The chemical repertoire of natural ribozymes

Cited by (745)

Items 201–300 of 745

1. Emergence of information transmission in a prebiotic RNA reactor.
   Obermayer, Benedikt, Krammer, Hubert, Braun, Dieter, Gerland, Ulrich · 2011 · Physical Review Letters
2. In Vitro Selection of Adenine-dependent Hairpin Ribozymes
   Marc Meli, Jacques Vergne, Marie‐Christine Maurel · 2003 · Journal of Biological Chemistry
3. Evolution of Tetrahymena ribozyme mutants with increased structural stability
   Feng Guo, Thomas R. Cech · 2002 · Nature Structural Biology
4. Boltzmann probability of RNA structural neighbors and riboswitch detection
   Eva Freyhult, Vincent Moulton, Peter Clote · 2007 · Bioinformatics
5. Origin of Informational Polymers
   Raffaele Saladino, Claudia Crestini, Fabiana Ciciriello, Ernesto Di Mauro, Giovanna Costanzo · 2006 · Journal of Biological Chemistry
6. The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure
   Sylvia Tobé · 2005 · Nucleic Acids Research
7. MOLECULAR REPLICATOR DYNAMICS
   Bärbel M. R. Stadler, Peter Florian Stadler · 2003 · Advances in Complex Systems
8. A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs
   Simón Poblete, Sandro Bottaro, Giovanni Bussi · 2017 · Nucleic Acids Research
9. The ARTS web server for aligning RNA tertiary structures
   O. Dror, Ruth Nussinov, Haim J. Wolfson · 2006 · Nucleic Acids Research
10. AAV-mediated gene transfer for retinal diseases
    Mariacarmela Allocca, Alessandra Tessitore, Gabriella Cotugno, Alberto Auricchio · 2006 · Expert Opinion on Biological Therapy
11. The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation
    Aleksandar Spasic, John R. Serafini, David H. Mathews · 2012 · Journal of Chemical Theory and Computation
12. Systematic Evaluation of the Dependence of Deoxyribozyme Catalysis on Random Region Length
    Tania E. Velez, Jaydeep Singh, Ying Xiao, Emily C. Allen, On Yi Wong, Madhavaiah Chandra, Sarah C. Kwon, Scott K. Silverman · 2012 · ACS Combinatorial Science
13. Adeno-associated viral vectors for retinal gene transfer
    Enrico Maria Surace, Alberto Auricchio · 2003 · Progress in Retinal and Eye Research
14. Asymptotics of RNA Shapes
    William Andrew Lorenz, Yann Ponty, Peter Clote · 2008 · Journal of Computational Biology
15. Terbium-mediated Footprinting Probes a Catalytic Conformational Switch in the Antigenomic Hepatitis Delta Virus Ribozyme
    D. Ahmasi Harris, Rebecca A. Tinsley, Nils G. Walter · 2004 · Journal of Molecular Biology
16. Bis-uracil based high efficient heat stabilizers used in super transparent soft poly (vinyl chloride)
    Bozhen Wu, Yating Wang, Si Chen, Muyan Wang, Meng Ma, Yanqin Shi, Xu Wang · 2018 · Polymer Degradation and Stability
17. The Roots of Genetic Coding in Aminoacyl-tRNA Synthetase Duality
    Charles W. Carter, Peter R. Wills · 2021 · Annual Review of Biochemistry
18. Quantifying the relationship between sequence and three-dimensional structure conservation in RNA
    Emidio Capriotti, Marc A. Martı́-Renom · 2010 · BMC Bioinformatics
19. Minimal Models for Proteins and RNA: From Folding to Function
    David L. Pincus, Samuel S. Cho, Changbong Hyeon, Dave Thirumalai · 2008 · Progress in molecular biology and translational science
20. Construction of photoresponsive RNA for photoswitching RNA hybridization
    Hiroshi Ito, Xingguo Liang, Hidenori Nishioka, Hiroyuki Asanuma · 2010 · Organic & Biomolecular Chemistry
21. Hydrolytic Activities of Crystalline Cellulose Nanofibers
    Takeshi Serizawa, Toshiki Sawada, Hiromichi Okura, Masahisa Wada · 2013 · Biomacromolecules
