The chemical repertoire of natural ribozymes

Cited by (745)

Items 401–500 of 745

  1. A Method to Predict the 3D Structure of an RNA Scaffold
    Xiaojun Xu, Shi‐Jie Chen · 2015 · Methods in molecular biology
  2. Allosteric Modulation of the Faecalibacterium prausnitzii Hepatitis Delta Virus-like Ribozyme by Glucosamine 6-Phosphate: The Substrate of the Adjacent Gene Product
    Luiz F. M. Passalacqua, Randi M. Jimenez, Jennifer Y. Fong, Andrej Lupták · 2017 · Biochemistry
  3. Process calculi for biological processes
    Andrea Bernini, Linda Brodo, Pierpaolo Degano, Moreno Falaschi, Diana Hermith · 2018 · Natural Computing
  4. LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2
    He Zhang, Sizhen Li, Liang Zhang, David H. Mathews, Liang Huang · 2022 · Nucleic Acids Research
  5. Antisense strategies in degenerative joint diseases: Sense or nonsense?☆
    Lars Christian Huber, Oliver Distler, R Gay, Steffen Gay · 2006 · Advanced Drug Delivery Reviews
  6. Reversed Assembly of Dyes in an RNA Duplex Compared with Those in DNA
    Taiga Fujii, Masaaki Urushihara, Hiromu Kashida, Hiroshi Ito, Xingguo Liang, Maho Yagi‐Utsumi, Koichi Kato, Hiroyuki Asanuma · 2012 · Chemistry - A European Journal
  7. Algebraic dynamic programming for multiple context-free grammars
    Maik Riechert, Christian Höner zu Siederdissen, Peter Florian Stadler · 2016 · Theoretical Computer Science
  8. Ribonuclease P as a Tool
    Fenyong Liu · 2009 · Springer eBooks
  9. New Tricks for an Old Dogma
    Gary D. Stormo · 2003 · Molecular Cell
  10. Language models enable zero-shot prediction of RNA secondary structures including pseudoknots
    Tiansu Gong, Dongbo Bu · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  11. Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations
    Elisa Posani, Pavel Janoš, Daniel B. Haack, Navtej Toor, Massimiliano Bonomi, Alessandra Magistrato, Giovanni Bussi · 2025 · Nature Communications
  12. Nucleophilic Substitution: A Charge Density Perspective
    Travis E. Jones · 2012 · The Journal of Physical Chemistry A
  13. Stabilizing DNAzymes through Encapsulation in a Metal–Organic Framework
    Huiye Zhong, Wei‐Shang Lo, Tiantian Man, Benjamin P. Williams, Dan Li, Sheng‐Yu Chen, Hao Pei, Li Li, Chia‐Kuang Tsung · 2020 · Chemistry - A European Journal
  14. New Trends in Organic Synthesis with Oxidative Enzymes
    Gonzalo de Gonzalo, Alejandro A. Orden, Fabricio R. Bisogno · 2012 · Current Organic Chemistry
  15. Proteins
    Gerald Litwack · 2017 · Elsevier eBooks
  16. Unusual DNA−DNA Cross-Links between a Photolyase Deoxyribozyme, UV1C, and Its Bound Oligonucleotide Substrate
    Gurpreet S. Sekhon, Dipankar Sen · 2009 · Biochemistry
  17. Ribozyme-Mediated Inhibition of 801-bp Deletion-Mutant Epidermal Growth Factor Receptor mRNA Expression in Glioblastoma Multiforme
    Georg Karpel‐Massler, Christian Rainer Wirtz, Marc‐Eric Halatsch · 2010 · Molecules
  18. An Unexpected Adenosine-Alkylating Ribozyme Emerged by Target Site Relocation during in Vitro Selection
    Carolin P. M. Scheitl, Evgeniia Dorinova, Sarah Christopher, Manisha B. Walunj, Takumi Okuda, Maksim V. Sednev, Claudia Höbartner · 2025 · Journal of the American Chemical Society
