The chemical repertoire of natural ribozymes

Cited by (745)

Items 301–400 of 745

1. On the aqueous origins of the condensation polymers of life
   Daniel E. Whitaker, Matthew W. Powner · 2024 · Nature Reviews Chemistry
2. Multiple Roles of Metal Ions in Large Ribozymes
   Daniela Donghi, Joachim Schnabl · 2011 · Royal Society of Chemistry eBooks
3. Fitness functions for RNA structure design
   Max Ward, Eliot Courtney, Elena Rivas · 2023 · Nucleic Acids Research
4. Hybridkatalysatoren auf DNA‐Basis für die asymmetrische organische Synthese
   Soyoung Park, Hiroshi Sugiyama · 2010 · Angewandte Chemie
5. Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs
   Uri Laserson · 2005 · Nucleic Acids Research
6. Novel organic antibacterial thermal stabilizers for transparent poly(vinyl chloride)
   Xiaopeng Xu, Si Chen, Yanqin Shi, Bozhen Wu, Meng Ma, Xu Wang · 2015 · Journal of Thermal Analysis and Calorimetry
7. Investigation of a Deoxyribozyme As a Biofuel Cell Catalyst
   Mi Zhang, Shuai Xu, Shelley D. Minteer, Dana A. Baum · 2011 · Journal of the American Chemical Society
8. RNA Protection is Effectively Achieved by Pullulan Film Formation
   Ping‐Yao Hsieh, M. Monsur Ali, Kha Tram, Sana Jahanshahi‐Anbuhi, Christine L. Brown, John D. Brennan, Carlos D. M. Filipe, Yingfu Li · 2017 · ChemBioChem
9. RNA finds a simpler way
   Thomas R. Cech · 2004 · Nature
10. Engineering of RNase P ribozyme for gene-targeting applications
    Stephen M.L. Raj, Fenyong Liu · 2003 · Gene
11. Oligonucleotide-Based Antiviral Strategies
    S. Schubert, Jens Kurreck · 2006 · Handbook of experimental pharmacology
12. Pressure modulates the self-cleavage step of the hairpin ribozyme
    Caroline Mello Pimentel Schuabb, Narendra Kumar, Salome Pataraia, Dominik Marx, Roland Winter · 2017 · Nature Communications
13. Aptamers, Riboswitches, and Ribozymes in S. cerevisiae Synthetic Biology
    Huanhuan Ge, Mario Andrea Marchisio · 2021 · Life
14. LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2
    Sizhen Li, He Zhang, Liang Zhang, Kaibo Liu, Boxiang Liu, David H. Mathews, Liang Huang · 2021 · Proceedings of the National Academy of Sciences
15. Self-Phosphorylating Deoxyribozyme Initiated Cascade Enzymatic Amplification for Guanosine-5′-triphosphate Detection
    Lida Wang, Yang Liu, Jinghong Li · 2014 · Analytical Chemistry
16. TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots
    Matthew G. Seetin, David H. Mathews · 2012 · Bioinformatics
17. The RNA‐Cleaving Bipartite DNAzyme Is a Distinctive Metalloenzyme
    Anat R. Feldman, Edward Ki Yun Leung, Andrew J. Bennet, Dipankar Sen · 2005 · ChemBioChem
18. Regulation by RNA
    M. Szymański, Jan Barciszewski · 2003 · International review of cytology
19. An RNA-making reactor for the origin of life
    Eugene V. Koonin · 2007 · Proceedings of the National Academy of Sciences
20. The First Example of an RNA Urea Synthase: Selection through the Enzyme Active Site of Human Neutrophile Elastase
    Dan Nieuwlandt, Madeline West, Xiaoqin Cheng, Gary Kirshenheuter, Bruce E. Eaton · 2003 · ChemBioChem
21. Coupling of Fast and Slow Modes in the Reaction Pathway of the Minimal Hammerhead Ribozyme Cleavage
    Ravi Radhakrishnan · 2007 · Biophysical Journal
22. Topology independent comparison of RNA 3D structures using the CLICK algorithm
    Minh N. Nguyen, Adelene Y. L. Sim, Yue Wan, Mallur Srivatsan Madhusudhan, Chandra Shekhar Verma · 2016 · Nucleic Acids Research
