The chemical repertoire of natural ribozymes
DOI 10.1038/418222a
Cited by (745)
Items 401–500 of 745
- A Method to Predict the 3D Structure of an RNA ScaffoldXiaojun Xu, Shi‐Jie Chen · 2015 · Methods in molecular biology
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- Oligonucleotides and Derivatives as Gene-Specific Control AgentsJian‐Sheng Sun, Claude Hélène · 2003 · Nucleosides Nucleotides & Nucleic Acids
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- How Does Mg 2+ Modulate the RNA Folding Mechanism: A Case Study of the G:C W:W Trans BasepairAntarip Halder, Rohit Roy, Dhananjay Bhattacharyya, Abhijit Mitra · 2017 · Biophysical Journal
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- Nucleic acid-based techniques for post-transcriptional regulation of molecular targetsGeorge Jarad, Jeffrey S. Simske, John R. Sedor, Jeffrey R. Schelling · 2003 · Current Opinion in Nephrology & Hypertension
- In Vitro Selection of Functional Oligonucleotides and the Origins of Biochemical ActivityJames M. Carothers, Jack W. Szostak · 2006 · Wiley eBooks
- Origin & influence of autocatalytic reaction networks at the advent of the RNA worldStephen A. Zorc, Raktim N. Roy · 2024 · RNA Biology
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- Biomimetic and bioinspired design of collective systemsThomas Schmickl, Karl Crailsheim, Jean‐Louis Deneubourg, José Halloy · 2011 · VU Research Portal
- A Specific Scenario for the Origin of Life and the Genetic Code Based on Peptide/Oligonucleotide InterdependenceRobert W. Griffith · 2009 · Origins of Life and Evolution of Biospheres
- Ribozyme-Catalyzed GeneticsDonald H. Burke · 2004 · Springer eBooks
- Relicts and models of the RNA worldKirsi M. Lehto, Alexey Karetnikov · 2005 · International Journal of Astrobiology
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- Structure-based RNA Function Prediction Using Elastic Shape AnalysisJosé Laborde, Anuj Srivastava, Jinfeng Zhang · 2011 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
- Targeting RNA G-Quadruplexes for Potential Therapeutic ApplicationsSatyaprakash Pandey, Prachi Agarwala, Souvik Maiti · 2017 · Topics in medicinal chemistry
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- Structural variants and modifications of hammerhead ribozymes targeting influenza A virus conserved structural motifsTomasz Czapik, Julita Piasecka, Ryszard Kierzek, Elżbieta Kierzek · 2022 · Molecular Therapy — Nucleic Acids
- Reflections on the Origin and Early Evolution of the Genetic CodeJuan Carlos Fontecilla-Camps · 2023 · ChemBioChem
- Finding aptamers and small ribozymes in unexpected placesKatarzyna Matylla-Kulińska, Jennifer L. Boots, Bob Zimmermann, Renée Schroeder · 2011 · Wiley Interdisciplinary Reviews - RNA
- Computational prediction of nucleic acid secondary structure: Methods, applications, and challengesAnne Condon, Hosna Jabbari · 2008 · Theoretical Computer Science
- Accelerating calculations of RNA secondary structure partition functions using GPUsHarry A. Stern, David H. Mathews · 2013 · Algorithms for Molecular Biology
- Origins of Life StudiesJames R. Griesemer · 2009 · Oxford University Press eBooks
- HSRNAFold: A harmony search algorithm for RNA secondary structure prediction based on minimum free energyAbdulqader M. Mohsen, Ahamad Tajudin Khader, Dhanesh Ramachandram · 2008 · International Conference on Innovations in Information Technology
- A Possible Role of DNA Superstructures in Genome EvolutionClaudio Anselmi, Pasquale De Santis, Raffaella Paparcone, Maria Savino, Anita Scipioni · 2003 · Origins of Life and Evolution of Biospheres