22. Light-activation of gene function in mammalian cells viaribozymes
    Douglas D. Young, Ronald A. Garner, Jeffrey A. Yoder, Alexander Deiters · 2008 · Chemical Communications
23. Cross talk between the +73/294 interaction and the cleavage site in RNase P RNA mediated cleavage
    Mathias Brännvall · 2004 · Nucleic Acids Research
24. MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery
    Rongzhong Li, Lindsay M. MacNamara, Jessica D. Leuchter, Rebecca W. Alexander, Samuel Cho · 2015 · International Journal of Molecular Sciences
25. The origins of life – the ‘protein interaction world’ hypothesis: protein interactions were the first form of self-reproducing life and nucleic acids evolved later as memory molecules
    Péter András, Csaba Dezső András · 2005 · Medical Hypotheses
26. Genetic therapies for cardiovascular diseases
    Luis Gabriel Melo, Alok S. Pachori, Massimiliano Gnecchi, Victor J. Dzau · 2005 · Trends in Molecular Medicine
27. Pseudorotation of Natural and Chemically Modified Biological Phosphoranes: Implications for RNA Catalysis
    Carlos Silva López, Olalla Nieto Faza, Brent A. Gregersen, Xabier López, Ángel R. de Lera, Darrin M. York · 2004 · ChemPhysChem
28. Translational control of gene function through optically regulated nucleic acids
    Kristie E. Darrah, Alexander Deiters · 2021 · Chemical Society Reviews
29. Reversible Photo-regulation of a Hammerhead Ribozyme Using a Diffusible Effector
    Hyun‐Wu Lee, Stephen G. Robinson, Subhajit Bandyopadhyay, Reginald Harry Mitchell, Dipankar Sen · 2007 · Journal of Molecular Biology
30. Importance of RNA‐protein interactions in bacterial ribonuclease P structure and catalysis
    J. Kristin Smith, John Hsieh, Carol A. Fierke · 2007 · Biopolymers
31. Annotating Non‐Coding RNAs with Rfam
    Sam Griffiths‐Jones · 2005 · Current Protocols in Bioinformatics
32. Expanding the Scope of Protein Synthesis Using Modified Ribosomes
    Larisa M. Dedkova, Sidney M. Hecht · 2019 · Journal of the American Chemical Society
33. Interpretation of pH–Activity Profiles for Acid–Base Catalysis from Molecular Simulations
    Thakshila Dissanayake, Jason Swails, Michael E. Harris, Adrián E. Roitberg, Darrin M. York · 2015 · Biochemistry
34. Preparation of Small RNAs Using Rolling Circle Transcription and Site-Specific RNA Disconnection
    Xingyu Wang, Can Li, Xiaomeng Gao, Jing Wang, Xingguo Liang · 2015 · Molecular Therapy — Nucleic Acids
35. Computational RNA Structure Prediction
    Marc A. Martı́-Renom, Emidio Capriotti · 2008 · Current Bioinformatics
36. A More Complex Isoleucine Aptamer with a Cognate Triplet
    Michał Łęgiewicz, Michael Yarus · 2005 · Journal of Biological Chemistry
37. Activation of Oxygen Nucleophiles in Enzyme Catalysis
    Vernon E. Anderson, Mark Walter Ruszczycky, Michael E. Harris · 2006 · Chemical Reviews
38. SARA: a server for function annotation of RNA structures
    Emidio Capriotti, Marc A. Martı́-Renom · 2009 · Nucleic Acids Research
39. Templated Self‐Replication in Biomimetic Systems
    Kristian Kyle Le Vay, Laura I. Weise, Kai Libicher, Judita Mascarenhas, Hannes Mutschler · 2019 · Advanced Biosystems
40. Machine learning a model for RNA structure prediction
    Nicola Calonaci, Alisha Jones, Francesca Cuturello, Michael Sattler, Giovanni Bussi · 2020 · NAR Genomics and Bioinformatics
41. Rolling-circle and strand-displacement mechanisms for non-enzymatic RNA replication at the time of the origin of life
    Andrew S. Tupper, Paul G. Higgs · 2021 · Journal of Theoretical Biology
