (33) : 644-649
68.	Prediction of functional tertiary interactions and intermolecular interfaces from primary sequence data Phillip S. Pang, Eckhard Jankowsky, Leven M. Wadley and Anna Marie Pyle J. Exp. Zoolog B Mol Dev Evol. 2005 (304) : 50-63
67.	The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery Leven M. Wadley and Anna Marie Pyle Nucl. Acids Res. 2004 (32) : 50-63
66.	DNA repair: big engine finds small breaks Anna Marie Pyle Nature 2004 (432) : 157-158
65.	Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase Victor Serebrov and Anna Marie Pyle Nature 2004 (430) : 476-480
64.	Backbone tracking by the SF2 helicase NPH-II Jane Kawaoka, Eckhard Jankowsky, E. and Anna Marie Pyle Nature Structural & Molecular Biology 2004 (11) : 526-530
63.	Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif Roland K.O. Sigel, Dipali G. Sashital, Dana L. Abramovitz, Arthur G. Palmer III, Samuel E. Butcher and Anna Marie Pyle Nature Structural & Molecular Biology 2004 (11) : 187-192
62.	An alternative route for the folding of large RNAs: Apparent two-state folding by a group II intron ribozyme Linhui J. Su, Michael Brenowitz and Anna Marie Pyle J Mol Biol. 2003 (334) : 639-652
61.	RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space Carlos M. Duarte, Leven M. Wadley and Anna Marie Pyle Nucleic Acids Research 2003 (31) : 4755-4761
60.	Domains 2 and 3 interact to form critical elements of the group II intron active-site Olga Fedorova and Anna Marie Pyle J Mol Biol. 2003 (330) : 197-209
59.	Lanthanide ions as probes for metal ions in the structure and catalytic mechanism of ribozymes Roland Sigel and Anna Marie Pyle Met Ions Biol Syst. 2003 (40) : 477-512
58.	A group II intron inserted into a bacterial heat-shock operon shows autocatalytic activity and unusual thermostability Catherine Adamidi, Olga Fedorova, and Anna Marie Pyle Biochemistry 2003 (42) : 3409-3418
57.	The pathway for DNA recognition and RNA integration by a group II intron retrotransposon Yasunori Aizawa, Qing Xiang, Alan M. Lambowitz and Anna Marie Pyle Molecular Cell 2003 (11) : 795-805
56.	Group II introns: highly specific endonucleases with modular structures and diverse catalytic functions Olga Fedorova, Linhui Julie Su and Anna Marie Pyle Methods 2002 (28) : 323-335
55.	Metal ions in the structure and function of RNA Anna Marie Pyle J Biol Inorg Chem. 2002 (7) : 679-690
54.	The Hepatitis C Viral NS3 Protein is a Processive DNA Helicase with Cofactor Enhanced RNA Unwinding Philip S. Pang, Eckhard Jankowsky, Paul Planet and Anna Marie Pyle EMBO J. 2002 (21) : 1168-1176
53.	Mda-5, an interferon-inducible atypical putative RNA helicase with dsRNA-dependent ATPase activity and melanoma growth suppressive properties Dong-Chul Kang, Rahul V. Gopalkrishnan, Qingping Wu, Eckhard Jankowsky, Anna Marie Pyle and Paul B. Fisher PNAS 2002 (99) : 637-642
52.	Productive folding to the native state by a group II intron ribozyme Jennifer Swisher, Lin-Hui Julie Su, Michael Brenowitz, Vernon Anderson, and Anna Marie Pyle J. Mol. Biol. 2002 (315) : 297-310
51.	Kinetic dissection of the multistep process in L1.ltrB intron mobility Aizawa, Xiang and Anna Marie Pyle Nucleic Acids Res. Suppl. 2001 () : 249-250
50.	Control of branch-site choice by a group II intron Vi T. Chu, Catherine Adamidi, Qiaolian Liu, Philip S. Perlman, and Anna Marie Pyle EMBO J. 2001 (20) : 6866-6876
49.	Visualizing the solvent inaccessible core of a group II intron ribozyme Jennifer Swisher, Carlos Duarte, Linhui Julie Su, and Anna Marie Pyle EMBO J. 2001 (20) : 2051-2061
48.	Guiding ribozyme cleavage through motif recognition: the mechanism of cleavage site selection by a group II intron ribozyme Linhui Julie Su, Peter Z. Qin, William J. Michels and Anna Marie Pyle J. Mol. Biol. 2001 (306) : 655-668
47.	Active disruption of an RNA-protein interaction by a DExH/D RNA Helicase Eckhard Jankowsky, Christian H. Gross, Stewart Shuman and Anna Marie Pyle Science 2001 (291) : 121-125
46.	Metal ion binding sites in a group II intron core Roland K.O. Sigel, Anand Vaidya and Anna Marie Pyle Nature Structural Biology 2000 (7) : 1111-1116