- Riboactivators: Transcription activation by noncoding RNAAseem Z. Ansari · 2009 · Critical Reviews in Biochemistry and Molecular Biology
- Group I intron-like insertions in SSU rDNA of Cladonia gracilis and C. rangiferinaMichele D. Piercey‐Normore, Georg Hausner, Ewan A. Gibb · 2004 · The Lichenologist
- Searching for 2D RNA geometries in bacterial genomesUri Laserson, Hin Hark Gan, Tamar Schlick A · 2004 · Annual Symposium on Computational Geometry (SoCG)
- Methods for Multiple Alignment and Consensus Structure Prediction of RNAs Implemented in MARNASven Siebert, Rolf Backofen · 2007 · Methods in molecular biology
- Deformations of promoter DNA bound to carcinogens help interpret effects on TATA-element structure and activityQing Zhang, Suse B. Broyde, Tamar Schlick A · 2004 · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences
- Assessing adenoviral hammerhead ribozyme and small hairpin RNA cassettes in neurons: Inhibition of endogenous caspase‐3 activity and protection from apoptotic cell deathIoannis Bantounas, Colin P. J. Glover, Stephen Kelly, Sachiko Iseki, Leonidas A. Phylactou, James B. Uney · 2005 · Journal of Neuroscience Research
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- Linear-Time Algorithms for RNA Structure PredictionHe Zhang, Liang Zhang, Kaibo Liu, Sizhen Li, David H. Mathews, Liang Huang · 2022 · Methods in molecular biology
- Fungal Intervening SequencesStefanie Pöggeler · 2005 · Applied mycology and biotechnology
- Self-organizing proto-replicators and the origin of lifeRichard M.P. Sayer · 2006 · Biosystems
- Multi-agent approach to sequence structure simulation in the RNA World hypothesisJaroslaw Synak, Agnieszka Rybarczyk, Jacek Błażewicz · 2020 · PLoS ONE
- RNA-like polymer model: Exact calculation on the Bethe latticeMarco Pretti · 2006 · Physical Review E
- Replication elongates short DNA, reduces sequence bias and develops trimer structureAdriana Calaça Serrão, Felix Dänekamp, Zsófia Meggyesi, Dieter Braun · 2023 · Nucleic Acids Research
- Efficient Assembly of Functional RNA by in Situ Phosphate Activation and Loop-Closing LigationJian Zhang, Aleksandar Radakovic, Filip Bošković, Harry R. M. Aitken, Long-Fei Wu, Jack W. Szostak · 2025 · Journal of the American Chemical Society
- SamplingDesign: RNA design via continuous optimization with coupled variables and Monte-Carlo samplingWei Yu Tang, Ning Dai, Tianshuo Zhou, David H. Mathews, Liang Huang · 2026 · Nature Communications
- Undesignable RNA Structure Identification via Rival Structure Generation and Structure DecompositionTianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang · 2024 · Lecture notes in computer science
- memerna: Sparse RNA folding including coaxial stackingEliot Courtney, Amitava Datta, David H. Mathews, Max Ward · 2024 · Journal of Molecular Biology
- Shields for small moleculesScott K. Silverman · 2012 · Nature Chemistry
- Coordination of two sequential ester-transfer reactions: exogenous guanosine binding promotes the subsequent ωG binding to a group I intronPenghui Bao, Qijia Wu, Ping Yin, Yanfei Jiang, Xu Wang, Maohua Xie, Tao Sun, Lin Huang, Dingding Mo, Yi Zhang · 2008 · Nucleic Acids Research
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- Translational control of enzyme scavenger expression with toxin-induced micro RNA switchesNina M. Pollak, Justin John Cooper-White, Joanne Macdonald · 2021 · Scientific Reports
- Biomolecule Recognition Using Transition Metal Ions and Hydrogen BondingAdam J. Plaunt, Lourdes Betancourt-Mendiola, Bradley D. Smith · 2016 · Elsevier eBooks
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