  19. Mechanistic role of nucleobases in self-cleavage catalysis of hairpin ribozyme at ambient versus high-pressure conditions
    Narendra Kumar, Dominik Marx · 2018 · Physical Chemistry Chemical Physics
  20. A general strategy for engineering GU base pairs to facilitate RNA crystallization
    Yuan Ren, Xiaowei Lin, Wenjian Liao, Xuemei Peng, Jie Deng, Zhe Zhang, Jian Zhan, Yaoqi Zhou, Éric Westhof, David M.J. Lilley et al. · 2024 · Nucleic Acids Research
  21. Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides
    Vojtěch Mlýnský, Giovanni Bussi · 2017 · RNA
  22. Structure-Specific Ribonucleases for MS-Based Elucidation of Higher-Order RNA Structure
    Matteo Scalabrin, Yik Siu, Papa Nii Asare‐Okai, Daniele Fabris · 2014 · Journal of the American Society for Mass Spectrometry
  23. Error thresholds for self- and cross-specific enzymatic replication
    Benedikt Obermayer, Erwin Frey · 2010 · Journal of Theoretical Biology
  24. Synthesis of 5′-Thiamine-Capped RNA
    Marvin Möhler, Katharina Höfer, Andres Jäschke · 2020 · Molecules
  25. Knotify: An Efficient Parallel Platform for RNA Pseudoknot Prediction Using Syntactic Pattern Recognition
    Christos Andrikos, Evangelos Makris, Angelos Kolaitis, Georgios Rassias, Christos Pavlatos, Panayiotis D. Tsanakas · 2022 · Methods and Protocols
  26. Splicing and evolution of an unusually small group I intron
    Lorena Harris, Scott Orland Rogers · 2008 · Current Genetics
  27. Unusual Properties of Adenovirus E2E Transcription by RNA Polymerase III
    Wenlin Huang, Sarah Jane Flint · 2003 · Journal of Virology
  28. The evolution of catalytic function
    Marie‐Christine Maurel, Jacques Ricard · 2006 · Physics of Life Reviews
  29. In Vivo Evolution of an RNA-Based Transcriptional Silencing Domain in S. cerevisiae
    Polina D. Kehayova, David R. Liu · 2007 · Chemistry & Biology
  30. RNA GG·UU Motif Binds K+ but Not Mg2+
    Yupeng Fan, Barbara L. Gaffney, Roger A. Jones · 2005 · Journal of the American Chemical Society
  31. A peripheral element assembles the compact core structure essential for group I intron self-splicing
    Mu Xiao · 2005 · Nucleic Acids Research
  32. Oligonucleotides and Derivatives as Gene-Specific Control Agents
    Jian‐Sheng Sun, Claude Hélène · 2003 · Nucleosides Nucleotides & Nucleic Acids
  33. LinearAlifold: Linear-time consensus structure prediction for RNA alignments
    Apoorv Malik, Liang Zhang, Milan Gautam, Ning Dai, Sizhen Li, He Zhang, David H. Mathews, Liang Huang · 2024 · Journal of Molecular Biology
  34. Cell-Free Biosensing Genetic Circuit Coupled with Ribozyme Cleavage Reaction for Rapid and Sensitive Detection of Small Molecules
    Wenxing Li, Yiming Xu, Yue Zhang, Pengfei Li, Xiaoli Zhu, Chang Feng · 2023 · ACS Synthetic Biology
  35. Engineered Ribozymes as Molecular Tools for Site‐Specific Alteration of RNA Sequence
    Sabine Müller · 2003 · ChemBioChem
  36. How Does Mg 2+ Modulate the RNA Folding Mechanism: A Case Study of the G:C W:W Trans Basepair
    Antarip Halder, Rohit Roy, Dhananjay Bhattacharyya, Abhijit Mitra · 2017 · Biophysical Journal
  37. Modulation of RNA Metal Binding by Flanking Bases: 15N NMR Evaluation of GC, Tandem GU, and Tandem GA Sites
    Weimin Wang, Jianwei Zhao, Qianwei Han, Gang Wang, Gengcheng J. Yang, Anthony J. Shallop, Jane Liu, Barbara L. Gaffney, Roger A. Jones · 2009 · Nucleosides Nucleotides & Nucleic Acids