23. Developing RNase P ribozymes for gene-targeting and antiviral therapy
    Phong Trang, Kihoon Kim, Fenyong Liu · 2004 · Cellular Microbiology
24. The naturally trans-acting ribozyme RNase P RNA has leadzyme properties
    Ema Kikovska · 2005 · Nucleic Acids Research
25. Active Site Labeling of G8 in the Hairpin Ribozyme: Implications for Structure and Mechanism
    Jason M. Thomas, David M. Perrin · 2006 · Journal of the American Chemical Society
26. Three critical hydrogen bonds determine the catalytic activity of the Diels–Alderase ribozyme
    Stefanie Kraut, Dirk Bebenroth, Alexander Nierth, Andrei Yu Kobitski, Gerd Ulrich Nienhaus, Andres Jäschke · 2011 · Nucleic Acids Research
27. Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications
    Markus E. Nebel, Frank Weinberg · 2012 · Journal of Computational Biology
28. Multiscale Methods for Computational RNA Enzymology
    Maria T. Panteva, Thakshila Dissanayake, Haoyuan Chen, Brian K. Radak, Erich R. Kuechler, George M. Giambaşu, Tai‐Sung Lee, Darrin M. York · 2015 · Methods in enzymology on CD-ROM/Methods in enzymology
29. RNAbor: a web server for RNA structural neighbors
    Eva Freyhult, Vincent Moulton, Peter Clote · 2007 · Nucleic Acids Research
30. Linkage between proton binding and folding in RNA: implications for RNA catalysis
    Philip C. Bevilacqua, Trevor S. Brown, Durga M. Chadalavada, Juliette T. J. Lecomte, Ellen M. Moody, Shu‐ichi Nakano · 2005 · Biochemical Society Transactions
31. Cooperative binding and self-assembling behavior of cationic low molecular-weight dendrons with RNA molecules
    Jiehua Zhou, Jiangyu Wu, Xiaoxuan Liu, Fanqi Qu, Mu Xiao, Yi Zhang, Laurence Charles, Cheng‐Cai Zhang, Ling Peng · 2006 · Organic & Biomolecular Chemistry
32. Selection In Vitro of Allosteric Ribozymes
    Adam Roth, Ronald R. Breaker · 2004 · Humana Press eBooks
33. Role of Ion Valence in the Submillisecond Collapse and Folding of a Small RNA Domain
    Suzette A. Pabit, Julie L. Sutton, Huimin Chen, Lois Pollack · 2013 · Biochemistry
34. Step-Growth Control in Template-Directed Polymerization
    David G. Lynn, Xiaoyu Li, Andres F. Hernandez, Martha A. Grover, Nicholas V. Hud · 2010 · Heterocycles
35. Functional Nucleic Acids Under Unusual Conditions
    Tianjun Chang, Sisi He, Ryan Amini, Yingfu Li · 2021 · ChemBioChem
36. An Optimization Algorithm Based on Harmony Search for RNA Secondary Structure Prediction
    Abdulqader M. Mohsen, Ahamad Tajudin Khader, Dhanesh Ramachandram · 2010 · Studies in computational intelligence
37. A thiamin-utilizing ribozyme decarboxylates a pyruvate-like substrate
    Paul Cernak, Dipankar Sen · 2013 · Nature Chemistry
38. DNA Catalysis of a Normally Disfavored RNA Hydrolysis Reaction
    Darren J. Parker, Ying Xiao, John M. Aguilar, Scott K. Silverman · 2013 · Journal of the American Chemical Society
39. Electrochemical Surface Plasmon Resonance Measurement in a Microliter Volume Flow Cell for Evaluating the Affinity and Catalytic Activity of Biomolecules
    Ryoji Kurita, Yoshimi Yokota, Akio Ueda, Osamu Niwa · 2007 · Analytical Chemistry
40. Evolution of the capacity to evolve
    Robert L. Carroll · 2002 · Journal of Evolutionary Biology
41. The Role of Terahertz and Far-IR Spectroscopy in Understanding the Formation and Evolution of Interstellar Prebiotic Molecules
