The chemical repertoire of natural ribozymes

The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution

Ban, N., Nissen, P., Hansen, J., Moore, P. B., & Steitz, T. A. (2000) · Science · doi:10.1126/science.289.5481.905 · Cited by 3,327

The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme

Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N., & Altman, S. (1983) · Cell · doi:10.1016/0092-8674(83)90117-4 · Cited by 2,684

Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena

Kruger, K., Grabowski, P. J., Zaug, A. J., Sands, J., Gottschling, D. E., & Cech, T. R. (1982) · Cell · doi:10.1016/0092-8674(82)90414-7 · Cited by 2,331

The Structural Basis of Ribosome Activity in Peptide Bond Synthesis

Nissen, P., Hansen, J., Ban, N., Moore, P. B., & Steitz, T. A. (2000) · Science · doi:10.1126/science.289.5481.920 · Cited by 2,269

Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing

Cate, J. H. D., Gooding, A. R., Podell, E. R., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R., & Doudna, J. A. (1996) · Science · doi:10.1126/science.273.5282.1678 · Cited by 1,249

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

Michel, F., & Westhof, É. (1990) · Journal of Molecular Biology · doi:10.1016/0022-2836(90)90386-z · Cited by 1,239

In Vitro Selection of Functional Nucleic Acids

Wilson, D. S., & Szostak, J. W. (1999) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.68.1.611 · Cited by 1,217

Three-dimensional structure of a hammerhead ribozyme

Pley, H. W., Flaherty, K. M., & McKay, D. (1994) · Nature · doi:10.1038/372068a0 · Cited by 946

Reversible Unfolding of Single RNA Molecules by Mechanical Force

Liphardt, J., Onoa, B., Smith, S. B., Tinoco, I., & Bustamante, C. (2001) · Science · doi:10.1126/science.1058498 · Cited by 931

Crystal structure of a hepatitis delta virus ribozyme

Ferré-D’Amaré, A. R., Zhou, K., & Doudna, J. A. (1998) · Nature · doi:10.1038/26912 · Cited by 790

siRNA FOR ERECTILE DYSFUNCTION

Christ, G. J. (2005) · The Journal of Urology · doi:10.1097/01.ju.0000174934.17803.5b · Cited by 1

Comparison of HSRNAFold and RNAFold algorithms for RNA secondary structure prediction

Mohsen, A. M., Khader, A. T., & Ramachandram, D. (2009) · IEEE Region 10 Conference (TENCON) · doi:10.1109/tencon.2009.5395933 · Cited by 1

Vocabulario inglés-español de bioquímica y biología molecular (8.ª y 9.ª entregas)

Saladrigas, M. V. (2005) · Panace@: Revista de Medicina, Lenguaje y Traducción · Cited by 1

Detection of single enzyme molecules and catalytic nucleic acids using microfluidics and selection of aptamers using capillary electrophoresis-SELEX

Yang, J. (2014) · University of Minnesota Digital Conservancy (University of Minnesota) · Cited by 1

RNA Secondary Structures

Reidys, C. M. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-801213-0.00014-9 · Cited by 1

Molecular Genetics of Corneal Disease

Stamler, J. F., & Fingert, J. H. (2011) · Elsevier eBooks · doi:10.1016/b978-0-323-06387-6.00019-2 · Cited by 1

Regulating Gene Expression through Engineered RNA Technologies

Win, M. N. (2009) · CRC Press eBooks · doi:10.1201/9781420077667.ch8 · Cited by 1

From ancient to modern RNA world: a metabolic story.

Li, Y. L., Tobé, S., Chabauty, A., & Maurel, M. (2006) · HAL · Cited by 1

Nucleic Acids

Rehmann, J. P. (2005) · Kirk-Othmer Encyclopedia of Chemical Technology · doi:10.1002/0471238961.1421031218050813.a01.pub2 · Cited by 1

Nuclease

Zhang, L., & Reha-Krantz, L. J. (2013) · Elsevier eBooks · doi:10.1016/b978-0-12-374984-0.01069-x · Cited by 1

Ribozyme Mechanisms

Hsieh, J., & Fierke, C. A. (2004) · Encyclopedia of Biological Chemistry · doi:10.1016/b0-12-443710-9/00077-6 · Cited by 1

Amino acids catalyze RNA formation under ambient alkaline conditionsPreprint

Braun, D., Rout, S. K., Wunnava, S., Powner, M. W., Šponer, J. E., & Mast, C. B. (2024) · Research Square · doi:10.21203/rs.3.rs-4343389/v1 · Cited by 1

Raman spectroscopic studies of the hepatitis delta virus (HDV) ribozyme

Gong, B. (2009) · OhioLink ETD Center (Ohio Library and Information Network)

GPU-optimized hybrid neighbor/cell list algorithm for coarse-grained molecular dynamics simulations