  38. Atomic Force Microscopy and Anodic Voltammetry Characterization of a 49-Mer Diels-Alderase Ribozyme
    Ana-Maria Chiorcea Paquim, J.A.P. Piedade, Richard Wombacher, Andres Jäschke, Ana Maria Oliveira‐Brett · 2006 · Analytical Chemistry
  39. Identification and annotation of noncoding RNAs in Saccharomycotina
    José Almeida Cruz, Éric Westhof · 2011 · Comptes Rendus Biologies
  40. Non-identical electronic characters of the internucleotidic phosphates in RNA modulate the chemical reactivity of the phosphodiester bonds
    Jharna Barman, Sandipta Acharya, Chuanzheng Zhou, Subhrangsu Chatterjee, Åke Engström, JYOTI B. CHATTOPADHYAYA · 2006 · Organic & Biomolecular Chemistry
  41. ThreshKnot: Thresholded ProbKnot for Improved RNA Secondary Structure Prediction
    Liang Zhang, He Zhang, D. Mathews, Liang Huang · 2019 · arXiv (Cornell University)
  42. RNA Through Time: From the Origin of Life to Therapeutic Frontiers in Transcriptomics and Epitranscriptional Medicine
    Cecilia Martinez Campos, Humberto Lanz‐Mendoza, Jorge Cime‐Castillo, Óscar Peralta-Zaragoza, Vicente Madrid‐Marina · 2025 · International Journal of Molecular Sciences
  43. Minimal models for RNA simulations
    Dave Thirumalai, Naoto Hori, Hung Tan Nguyen · 2025 · Current Opinion in Structural Biology
  44. Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation
    Aleksandar Spasic, Scott D. Kennedy, Laura L. Needham, Muthiah Manoharan, Ryszard Kierzek, Douglas H. Turner, David H. Mathews · 2018 · RNA
  45. Determining parameters for non-linear models of multi-loop free energy change
    Max Ward, Hongying Sun, Amitava Datta, Michael J. Wise, David H. Mathews · 2019 · Bioinformatics
  46. An Overview of RNA Structure Prediction and Applications to RNA Gene Prediction and RNA i Design
    Gary D. Stormo · 2006 · Current Protocols in Bioinformatics
  47. Disorder to Order, Nonlife to Life: In the Beginning There Was a Mistake
    Ernesto Di Mauro, A. Keith Dunker, Edward N. Trifonov · 2012 · Cellular origin and life in extreme habitats
  48. Computational Approaches to Predicting the Impact of Novel Bases on RNA Structure and Stability
    Jason G. Harrison, Yvonne B. Zheng, Peter A. Beal, Dean Joseph Tantillo · 2013 · ACS Chemical Biology
  49. Nucleic acid-based techniques for post-transcriptional regulation of molecular targets
    George Jarad, Jeffrey S. Simske, John R. Sedor, Jeffrey R. Schelling · 2003 · Current Opinion in Nephrology & Hypertension
  50. In Vitro Selection of Functional Oligonucleotides and the Origins of Biochemical Activity
    James M. Carothers, Jack W. Szostak · 2006 · Wiley eBooks
  51. Origin & influence of autocatalytic reaction networks at the advent of the RNA world
    Stephen A. Zorc, Raktim N. Roy · 2024 · RNA Biology
  52. DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters
    Tuan Minh Pham, Terrel Miffin, Hongying Sun, Kenneth K. Sharp, Xiaoyu Wang, Mingyi Zhu, Shuichi Hoshika, Raymond J. Peterson, Steven A. Benner, Jason D. Kahn et al. · 2023 · ACS Synthetic Biology
  53. Biomimetic and bioinspired design of collective systems
    Thomas Schmickl, Karl Crailsheim, Jean‐Louis Deneubourg, José Halloy · 2011 · VU Research Portal