    Duncan V. Mifsud, Perry A. Hailey, Alejandra Traspas Muiña, Olivier Auriacombe, Nigel John Mason, S. Ioppolo · 2021 · Frontiers in Astronomy and Space Sciences
42. What are inorganic nanozymes? Artificial or inorganic enzymes
    Xiaolan Huang · 2022 · New Journal of Chemistry
43. Computational drug discovery under RNA times
    Mattia Bernetti, Riccardo Aguti, Stefano Bosio, Maurizio Recanatini, Matteo Masetti, Andrea Cavalli · 2022 · QRB Discovery
44. Exploring ribozyme conformational changes with X-ray crystallography
    Robert C. Spitale, Joseph E. Wedekind · 2009 · Methods
45. Early evolution of efficient enzymes and genome organization
    András Szilágyi, Ádám Kun, Eörs Szathmáry · 2012 · Biology Direct
46. One-Pot Production of RNA in High Yield and Purity Through Cleaving Tandem Transcripts
    Hannes Feyrer, Raluca Munteanu, Lorenzo Baronti, Katja Petzold · 2020 · Molecules
47. Evolving towards the hypercycle: A spatial model of molecular evolution
    Camille Stephan‐Otto Attolini, Peter Florian Stadler · 2006 · Physica D Nonlinear Phenomena
48. “RNA World”, a highly improbable scenario of the origin and early evolution of life on earth
    Piotr D. Bregestovski · 2015 · Journal of Evolutionary Biochemistry and Physiology
49. Convergent donor and acceptor substrate utilization among kinase ribozymes
    Elisa Biondi, David G. Nickens, Samantha Warren, Dayal Saran, Donald H. Burke · 2010 · Nucleic Acids Research
50. RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
    Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote · 2009 · Nucleic Acids Research
51. Bacterial Riboswitches and Ribozymes Potently Activate the Human Innate Immune Sensor PKR
    Chelsea M. Hull, Ananya Anmangandla, Philip C. Bevilacqua · 2016 · ACS Chemical Biology
52. Predicting RNA–RNA Interactions Using RNAstructure
    Laura DiChiacchio, David H. Mathews · 2016 · Methods in molecular biology
53. RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism, and Molecular Tensegrity
    Jong-Chin Lin, Changbong Hyeon, Dave Thirumalai · 2016
54. Highly Active Low Magnesium Hammerhead Ribozyme
    Agnieszka Fedoruk‐Wyszomirska, M. Szymański, Eliza Wyszko, Mirosława Z. Barciszewska, Jan Barciszewski · 2009 · The Journal of Biochemistry
55. An alternative to the RNA World Hypothesis
    Brian R. Francis · 2011 · Trends in Evolutionary Biology
56. Inherently Chiral Uranyl-Salophen Macrocycles: Computer-Aided Design and Resolution
    Antonella Dalla Cort, Luigi Mandolini, Chiara Pasquini, Luca Schiaffino · 2005 · The Journal of Organic Chemistry
57. Mimicking the First Step of RNA Splicing: An Artificial DNA Enzyme Can Synthesize Branched RNA Using an Oligonucleotide Leaving Group as a 5‘-Exon Analogue
    Rebecca L. Coppins, Scott K. Silverman · 2005 · Biochemistry
58. Deep generalizable prediction of RNA secondary structure via base pair motif energy
    Zhu, Heqin, Tang, Fenghe, Quan, Quan, Chen, Ke, Xiong, Peng, Zhou, S. Kevin · 2025 · Nature Communications
59. Magnesium-Dependent Active-Site Conformational Selection in the Diels−Alderase Ribozyme
    Tomasz Bereźniak, Maï Zahran, Petra Imhof, Andres Jäschke, Jeremy C. Smith · 2010 · Journal of the American Chemical Society
60. RNA global alignment in the joint sequence–structure space using elastic shape analysis
    José Laborde, Daniel Robinson, Anuj Srivastava, Eric Paul Klassen, Jinfeng Zhang · 2013 · Nucleic Acids Research
