Publications

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
Nature Chemical Biology 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 Biol Crystallogr 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 Cryst. 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
T. 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 ai5 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. The 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
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
A.M. Pyle, J.P. Rehmann, R. Meshoyrer, C.V. Kumar, N.J. Turro, and J.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
Nucl. 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