The chemical repertoire of natural ribozymes

Cited by (745)

Items 101–200 of 745

1. The Structural Basis of Ribozyme-Catalyzed RNA Assembly
   Robertson, Michael P., Scott, William G. · 2007 · Science
2. Review of machine learning methods for RNA secondary structure prediction
   Qi Zhao, Zheng Zhao, Xiaoya Fan, Zhengwei Yuan, Qian Mao, Yudong Yao · 2021 · PLoS Computational Biology
3. Observation of internal cleavage and ligation reactions of a ribozyme
   Michelle K. Nahas, Timothy J. Wilson, Sungchul Hohng, Kaera Jarvie, David M.J. Lilley, Taekjip Ha · 2004 · Nature Structural & Molecular Biology
4. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins
   Lakshminarayan M. Iyer, Saraswathi Abhiman, Alexander Maxwell Burroughs, Lakshminarayanan Aravind · 2009 · Molecular BioSystems
5. Topology and prediction of RNA pseudoknots
   Christian M. Reidys, Fenix W. D. Huang, Jørgen Ellegaard Andersen, Robert Penner, Peter Florian Stadler, Markus E. Nebel · 2011 · Bioinformatics
6. RNase P RNA mediated cleavage: Substrate recognition and catalysis
   Leif A. Kirsebom · 2007 · Biochimie
7. Forced-Unfolding and Force-Quench Refolding of RNA Hairpins
   Changbong Hyeon, Dave Thirumalai · 2006 · Biophysical Journal
8. Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures
   Samuel S. Cho, David L. Pincus, Dave Thirumalai · 2009 · Proceedings of the National Academy of Sciences
9. Modeling RNA secondary structure folding ensembles using SHAPE mapping data
   Aleksandar Spasic, Sarah M. Assmann, Philip C. Bevilacqua, David H. Mathews · 2017 · Nucleic Acids Research
10. RNA Recombination In Vivo in the Absence of Viral Replication
    Andreas Gallei, Alexander Pankraz, Heinz‐Jürgen Thiel, Paul Becher · 2004 · Journal of Virology
11. Direct Measurement of a pKa near Neutrality for the Catalytic Cytosine in the Genomic HDV Ribozyme Using Raman Crystallography
    Bo Gong, Jui-Hui Chen, Elaine S. Chase, Durga M. Chadalavada, Rieko Yajima, Barbara L. Golden, Philip C. Bevilacqua, PAUL R. CAREY · 2007 · Journal of the American Chemical Society
12. Structure and assembly of group I introns
    Sarah A. Woodson · 2005 · Current Opinion in Structural Biology
13. RNAiFOLD: A CONSTRAINT PROGRAMMING ALGORITHM FOR RNA INVERSE FOLDING AND MOLECULAR DESIGN
    Juan Antonio García-Martín, Peter Clote, Iván Dotú · 2012 · Journal of Bioinformatics and Computational Biology