61. Base-specific RNA force field improving the dynamics conformation of nucleotide
    Zhengxin Li, Junxi Mu, Jun Chen, Haifeng Chen · 2022 · International Journal of Biological Macromolecules
62. RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism, and Molecular Tensegrity
    Jong-Chin Lin, Changbong Hyeon, Dave Thirumalai · 2012 · The Journal of Physical Chemistry Letters
63. Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA
    Asaminew H. Aytenfisu, Aleksandar Spasic, Matthew G. Seetin, John R. Serafini, David H. Mathews · 2014 · Journal of Chemical Theory and Computation
64. Exact solution of a RNA-like polymer model on the Husimi lattice
    Reginaldo A. Zara, Marco Pretti · 2007 · The Journal of Chemical Physics
65. Equilibrium Properties and Force-Driven Unfolding Pathways of RNA Molecules
    Alberto Imparato, Alessandro Pelizzola, Marco Zamparo · 2009 · Physical Review Letters
66. Generalized iterative annealing model for the action of RNA chaperones
    Changbong Hyeon, Dave Thirumalai · 2013 · The Journal of Chemical Physics
67. A Simple Molecular Model for Thermophilic Adaptation of Functional Nucleic Acids
    Joshua M. Blose, Scott K. Silverman, Philip C. Bevilacqua · 2007 · Biochemistry
68. Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data
    Zhen Tan, Gaurav Sharma A, David H. Mathews · 2017 · Biophysical Journal
69. Entropy and Mg2+ control ligand affinity and specificity in the malachite green binding RNA aptamer
    Jason Bernard Da Costa, Thorsten Dieckmann · 2011 · Molecular BioSystems
70. The significance of thermodynamic models in the accuracy improvement of RNA secondary structure prediction using permutation-based simulated annealing
    Herbert H. Tsang, Kay C. Wiese · 2007 · IEEE Congress on Evolutionary Computation (CEC)
71. RNA secondary structure prediction
    David H. Mathews, Michael Zuker · 2005 · Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics
72. Ribozymes: Flexible molecular devices at work
    Giulia Talini, Sergio Branciamore, Enzo Gallori · 2011 · Biochimie
73. Structural RNA alignment by multi-objective optimization
    Thomas Schnattinger, Uwe Schöning, Hans Armin Kestler · 2013 · Bioinformatics
74. Development of a ribonuclease containing a G4-specific binding motif for programmable RNA cleavage
    Dung Thanh Dang, Anh Tuân Phan · 2019 · Scientific Reports
75. Going beyond base-pairs: topology-based characterization of base-multiplets in RNA
    Sohini Bhattacharya, Ayush Jhunjhunwala, Antarip Halder, Dhananjay Bhattacharyya, Abhijit Mitra · 2019 · RNA
76. Evaluating the Catalytic Potential of a General RNA‐Cleaving FANA Enzyme
    Yajun Wang, Alexander Vorperian, Mouhamad Shehabat, John Charles Chaput · 2019 · ChemBioChem
77. Looking for the Primordial Genetic Honeycomb
    Enzo Gallori, Elisa Biondi, Sergio Branciamore · 2006 · Origins of Life and Evolution of Biospheres
78. Mobile Genetic Elements in Mycelial Fungi
    Stefanie Pöggeler, Frank Kempken · 2004 · Springer eBooks
79. Amino acids catalyse RNA formation under ambient alkaline conditions
    Rout, Saroj K., Wunnava, Sreekar, Krepl, Miroslav, Cassone, Giuseppe, Šponer, Judit E., Mast, Christof B., Powner, Matthew W., Braun, Dieter · 2025 · Nature Communications
80. Identification of metal ion-binding sites in RNA structures using deep learning method