  54. A Specific Scenario for the Origin of Life and the Genetic Code Based on Peptide/Oligonucleotide Interdependence
    Robert W. Griffith · 2009 · Origins of Life and Evolution of Biospheres
  55. Ribozyme-Catalyzed Genetics
    Donald H. Burke · 2004 · Springer eBooks
  56. Relicts and models of the RNA world
    Kirsi M. Lehto, Alexey Karetnikov · 2005 · International Journal of Astrobiology
  57. Disruption of glucose sensing and insulin secretion by ribozyme Kir6.2-gene targeting in insulin-secreting cells.
    Li Li, Asheebo Rojas, Jian-Ping Wu, Chun Jiang · 2004 · Endocrinology
  58. A group I intron-like sequence in the nuclear small ribosomal subunit gene of the ophiostomatoid fungus Gondwanamyces proteae
    Ewan A. Gibb, Georg Hausner · 2003 · Mycological Research
  59. Simulation-Guided Conformational Space Exploration to Assess Reactive Conformations of a Ribozyme
    Sélène Forget, Marie Juillé, Élise Duboué-Dijon, Guillaume Stirnemann · 2024 · Journal of Chemical Theory and Computation
  60. Structure-based RNA Function Prediction Using Elastic Shape Analysis
    José Laborde, Anuj Srivastava, Jinfeng Zhang · 2011 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  61. Targeting RNA G-Quadruplexes for Potential Therapeutic Applications
    Satyaprakash Pandey, Prachi Agarwala, Souvik Maiti · 2017 · Topics in medicinal chemistry
  62. Characterisation of a satellite RNA of Cucumber mosaic virus that induces chlorosis in Capsicum annuum
    Seung‐Kook Choi, Yong-Woon Jeon, Ju-Yeon Yoon, Jang-Kyung Choi · 2011 · Virus Genes
  63. Assessing Force Field Potential Energy Function Accuracy via a Multipolar Description of Atomic Electrostatic Interactions in RNA
    Yongna Yuan, Zhuangzhuang Zhang, Matthew J. L. Mills, Rongjing Hu, Ruisheng Zhang · 2018 · Journal of Chemical Information and Modeling
  64. Structural variants and modifications of hammerhead ribozymes targeting influenza A virus conserved structural motifs
    Tomasz Czapik, Julita Piasecka, Ryszard Kierzek, Elżbieta Kierzek · 2022 · Molecular Therapy — Nucleic Acids
  65. Reflections on the Origin and Early Evolution of the Genetic Code
    Juan Carlos Fontecilla-Camps · 2023 · ChemBioChem
  66. Finding aptamers and small ribozymes in unexpected places
    Katarzyna Matylla-Kulińska, Jennifer L. Boots, Bob Zimmermann, Renée Schroeder · 2011 · Wiley Interdisciplinary Reviews - RNA
  67. Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges
    Anne Condon, Hosna Jabbari · 2008 · Theoretical Computer Science
  68. Accelerating calculations of RNA secondary structure partition functions using GPUs
    Harry A. Stern, David H. Mathews · 2013 · Algorithms for Molecular Biology
  69. Origins of Life Studies
    James R. Griesemer · 2009 · Oxford University Press eBooks
  70. HSRNAFold: A harmony search algorithm for RNA secondary structure prediction based on minimum free energy
    Abdulqader M. Mohsen, Ahamad Tajudin Khader, Dhanesh Ramachandram · 2008 · International Conference on Innovations in Information Technology
  71. A Possible Role of DNA Superstructures in Genome Evolution
    Claudio Anselmi, Pasquale De Santis, Raffaella Paparcone, Maria Savino, Anita Scipioni · 2003 · Origins of Life and Evolution of Biospheres
  72. Riboactivators: Transcription activation by noncoding RNA
    Aseem Z. Ansari · 2009 · Critical Reviews in Biochemistry and Molecular Biology
  73. Group I intron-like insertions in SSU rDNA of Cladonia gracilis and C. rangiferina
    Michele D. Piercey‐Normore, Georg Hausner, Ewan A. Gibb · 2004 · The Lichenologist
  74. Searching for 2D RNA geometries in bacterial genomes
    Uri Laserson, Hin Hark Gan, Tamar Schlick A · 2004 · Annual Symposium on Computational Geometry (SoCG)
  75. Methods for Multiple Alignment and Consensus Structure Prediction of RNAs Implemented in MARNA
    Sven Siebert, Rolf Backofen · 2007 · Methods in molecular biology
  76. Deformations of promoter DNA bound to carcinogens help interpret effects on TATA-element structure and activity
    Qing Zhang, Suse B. Broyde, Tamar Schlick A · 2004 · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences
  77. Assessing adenoviral hammerhead ribozyme and small hairpin RNA cassettes in neurons: Inhibition of endogenous caspase‐3 activity and protection from apoptotic cell death
    Ioannis Bantounas, Colin P. J. Glover, Stephen Kelly, Sachiko Iseki, Leonidas A. Phylactou, James B. Uney · 2005 · Journal of Neuroscience Research
  78. Origin of the RNA World in Cold Hadean Geothermal Fields Enriched in Zinc and Potassium: Abiogenesis as a Positive Fallout from the Moon-Forming Impact?
    Armen Y. Mulkidjanian, Daria V. Dibrova, A. Yu. Bychkov · 2025 · Life
  79. Synthetic regulatory RNAs as tools for engineering biological systems: Design and applications
    Sang Woo Seo, Gyoo Yeol Jung · 2013 · Chemical Engineering Science
  80. How do ribozymes accommodate additional water molecules upon hydrostatic compression deep into the kilobar pressure regime?