14. The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life
    Koonin, Eugene V · 2007 · Biology Direct
15. Nonreplicative homologous RNA recombination: Promiscuous joining of RNA pieces?
    Anatoly P. Gmyl, SERGEY A. KORSHENKO, Evgeny V. Belousov, Elena V. Khitrina, Vadim I. Agol · 2003 · RNA
16. Molecular Crowding Accelerates Ribozyme Docking and Catalysis
    Bishnu P. Paudel, David Rueda · 2014 · Journal of the American Chemical Society
17. TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences
    Arif O. Harmanci, Gaurav Sharma A, David H. Mathews · 2011 · BMC Bioinformatics
18. Engineering a Ligand-Dependent RNA Transcriptional Activator
    Allen R. Buskirk, Angela Landrigan, David R. Liu · 2004 · Chemistry & Biology
19. Replication of human hepatitis delta virus: recent developments
    John M. Taylor · 2003 · Trends in Microbiology
20. Evolution of a General RNA-Cleaving FANA Enzyme
    Yajun Wang, Arlene K. Ngor, Ali Nikoomanzar, John Charles Chaput · 2018 · Nature Communications
21. Selection of the simplest RNA that binds isoleucine
    Catherine Lozupone, Shankar Changayil, Irene H. Majerfeld, Michael Yarus · 2003 · RNA
22. Montmorillonite protection of an UV-irradiated hairpin ribozyme: evolution of the RNA world in a mineral environment
    Elisa Biondi, Sergio Branciamore, Marie‐Christine Maurel, Enzo Gallori · 2007 · BMC Evolutionary Biology
23. Light-regulated Catalysis by an RNA-cleaving Deoxyribozyme
    Yong Liu, Dipankar Sen · 2004 · Journal of Molecular Biology
24. Leaving Group Activation by Aromatic Stacking: An Alternative to General Acid Catalysis
    Wim Versées, Stefan Loverix, An Vandemeulebroucke, Paul Geerlings, Jan Steyaert · 2004 · Journal of Molecular Biology
25. Deep learning models for RNA secondary structure prediction (probably) do not generalize across families
    Marcell Szikszai, Michael J. Wise, Amitava Datta, Max Ward, David H. Mathews · 2022 · Bioinformatics
26. Mechanical Unfolding of RNA: From Hairpins to Structures with Internal Multiloops
    Changbong Hyeon, Dave Thirumalai · 2006 · Biophysical Journal
27. RNA splicing: group I intron crystal structures reveal the basis of splice site selection and metal ion catalysis
    Mary R. Stahley, Scott A. Strobel · 2006 · Current Opinion in Structural Biology
28. RNA Sensors and Riboswitches: Self-Regulating Messages
    Eric C. Lai · 2003 · Current Biology
29. Engineering polymerases for applications in synthetic biology
    Ali Nikoomanzar, Nicholas Chim, Eric J. Yik, John Charles Chaput · 2020 · Quarterly Reviews of Biophysics
30. All-atom knowledge-based potential for RNA structure prediction and assessment
    Emidio Capriotti, Tomás Norambuena, Marc A. Martı́-Renom, Francisco Melo · 2011 · Bioinformatics
31. The Varkud satellite ribozyme
    David M.J. Lilley · 2004 · RNA
32. Thermodynamic and Kinetic Aspects of RNA Pulling Experiments
    Maria Mañosas, Félix Ritort · 2005 · Biophysical Journal
33. LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities
    He Zhang, Liang Zhang, David H. Mathews, Liang Huang · 2020 · Bioinformatics
34. Eukaryotic RNase P
    Hagit Mann, Yitzhak Ben-Asouli, Aleks Schein, Sana Moussa, Nayef Jarrous · 2003 · Molecular Cell
35. Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes
    Changbong Hyeon, Greg Morrison, Dave Thirumalai · 2008 · Proceedings of the National Academy of Sciences
36. The evolving ribosome: from non-coded peptide bond formation to sophisticated translation machinery
    Chen Davidovich, Matthew J. Belousoff, Anat Bashan, Ada Yonath · 2009 · Research in Microbiology
37. DNA Catalysis: Potential, Limitations, Open Questions
    Alessio Peracchi · 2005 · ChemBioChem