    Yanpeng Zhao, Jingjing Wang, Fubin Chang, Weikang Gong, Yang Liu, Chunhua Li · 2023 · Briefings in Bioinformatics
81. Differentiable partition function calculation for RNA
    2023
82. Comprehensive Comparison and Critical Assessment of RNA-Specific Force Fields
    Taeyoung Choi, Zhengxin Li, Ge Song, Haifeng Chen · 2024 · Journal of Chemical Theory and Computation
83. Flexizymes-facilitated Genetic Code Reprogramming Leading to the Discovery of Drug-like Peptides
    Naohiro Terasaka, Hiroaki Suga · 2013 · Chemistry Letters
84. Coarse‐Grained and Atomistic MD Simulations of RNA and DNA Folding
    Jessica D. Leuchter, Adam T. Green, Julian Gilyard, Cecilia G. Rambarat, Samuel S. Cho · 2014 · Israel Journal of Chemistry
85. A genetic algorithm for RNA secondary structure prediction using stacking energy thermodynamic models
    A. Deschenes · 2005 · Summit (Simon Fraser University)
86. Estimating uncertainty in predicted folding free energy changes of RNA secondary structures
    Jeffrey Zuber, David H. Mathews · 2019 · RNA
87. Deciphering the Self-Cleavage Reaction Mechanism of Hairpin Ribozyme
    Narendra Kumar, Dominik Marx · 2020 · The Journal of Physical Chemistry B
88. Why DNA Is a More Effective Scaffold than RNA in Nucleic Acid‐Based Asymmetric Catalysis—Supramolecular Control of Cooperative Effects
    Jasmin J. Marek, Ulrich Hennecke · 2017 · Chemistry - A European Journal
89. RNA independent fragment partition method based on deep learning for RNA secondary structure prediction
    Qi Zhao, Qian Mao, Zheng Zhao, Wenxuan Yuan, Qiang He, Qixuan Sun, Yudong Yao, Xiaoya Fan · 2023 · Scientific Reports
90. Developing parallel ant colonies filtered by deep learned constrains for predicting RNA secondary structure with pseudo-knots
    Lijun Quan, Leixin Cai, Yu Chen, Jie Mei, Xiaoyu Sun, Qiang Lyu · 2019 · Neurocomputing
91. Selfishness in Moderation: Evolutionary Success of the Yeast Plasmid
    Vel Murugan, Shwetal V. Mehta, Makkuni Jayaram · 2003 · Current topics in developmental biology/Current Topics in Developmental Biology
92. Fitness Landscapes of Functional RNAs
    Ádám Kun, Eörs Szathmáry · 2015 · Life
93. Diverse Mechanisms of RNA Recombination
    Anatoly P. Gmyl, Vadim I. Agol · 2005 · Molecular Biology
94. RNALOSS: a web server for RNA locally optimal secondary structures
    Peter Clote · 2005 · Nucleic Acids Research
95. tRNA-dependent cleavage of the ColE1 plasmid-encoded RNA I
    Zhijun Wang, Zhenghong Yuan, Li Xiang, Junjie Shao, Grzegorz Węgrzyn · 2006 · Microbiology
96. Non-enzymatic Polymerization of Nucleic Acids from Monomers: Monomer Self- Condensation and Template-Directed Reactions
    Mark Dörr, Philipp M. G. Löffler, Pierre‐Alain Monnard · 2012 · Current Organic Synthesis
97. Technologies for the study of epididymal-specific genes
    R. John Lye, Barry T. Hinton · 2003 · Molecular and Cellular Endocrinology
98. Deep dive into RNA: a systematic literature review on RNA structure prediction using machine learning methods
    Michał Budnik, Jakub Wawrzyniak, Łukasz Grala, Miłosz Kadziński, Natalia Szóstak · 2024 · Artificial Intelligence Review
99. Force-induced misfolding in RNA
    Maria Mañosas, Ivan Junier, Félix Ritort · 2008 · Physical Review E
100. Theory of RNA Folding: From Hairpins to Ribozymes
     Dave Thirumalai, Changbong Hyeon · 2008 · Springer series in biophysics