    Narendra Kumar, Dominik Marx · 2019 · Biophysical Chemistry
  81. Virus-associated ribozymes and nano carriers against COVID-19
    Beyza Dönmüş, Sinan ÜNAL, Fatma Ceren Kırmızıtaş, Nelisa Türkoğlu Laçin · 2021 · Artificial Cells Nanomedicine and Biotechnology
  82. Linear-Time Algorithms for RNA Structure Prediction
    He Zhang, Liang Zhang, Kaibo Liu, Sizhen Li, David H. Mathews, Liang Huang · 2022 · Methods in molecular biology
  83. Fungal Intervening Sequences
    Stefanie Pöggeler · 2005 · Applied mycology and biotechnology
  84. Self-organizing proto-replicators and the origin of life
    Richard M.P. Sayer · 2006 · Biosystems
  85. Multi-agent approach to sequence structure simulation in the RNA World hypothesis
    Jaroslaw Synak, Agnieszka Rybarczyk, Jacek Błażewicz · 2020 · PLoS ONE
  86. RNA-like polymer model: Exact calculation on the Bethe lattice
    Marco Pretti · 2006 · Physical Review E
  87. Replication elongates short DNA, reduces sequence bias and develops trimer structure
    Adriana Calaça Serrão, Felix Dänekamp, Zsófia Meggyesi, Dieter Braun · 2023 · Nucleic Acids Research
  88. Efficient Assembly of Functional RNA by in Situ Phosphate Activation and Loop-Closing Ligation
    Jian Zhang, Aleksandar Radakovic, Filip Bošković, Harry R. M. Aitken, Long-Fei Wu, Jack W. Szostak · 2025 · Journal of the American Chemical Society
  89. SamplingDesign: RNA design via continuous optimization with coupled variables and Monte-Carlo sampling
    Wei Yu Tang, Ning Dai, Tianshuo Zhou, David H. Mathews, Liang Huang · 2026 · Nature Communications
  90. Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition
    Tianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang · 2024 · Lecture notes in computer science
  91. memerna: Sparse RNA folding including coaxial stacking
    Eliot Courtney, Amitava Datta, David H. Mathews, Max Ward · 2024 · Journal of Molecular Biology
  92. Shields for small molecules
    Scott K. Silverman · 2012 · Nature Chemistry
  93. Coordination of two sequential ester-transfer reactions: exogenous guanosine binding promotes the subsequent ωG binding to a group I intron
    Penghui Bao, Qijia Wu, Ping Yin, Yanfei Jiang, Xu Wang, Maohua Xie, Tao Sun, Lin Huang, Dingding Mo, Yi Zhang · 2008 · Nucleic Acids Research
  94. Identification, molecular characterization, and evolution of group I introns at the expansion segment D11 of 28S rDNA in Rhizoctonia species
    Dolores González · 2013 · Fungal Biology
  95. Mechanistic Analysis of the Hepatitis Delta Virus (HDV) Ribozyme: Methods for RNA Preparation, Structure Mapping, Solvent Isotope Effects, and Co-transcriptional Cleavage
    Durga M. Chadalavada, Andrea L. Cerrone-Szakal, Jennifer L. Wilcox, Nathan A. Siegfried, Philip C. Bevilacqua · 2012 · Methods in molecular biology
  96. Hairpin Ribozyme Genes Curtail Alcohol Drinking: from Rational Design to in vivo Effects in the Rat
    Amalia Sapag, Thergiory Irrazábal, Lorena Lobos‐González, Carlos R Muñoz-Brauning, Marı́a Elena Quintanilla, Lutske Tampier · 2016 · Molecular Therapy — Nucleic Acids
  97. Nature inspired optimization algorithm for prediction of “minimum free energy” “RNA secondary structure”
    Ashish Tripathi, K. K. Mishra, Shailesh Tiwari, Prem Chand Vashist · 2019 · Journal of Reliable Intelligent Environments
  98. Translational control of enzyme scavenger expression with toxin-induced micro RNA switches
    Nina M. Pollak, Justin John Cooper-White, Joanne Macdonald · 2021 · Scientific Reports
  99. Biomolecule Recognition Using Transition Metal Ions and Hydrogen Bonding
    Adam J. Plaunt, Lourdes Betancourt-Mendiola, Bradley D. Smith · 2016 · Elsevier eBooks
  100. Application of NIR Raman Spectroscopy to Probe the Flexibility of RNA Structure
    Hui Bon Hoa Gaston · 2020 · Methods in molecular biology