38. Metalloprotein and Metallo-DNA/RNAzyme Design: Current Approaches, Success Measures, and Future Challenges
    Yi Lu · 2006 · Inorganic Chemistry
39. An Interpretive Review of the Origin of Life Research
    David Penny · 2005 · Biology & Philosophy
40. Characterization of a native hammerhead ribozyme derived from schistosomes
    Edith M. Osborne, Janell E. Schaak, Victoria J. DeRose · 2005 · RNA
41. Polycationic dendrimers interact with RNA molecules: polyamine dendrimers inhibit the catalytic activity of Candida ribozymes
    Jiangyu Wu, Jiehua Zhou, Fanqi Qu, Penghui Bao, Yi Zhang, Ling Peng · 2004 · Chemical Communications
42. Evolutionary patterns of non-coding RNAs
    Athanasius F. Bompfünewerer · 2005 · Theory in Biosciences
43. Chemical and functional diversity of small molecule ligands for RNA
    Thomas Hermann · 2003 · Biopolymers
44. Gene and cell‐based therapies for heart disease
    Luis Gabriel Melo, Alok S. Pachori, Deling Kong, Massimiliano Gnecchi, Kai Wang, Richard E. Pratt, Victor J. Dzau · 2004 · The FASEB Journal
45. Unraveling Mg2+–RNA binding with atomistic molecular dynamics
    Richard A. Cunha, Giovanni Bussi · 2017 · RNA
46. Roles of protein subunits in RNA–protein complexes: Lessons from ribonuclease P
    John Hsieh, Andy J. Andrews, Carol A. Fierke · 2003 · Biopolymers
47. How to benchmark RNA secondary structure prediction accuracy
    David H. Mathews · 2019 · Methods
48. Predicting helical coaxial stacking in RNA multibranch loops
    Rahul Tyagi, David H. Mathews · 2007 · RNA
49. Two Decades of RNA Catalysis
    Victoria J. DeRose · 2002 · Chemistry & Biology
50. Endothelium-Targeted Gene and Cell-Based Therapies for Cardiovascular Disease
    Luis Gabriel Melo, Massimiliano Gnecchi, Alok S. Pachori, Deling Kong, Kai Wang, Xiaoli Liu, Richard E. Pratt, Victor J. Dzau · 2004 · Arteriosclerosis Thrombosis and Vascular Biology
51. RNAi: a novel antisense technology and its therapeutic potential.
    Anne Dallas, Alexander V. Vlassov · 2006 · PubMed
52. Catalytic RNA, ribozyme, and its applications in synthetic biology
    Soyeon V. Park, Jae‐Seong Yang, Hyesung Jo, Byunghwa Kang, Seung Soo Oh, Gyoo Yeol Jung · 2019 · Biotechnology Advances
53. Structure-based mechanistic insights into catalysis by small self-cleaving ribozymes
    Aiming Ren, Ronald Micura, Dinshaw J. Patel · 2017 · Current Opinion in Chemical Biology
54. ARTS: alignment of RNA tertiary structures
    Oranit Dror, Ruth Nussinov, Haim J. Wolfson · 2005 · Bioinformatics
55. Fungal Mitochondrial Genomes, Plasmids and Introns
    Georg Hausner · 2003 · Applied mycology and biotechnology
56. In Vivo Evolution of an RNA-Based Transcriptional Activator
    Allen R. Buskirk, Polina D. Kehayova, Angela Landrigan, David R. Liu · 2003 · Chemistry & Biology
57. Extracting Stacking Interaction Parameters for RNA from the Data Set of Native Structures
    Ruxandra I. Dima, Changbong Hyeon, Dave Thirumalai · 2005 · Journal of Molecular Biology
58. Hepatitis D Virus Replication
    John M. Taylor · 2015 · Cold Spring Harbor Perspectives in Medicine
59. Quaternized starch-based carrier for siRNA delivery: From cellular uptake to gene silencing
    Eliz Amar‐Lewis, Aharon Azagury, Ramesh Chintakunta, Riki Goldbart, Tamar Traitel, Jackson Prestwood, Dalit Landesman‐Milo, Dan Peer, Joseph Kost · 2014 · Journal of Controlled Release
60. Lipid vesicles chaperone an encapsulated RNA aptamer
    Ranajay Saha, Samuel Verbanic, Irene A. Chen · 2018 · Nature Communications
61. NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site
    Bernd Hoffmann, G. Thomas Mitchell, Patrick Gendron, François Major, Angela A. Andersen, Richard A. Collins, Pascale Legault · 2003 · Proceedings of the National Academy of Sciences
62. The dynamics of the RNA world: insights and challenges