45.	A tertiary interaction that links active-site domains to the 5’-splice site of a group II intron Marc Boudvillain, Alexandre de Lencastre and Anna Marie Pyle Nature 2000 (406) : 315-317
44.	Using DNAzymes to Cut, Process and Map RNA Molecules for Structural Studies or Modification Anna Marie Pyle, Vi T. Chu, Eckhard Jankowsky and Marc Boudvillain Methods in Enz. 2000 (317) : 140-146
43.	New tricks from an itinerant intron Anna Marie Pyle Nature Structural Biology 2000 (7) : 352-354
42.	The DExH/D protein NPH-II is a processive and directional motor for unwinding RNA Eckhard Jankowsky, Christian H. Gross, Stewart Shuman and Anna Marie Pyle Nature 2000 (403) : 447-451
41.	Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function Kevin Chin, Kim A. Sharp, Barry Honig and Anna Marie Pyle Nature Structural Biology 1999 (6) : 1055-1061
40.	Antagonistic substrate binding by a group II intron ribozyme Peter Z. Qin and Anna Marie Pyle J. Mol. Biol. 1999 (291) : 15-27
39.	Site specific labeling of RNA with fluorophores and other structural probes Peter Z. Qin and Anna Marie Pyle Methods 1999 (18) : 60-70
38.	Stepping through an RNA structure: a novel approach to conformational analysis Chuck Duarte and Anna Marie Pyle J. Mol. Biol. 1998 (284) : 1465-1478
37.	Analysis of putative RNase sensitivity and protease insensitivity of demethylation activity in extracts from rat myoblasts Jennifer A. Swisher, Eyal Rand, Howard Cedar and Anna Marie Pyle Nucl. Acids Res. 1998 (26) : 5573-5580
36.	A map of the binding site for catalytic domain 5 in the core of a group II intron ribozyme Boyana B. Konforti, Qiaolian Liu and Anna Marie Pyle EMBO J. 1998 (17) : 7105-7117
35.	Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis Marc Boudvillain and Anna Marie Py EMBO J. 1998 (17) : 7091-7104
34.	More than one way to splice an RNA: Branching without a bulge and splicing without branching in group II introns Vi T. Chu, Qiaolian Liu, Mircea Podar, Philip S. Perlman and Anna Marie Pyle RNA 1998 (4) : 1186-1202
33.	The architectural organization and mechanistic function of group II intron structural elements Peter Zhifeng Qin and Anna Marie Pyle Current Opinion in Structural Biology 1998 (8) : 301-308
32.	The DEAH-box protein Prp22 is an ATPase that mediates ATP-dependent mRNA release from the spliceosome and unwinds RNA duplexes John D.O. Wagner, Eckhard Jankowsky, Mahshid Company, Anna Marie Pyle and John N. Abelson EMBO J. 1998 (17) : 2926-2937
31.	The sequence specificity of a group II intron ribozyme: multiple mechanisms for promoting unusually high discrimination against mismatched targets Qing Xiang, Peter Z. Qin, William J. Michels, Keri Freeland and Anna Marie Pyle Biochemistry 1998 (37) : 3839-3849
30.	Group II intron splicing in-vivo through first step hydrolysis Mircea Podar, Vi T. Chu, Anna Marie Pyle and Philip S. Perlman Nature 1998 (391) : 915-918
29.	Ribozyme catalysis from the major groove of group II intron domain 5 Boyana B. Konforti, Dana L. Abramovitz, Carlos M. Duarte, Alex Karpeisky, Leonid Beigelman and Anna Marie Pyle Molecular Cell 1998 (1) : 433-442
28.	Stopped-flow fluorescence spectroscopy reveals that domain 1 of a group II intron is an independent folding unit Peter Z. Qin and Anna Marie Pyle Biochemistry 1997 (36) : 4718-4730
27.	Branch-site selection in a group II intron mediated by active recognition of the adenine amino group and exclusion of non-adenine functionalities Qiaolian Liu, Justin B. Green, Arbi Khodadadi, Leonid Beigelman, Peter Haeberli and Anna Marie Pyle J. Mol. Biol. 1997 (267) : 163-171
26.	Remarkable morphological variability of a common RNA folding motif: the GNRA tetraloop-receptor interaction Dana L. Abramovitz and Anna Marie Pyle J. Mol. Biol. 1997 (266) : 493-506
25.	Mobile genetic elements. Inside an intron invasion Anna Marie Pyle Nature 1996 (381) : 280-281
24.	Catalytic role of 2'-hydroxyl groups within a group II intron active site Dana L. Abramovitz, Richard A. Friedman and Anna Marie Pyle Science 1996 (271) : 1410-1413
23.	Two competing pathways for self-splicing by group II introns; a quantitative analysis of in-vitro reaction rates and products Danette Daniels, William J. Michels Jr. and Anna Marie Pyle Journal of Molecular Biology 1996 (256) : 31-49