42. Antisense regulation in X inactivation and autosomal imprinting
    Yuya Ogawa, Jeannie T. Lee · 2002 · Cytogenetic and Genome Research
43. 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
44. Catalytic activity of hammerhead ribozymes in a clay mineral environment: Implications for the RNA world
    Elisa Biondi, Sergio Branciamore, Luca Fusi, Selma Gago‐Zachert, Enzo Gallori · 2006 · Gene
45. Gene Therapy for Autosomal Dominant Disorders of Keratin
    Alfred S. Lewin, Peter M. Glazer, Leonard M. Milstone · 2005 · Journal of Investigative Dermatology Symposium Proceedings
46. Synthetic circRNA therapeutics: innovations, strategies, and future horizons
    Jingsheng Cai, Zonghao Qiu, William Chi Shing Cho, Zheng Liu, Shaoyi Chen, Haoran Li, Kezhong Chen, Yun Li, Chijian Zuo, Mantang Qiu · 2024 · MedComm
47. Eutectic Phase in Water‐Ice: A Self‐Assembled Environment Conducive to Metal‐Catalyzed Non‐Enzymatic RNA Polymerization
    Pierre‐Alain Monnard, Hans J. Ziock · 2008 · Chemistry & Biodiversity
48. A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction
    Jeffrey Zuber, Hongying Sun, Xiaoju Zhang, Iain J. McFadyen, David H. Mathews · 2017 · Nucleic Acids Research
49. Non-Nearest-Neighbor Dependence of the Stability for RNA Bulge Loops Based on the Complete Set of Group I Single-Nucleotide Bulge Loops
    Joshua M. Blose, Michelle L. Manni, Kelly A. Klapec, Yukiko Stranger-Jones, Allison C. Zyra, Vasiliy Sim, Chad A. Griffith, Jason D. Long, Martin J. Serra · 2007 · Biochemistry
50. Vesicle encapsulation stabilizes intermolecular association and structure formation of functional RNA and DNA
    Huan Peng, Amandine Lelievre, Katharina Landenfeld, Sabine Müller, Irene A. Chen · 2021 · Current Biology
51. Building objects from nucleic acids for a nanometer world
    Alexander Heckel, Michael Famulok · 2008 · Biochimie
52. AccessFold: predicting RNA–RNA interactions with consideration for competing self-structure
    Laura DiChiacchio, Michael F. Sloma, David H. Mathews · 2015 · Bioinformatics
53. Intracellular selection of trans-cleaving hammerhead ribozymes
    Xin Huang, Yongyun Zhao, Qinlin Pu, Getong Liu, Yan Peng, Fei Wang, Gangyi Chen, Meiling Sun, Feng Du, Juan Dong et al. · 2019 · Nucleic Acids Research
54. Effects of Polyethylene Glycol on DNA Duplex Stability at Different NaCl Concentrations
    Hisae Tateishi Karimata, Shu‐ichi Nakano, Naoki Sugimoto · 2007 · Bulletin of the Chemical Society of Japan
55. Inhibition of gene expression in human cells using RNase P-derived ribozymes and external guide sequences
    Kihoon Kim, Fenyong Liu · 2007 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
56. Electron Hole Flow Patterns through the RNA-Cleaving 8-17 Deoxyribozyme Yield Unusual Information about Its Structure and Folding
    Edward Ki Yun Leung, Dipankar Sen · 2007 · Chemistry & Biology
57. Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best
    Max Ward, Amitava Datta, Michael J. Wise, David H. Mathews · 2017 · Nucleic Acids Research
58. Self-Transfecting Micellar RNA: Modulating Nanoparticle Cell Interactions via High Density Display of Small Molecule Ligands on Micelle Coronas
    Alexander Roloff, David A. Nelles, Matthew P. Thompson, Gene Wei-Ming Yeo, Nathan C. Gianneschi · 2017 · Bioconjugate Chemistry
59. Predicting RNA secondary structure by free energy minimization
    David H. Mathews · 2005 · Theoretical Chemistry Accounts
60. Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs
    Samuela Pasquali · 2005 · Nucleic Acids Research
61. An Overview of RNA Sequence Analyses: Structure Prediction, ncRNA Gene Identification, and RNAi Design
    Gary D. Stormo · 2013 · Current Protocols in Bioinformatics
62. Ribozymes that can be regulated by external stimuli
    Jennifer Frommer, Bettina Appel, Sabine Müller · 2014 · Current Opinion in Biotechnology
63. Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction
    Jeffrey Zuber, B. Joseph Cabral, Iain J. McFadyen, David Mauger, David H. Mathews · 2018 · RNA
64. RNA-Specific Force Field Optimization with CMAP and Reweighting
    Jun Chen, Hao Liu, Xiaochen Cui, Zhengxin Li, Haifeng Chen · 2022 · Journal of Chemical Information and Modeling
65. Guanosine triphosphate acts as a cofactor to promote assembly of initial P-element transposase–DNA synaptic complexes
    Mei Tang, Ciro Cecconi, Helen Kim, Carlos Bustamante, Donald C. Rio · 2005 · Genes & Development
66. RNA–Small-Molecule Interaction: Challenging the “Undruggable” Tag
    Jaskirat Kaur, Akanksha Sharma, Poonam Mundlia, Vikas Sood, Ankur Pandey, Gurpal Singh, Ravi Pratap Barnwal · 2024 · Journal of Medicinal Chemistry
67. Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot
    Jorjethe Roca, Naoto Hori, Saroj Baral, Yogambigai Velmurugu, Ranjani Narayanan, Prasanth Narayanan, Dave Thirumalai, Anjum Ansari · 2018 · Proceedings of the National Academy of Sciences
68. The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer
    D. Morozov, V. Mironov, R. Moryachkov, I. Shchugoreva, P. Artyushenko, G. Zamay, O. Kolovskaya, T. Zamay, A. Krat, D. Molodenskiy et al. · 2021 · Molecular Therapy: Nucleic Acids
69. The separation between the 5′-3′ ends in long RNA molecules is short and nearly constant
    Nehemías Leija-Martínez, Sergio Casas‐Flores, Ruben Dario Cadena-Nava, Joan Anto i Roca, José Alfredo Tirado Méndez, E. Gómez, Jaime Ruiz-Garcia · 2014 · Nucleic Acids Research
70. Site-Selective RNA Cleavage by DNA Bearing a Base Pair-Mimic Nucleoside
    Shu‐ichi Nakano, Yuuki Uotani, Kazuya Uenishi, Masayuki Fujii, Naoki Sugimoto · 2004 · Journal of the American Chemical Society
71. Sensing complex regulatory networks by conformationally controlled hairpin ribozymes
    Seyed Hani Najafi-Shoushtari · 2004 · Nucleic Acids Research
72. The chemical versatility of RNA
    David A. Hiller, Scott A. Strobel · 2011 · Philosophical Transactions of the Royal Society B Biological Sciences
73. Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales
    Dawn K. Merriman, Yi Xue, Yang Shan, Isaac J. Kimsey, Anisha Shakya, Mary C. Clay, Hashim M. Al‐Hashimi · 2016 · Biochemistry
74. Primordial bioenergy sources: The two facets of adenosine triphosphate
    Juan Carlos Fontecilla-Camps · 2020 · Journal of Inorganic Biochemistry
75. Structure‐Switching RNAs: From Gene Expression Regulation to Small Molecule Detection
    Claire Husser, Natacha Dentz, Michaël Ryckelynck · 2021 · Small Structures
76. RNA Folding During Transcription: Protocols and Studies
    Terrence Neal Wong, Tao Pan · 2009 · Methods in enzymology on CD-ROM/Methods in enzymology
77. RNA Secondary Structure as a First Step for Rational Design of the Oligonucleotides towards Inhibition of Influenza A Virus Replication
    Marta Szabat, Dagny Lorent, Tomasz Czapik, Maria Nalewaj, Elżbieta Kierzek, Ryszard Kierzek · 2020 · Pathogens
78. The Exocyclic Amine at the RNase P Cleavage Site Contributes to Substrate Binding and Catalysis
    Ema Kikovska, Mathias Brännvall, Leif A. Kirsebom · 2006 · Journal of Molecular Biology
79. Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction
    Mu Xiao · 2003 · Nucleic Acids Research
80. Recombination in Primeval Genomes: A Step Forward but Still a Long Leap from Maintaining a Sizable Genome
    Mauro Santos A, Elias Zintzaras, E�rs Szathm�ry · 2004 · Journal of Molecular Evolution
81. The folding competence of HIV-1 Tat mediated by interaction with TAR RNA
    Jung Min ‍Kim, Hee Sun Choi, Baik Lin Seong · 2017 · RNA Biology
82. Metal‐Induced Specific and Nonspecific Oligonucleotide Folding Studied by FRET and Related Biophysical and Bioanalytical Implications
    Mehmet Murat Kiy, Zachary E. Jacobi, Juewen Liu · 2011 · Chemistry - A European Journal
83. A tale in molecular recognition: the hammerhead ribozyme
    Éric Westhof · 2006 · Journal of Molecular Recognition
84. Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials
    Tiansu Gong, Fusong Ju, Dongbo Bu · 2024 · Communications Biology
85. Application of RNAi to cancer research and therapy
    Fischer, L. Tan · 2005 · Frontiers in bioscience
86. RNA folding and the origins of catalytic activity in the hairpin ribozyme
    Timothy J. Wilson, Michelle K. Nahas, Lisa Araki, Shinya Harusawa, Taekjip Ha, David M.J. Lilley · 2006 · Blood Cells Molecules and Diseases
87. DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides
    Kenny Schlosser, Yingfu Li · 2008 · Nucleic Acids Research
88. Statistical evaluation of improvement in RNA secondary structure prediction
    Zhenjiang Zech Xu, Anthony Almudevar, David H. Mathews · 2011 · Nucleic Acids Research
89. Nucleic Acids Bind to Nanoparticulate iron (II) Monosulphide in Aqueous Solutions
    Bryan Hatton, David T. Rickard · 2008 · Origins of Life and Evolution of Biospheres
90. RNA as a Versatile and Powerful Platform for Engineering Genetic Regulatory Tools
    Maung Nyan Win, Christina D. Smolke · 2007 · Biotechnology and Genetic Engineering Reviews
91. The XNA alphabet
    John Charles Chaput, Martin Egli, Piet A. Herdewijn · 2025 · Nucleic Acids Research
92. Chirality-specific hydrolysis of amino acid substrates by cellulose nanofibers
    Takeshi Serizawa, Toshiki Sawada, Masahisa Wada · 2013 · Chemical Communications
93. Methods for identifying and characterizing interactions involving RNA
    Brett D. Blakeley, Sandra M. DePorter, Utpal Mohan, Ritwik Burai, Blanton S. Tolbert, Brian R. McNaughton · 2012 · Tetrahedron
94. RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone
    Xueyi Wang, Gary J. Kapral, Laura W. Murray, David C. Richardson, Jane S. Richardson, Jack Scott Snoeyink · 2007 · Journal of Mathematical Biology
95. Hydrostatic and osmotic pressure study of the hairpin ribozyme
    Guy Hervé, Sylvia Tobé, Thomas Heams, Jacques Vergne, Marie‐Christine Maurel · 2006 · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
96. Binding of Short Oligonucleotides to RNA: Studies of the Binding of Common RNA Structural Motifs to Isoenergetic Microarrays
    Elżbieta Kierzek · 2009 · Biochemistry
97. Origin of Informational Polymers
    Raffaele Saladino, Claudia Crestini, Vincenzo Busiello, Fabiana Ciciriello, Giovanna Costanzo, Ernesto Di Mauro · 2005 · Journal of Biological Chemistry
98. Looked at Life from Both Sides Now
    Jillian Smith, Allisandra K. Rha, Anil Mehta, David G. Lynn · 2014 · Life
99. Ribozyme Chemistry: To Be or Not To Be under High Pressure
    Marie‐Christine Maurel, Fabrice Leclerc, Guy Hervé · 2019 · Chemical Reviews
100. Polyamine derivatives as selective RNaseA mimics
     Sandra Fouace · 2004 · Nucleic Acids Research