    Kun, Ádám, Szilágyi, András, Könnyű, Balázs, Boza, Gergely, Zachar, István, Szathmáry, Eörs · 2015 · Annals of the New York Academy of Sciences
63. Biochemistry of Magnesium
    James Weston · 2009 · Patai's chemistry of functional groups
64. Catalytic DNA with phosphatase activity
    Jagadeeswaran Chandrasekar, Scott K. Silverman · 2013 · Proceedings of the National Academy of Sciences
65. Group II Intron Ribozymes and Metal Ions – A Delicate Relationship
    Roland K. O. Sigel · 2005 · European Journal of Inorganic Chemistry
66. A surface-mediated origin of the RNA world: biogenic activities of clay-adsorbed RNA molecules
    Marco Franchi, Enzo Gallori · 2005 · Gene
67. Ancient machinery embedded in the contemporary ribosome
    Matthew J. Belousoff, Chen Davidovich, Ella Zimmerman, Yaron Caspi, Itai Wekselman, Lin Rozenszajn, Tal Shapira, Ofir Sade-Falk, Leena Taha, Anat Bashan et al. · 2010 · Biochemical Society Transactions
68. DNA and RNA induced enantioselectivity in chemical synthesis
    Gérard Roelfes · 2006 · Molecular BioSystems
69. Gaining Target Access for Deoxyribozymes
    Steffen Schubert, Jens Peter Fürste, Denise Werk, Hans‐Peter Grunert, Heinz Zeichhardt, Volker A. Erdmann, Jens Kurreck · 2004 · Journal of Molecular Biology
70. Computational Exploration of Mobile Ion Distributions around RNA Duplex
    Serdal Kırmızıaltın, Ron Elber · 2010 · The Journal of Physical Chemistry B
71. Searching genomes for ribozymes and riboswitches
    Christian Hammann, Éric Westhof · 2007 · Genome biology
72. The 2′‐OH group of the peptidyl‐tRNA stabilizes an active conformation of the ribosomal PTC
    Hani S. Zaher, Jeffrey J Shaw, Scott A. Strobel, Rachel Green · 2011 · The EMBO Journal
73. RNA-based therapeutics for colorectal cancer: Updates and future directions
    Jingwen Liu, Bin Guo · 2019 · Pharmacological Research
74. Pursuing DNA Catalysts for Protein Modification
    Scott K. Silverman · 2015 · Accounts of Chemical Research
75. Candidates for Novel RNA Topologies
    Namhee Kim, Nahum Shiffeldrim, Hin Hark Gan, Tamar Schlick A · 2004 · Journal of Molecular Biology
76. RNase P RNA‐mediated cleavage
    Leif A. Kirsebom, Stefan Trobro · 2009 · IUBMB Life
77. Modular evolution and increase of functional complexity in replicating RNA molecules
    Susanna C. Manrubia, Carlos Briones · 2006 · RNA
78. The principles of guiding by RNA: chimeric RNA–protein enzymes
    Alexander Hüttenhofer, Peter Schattner · 2006 · Nature Reviews Genetics
79. Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling
    Richard I. McDonald, John P. Guilinger, Shankar Mukherji, Edward A. Curtis, Won I Lee, David R. Liu · 2014 · Nature Chemical Biology
80. Determining RNA Secondary Structure using Set-based Particle Swarm Optimization
    M. Neethling, Andries Petrus Engelbrecht · 2006 · IEEE Congress on Evolutionary Computation (CEC)
81. Crowders Perturb the Entropy of RNA Energy Landscapes to Favor Folding
    Duncan Kilburn, Joon Ho Roh, Reza Behrouzi, Robert M. Briber, Sarah A. Woodson · 2013 · Journal of the American Chemical Society
82. Targeting mortalin using conventional and RNA‐helicase‐coupled hammerhead ribozymes
    Renu Wadhwa, Hiroshi Andō, Hiroaki Kawasaki, Kazunari Taira, Sunil C. Kaul · 2003 · EMBO Reports
83. Structural insight into precursor ribosomal RNA processing by ribonuclease MRP
    Pengfei Lan, Bin Zhou, Ming Tan, Shaobai Li, Cao Mi, Jian Wu, Ming Lei · 2020 · Science
84. Two adjacent nuclear genes are required for functional complementation of a chloroplast trans‐splicing mutant from Chlamydomonas reinhardtii
    Carsten Balczun, Astrid Bunse, Daniela Hahn, Pierre Bennoun, Jörg Nickelsen, Ulrich Kück · 2005 · The Plant Journal