22.	Role of metal ions in ribozymes Anna Marie Pyle Metal Ions in Biological Systems 1996 (32) : 479-520
21.	Catalytic reaction mechanisms and structural features of group II intron ribozymes Anna Marie Pyle Nucleic Acids and Molecular Biology 1995 (10 Anniversary Volume) :
20.	Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts to substrate 2'-hydroxyl groups Edmund A. Griffin, Zhifeng Qin, William J. Michels Jr., and Anna Marie Pyle Chemistry and Biology 1995 (2) : 761-770
19.	RNA folding Anna Marie Pyle and Justin B. Green Current Opinion in Structural Biology 1995 (5) : 303-310
18.	Branch-point attack in group II introns is a highly reversible transesterification, providing a potential proof-reading mechanism for 5'-splice site selection Kevin Chin and Anna Marie Pyle RNA 1995 (1) : 391-406
17.	Conversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: Elucidation of reaction mechanism and structure/function relationships William J. Michels Jr. and Anna Marie Pyle Biochemistry 1995 (34) : 2965-2977
16.	Replacement of the conserved G-U with a G-C pair at the cleavage site of the Tetrahymena ribozyme decreases binding, reactivity and fidelity Anna Marie Pyle, Sean Moran, Scott A. Strobel, Theresa Chapman, Douglas H. Turner and Thomas R. Cech Biochemistry 1994 (33) : 13856-13863
15.	Building a Kinetic Framework for Group II Intron Ribozyme Activity: Quantitation of Inter-Domain Binding and Reaction Rate Anna Marie Pyle and Justin B Green Biochemistry 1994 (33) : 2716-2725
14.	Ribozymes: A Distinct Class of Metalloenzymes Anna Marie Pyle Science 1993 (261) : 709-714
13.	RNA catalysis by a Group I ribozyme: Developing a model for transition state stabilization Thomas R. Cech, Daniel Herschlag, Joseph A. Piccirilli and Anna Marie Pyle J. Biol. Chem. 1992 (267) : 17479-17482
12.	RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme Anna Marie Pyle, Felicia L. Murphy and Thomas R. Cech Nature 1992 (358) : 123-128
11.	DNA photocleavage by phenanthrenequinone diimine complexes of Rhodium ( III): Shape-selective recognition and reactivity Ayesha Sitlani, Eric C. Long, Anna Marie Pyle and Jacqueline K. Barton J. Am. Chem. Soc. 1992 (114) : 2303-2312
10.	Ribozyme recognition of RNA by tertiary interactions with specific ribose 2'-OH groups Anna Marie Pyle and Thomas R. Cech Nature 1991 (350) : 628-630
9.	Direct measurement of oligonucleotide substrate binding to wild-type and mutant ribozymes from Tetrahymena Anna Marie Pyle, James A. McSwiggen and Thomas R. Cech Proc. Natl. Acad. Sci. USA 1990 (87) : 8187-8191
8.	Probing microstructures in double-helical DNA with chiral metal complexes: Recognition of changes in base-pair propeller twisting in solution Anna Marie Pyle, Takashi Morii, and Jacqueline K. Barton J. Am. Chem. Soc. 1990 (112) : 9432-9434
7.	Synthesis and characterization of physical, electronic, and photochemical aspects of 9,10-phenanthrenequinone diimine complexes of Ruthenium (II) and Rhodium (III) Anna Marie Pyle, Michael Y. Chiang and Jacqueline K. Barton Inorg. Chem. 1990 (29) :
6.	Probing nucleic acids with transition metal complexes Anna Marie Pyle and Jacqueline K. Barton Progress in Inorganic Chemistry: Bioinorganic Chemistry 1990 (38) : 413-75
5.	Shape-selective targeting of DNA by (phenanthrenequinone diimine)rhodium (III) photocleaving agents Anna Marie Pyle, Eric C. Long, and Jacqueline K. Barton J. Am. Chem. Soc. 1989 (111) : 4520
4.	Mixed-ligand complexes of Ruthenium (II): Factors governing binding to DNA Anna Marie Pyle, Jill P Rehmann, R. Meshoyrer, Challa V Kumar, Nicholas J Turro, and Jacqueline K Barton J. Am. Chem. Soc. 1989 (111) : 3051
3.	High-resolution footprinting of EcoR1 and distamycin with Rh(phi)2(bpy)3+, a new photofootprinting reagent Kiyoshi Uchida, Anna Marie Pyle, Takashi Morii, and Jacqueline K. Barton Nucleic Acids Res. 1989 (17) : 10259-10279
2.	Synthesis and spectroscopic characterization of the purple tris (phenanthrenequinone diimine) ruthenium (II) ion Anna Marie Pyle and Jacqueline K. Barton Inorg. Chem. 1987 (26) : 3820
1.	H/D exchange in methane and other saturated hydrocarbons catalyzed by a supported zirconium complex Anna Marie Pyle and Klaus-Joachim Jens J. Molec. Catalysis 1986 (38) : 337