85. How do protein domains of low sequence complexity work?
    Masato Kato, Xiaoming Zhou, Steven Lanier McKnight · 2021 · RNA
86. Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects
    Jeffrey Zuber, Susan J. Schroeder, Hongying Sun, Douglas H. Turner, David H. Mathews · 2022 · Nucleic Acids Research
87. Methods for Computational Gene Prediction
    William H. Majoros · 2007 · Cambridge University Press eBooks
88. 7-Functionalized 7-deazapurine β-d and β-l-ribonucleosides related to tubercidin and 7-deazainosine: glycosylation of pyrrolo[2,3-d]pyrimidines with 1-O-acetyl-2,3,5-tri-O-benzoyl-β-d or β-l-ribofuranose
    Frank Seela, Xin Ming · 2007 · Tetrahedron
89. Spatial Models of Prebiotic Evolution: Soup Before Pizza?
    Scheuring, István, Czárán, Tamás, Szabó, Péter, Károlyi, György, Toroczkai, Zoltán · 2003 · Origins of life and evolution of the biosphere
90. Origin of self-replicating biopolymers: autocatalytic feedback can jump-start the RNA world
    Wu, Meng, Higgs, Paul G. · 2009 · Journal of Molecular Evolution
91. Single Nucleotide‐Catalyzed Biomimetic Reductive Amination
    Atul Kumar, Siddharth Sharma, Ram Awatar Maurya · 2010 · Advanced Synthesis & Catalysis
92. Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with ε/ζ Force Field Reparametrizations
    Vojtěch Mlýnský, Petra Kührová, Marie Zgarbová, Petr Jurečka, Nils G. Walter, Michal Otyepka, Jiřı́ Šponer, Pavel Banáš · 2015 · The Journal of Physical Chemistry B
93. Understanding the transition states of phosphodiester bond cleavage: Insights from heavy atom isotope effects
    Adam G. Cassano, Vernon E. Anderson, Michael E. Harris · 2003 · Biopolymers
94. Metal Ion Dependence, Thermodynamics, and Kinetics for Intramolecular Docking of a GAAA Tetraloop and Receptor Connected by a Flexible Linker
    Christopher D. Downey, Julie L. Fiore, Colby D. Stoddard, Jose Hector Hodak, David J. Nesbitt, Arthur Pardi · 2006 · Biochemistry
95. Architecture of a Diels-Alderase Ribozyme with a Preformed Catalytic Pocket
    Sonja Keiper, Dirk Bebenroth, Burckhard Seelig, Éric Westhof, Andres Jäschke · 2004 · Chemistry & Biology
96. Photochemical hammerhead ribozyme activation
    Douglas D. Young, Alexander Deiters · 2006 · Bioorganic & Medicinal Chemistry Letters
97. Dynalign II: common secondary structure prediction for RNA homologs with domain insertions
    Yinghan Fu, Gaurav Sharma A, David H. Mathews · 2014 · Nucleic Acids Research
98. Unwinding the twister ribozyme: from structure to mechanism
    Jennifer Gebetsberger, Ronald Micura · 2016 · Wiley Interdisciplinary Reviews - RNA
99. Ligand‐pKa Shifts through Metals: Potential Relevance to Ribozyme Chemistry
    Bernhard Lippert · 2008 · Chemistry & Biodiversity
100. Conformational change in the Bacillus subtilis RNase P holoenzyme–pre-tRNA complex enhances substrate affinity and limits cleavage rate
     John Hsieh, Carol A. Fierke · 2009 · RNA