Proctor, A. J. (2013) · WakeSpace Scholarship (Wake Forest University)

Mortalin Targeting Gadgets for Cancer Therapy

Yun, C., & Wadhwa, R. (2012) · Springer eBooks · doi:10.1007/978-94-007-3027-4_18

DNA, RNA, and Protein Metabolism

Fromm, H. J., & Hargrove, M. S. (2011) · Springer eBooks · doi:10.1007/978-3-642-19624-9_16

Purification and Characterization of Novel Nucleases from a Thermophilic Fungus

Landry, K. S. (2023) · ScholarWorks@UMassAmherst (University of Massachusetts Amherst) · doi:10.7275/2721109

Splicing in the RNA World

Buratti, E., Romano, M., & Baralle, F. E. (2012) · doi:10.1002/9783527636778.ch1

An Overview of RNA Structure Prediction

Stormo, G. D. (2003) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1201s04

Probing Structure and Binding Sites on RNA by Fenton Cleavage

Bauer, G., & Berens, C. (2005) · doi:10.1002/9783527619504.ch15

Basics of Molecular Biology, Genetic Engineering, and Metabolic Engineering

Wang, M., & Shi, H. (2009) · doi:10.1002/9780470437988.ch2

Peptidyltransfer Reaction Catalyzed by the Ribosome and the Ribozyme: a Dissertation

Sun, L. (2003) · The Journal of the American Medical Association (JAMA) Network (American Medical Association) · doi:10.13028/6ds0-4c54

RNA ‐Based Therapies

Pascolo, S. (2010) · Pharmaceutical Sciences Encyclopedia · doi:10.1002/9780470571224.pse028

DISSECTION DU MÉCANISME DE TERMINAISON/ANTITERMINAISON AU NIVEAU DU TERMINATEUR TRI DU PHAGE LAMBDA : APPLICATION A L'ÉTUDE DES COMPLEXES ARN-PROTÉINE IN VIVO

Vieu, E. (2004) · HAL

GROUP I INTRON-DERIVED RIBOZYME REACTIONS

Johnson, A. K. (2005) · UKnowledge (University of Kentucky)

High‐Technology Therapy Using Biomolecules or Synthetic Compounds for HIV Inhibition

Fosso‐Kankeu, E., Fonteh, P., & Mishra, A. K. (2013) · Wiley eBooks · doi:10.1002/9781118636299.ch1

IN VITRO AND IN VIVO CHARACTERIZATION OF A TRANS EXCISION-SPLICING RIBOZYME

Nusbaum, C. (2005) · UKnowledge (University of Kentucky)

Informatic Approaches to Molecular Translation

Ardell, D. H. (2006) · Springer eBooks · doi:10.1007/3-540-32392-9_77

Group I Ribozymes as a Paradigm for RNA Folding and Evolution

Woodson, S. A., & Chauhan, S. (2008) · Springer series in biophysics · doi:10.1007/978-3-540-70840-7_7

Development of an RNA-based theophylline-specific microarray biosensor

Jordan, K. M. (2008) · Deep Blue (University of Michigan)

Antisenes-, Ribozym- und RNA-Interferenz-Strstegien: Methoden des posttranskriptionellen Gene Silencing in der Molekularen Medizin

Kurreck, J., Schubert, S., & Erdmann, V. A. (2008) · Springer eBooks · doi:10.1007/978-3-540-69414-4_18

Switchable RNA Motifs as Drug Targets

Westhof, É., François, B., & Vicens, Q. (2006) · Springer eBooks · doi:10.1007/978-0-387-47257-7_7

Single-Molecule Kinetic and Thermodynamic Studies of Cation-Facilitated RNA Folding: Isolated Tertiary Interactions

Fiore, J. L. (2011) · CU Scholar (University of Colorado Boulder)

Engineering RNA-Based Circuits

Narayanaswamy, R., & Ellington, A. D. (2006) · Springer eBooks · doi:10.1007/3-540-27262-3_22 · Cited by 1

Replication Processes—From Autocatalysis to Systems Chemistry

Huck, J., & Philp, D. (2012) · Supramolecular chemistry · doi:10.1002/9780470661345.smc158

Riboswitches as Genetic Control Elements

Nahvi, A., & Breaker, R. R. (2006) · Springer eBooks · doi:10.1007/978-0-387-47257-7_6

Potential thermosensitive riboswitches in the genome of Salmonella

Limanskaya, O. Y., Муртазаева, Л. А., & Лиманский, А. П. (2013) · Cytology and Genetics · doi:10.3103/s009545271305006x

Genetics of Corneal Disease for the Ocular Surface Clinician

Sjoberg, S. A. (2005) · The Ocular Surface · doi:10.1016/s1542-0124(12)70197-0

Purification of mitochondrial RNase P in A. nidulans

Khomami, P. J. (2010) · Papyrus : Institutional Repository (Université de Montréal) · doi:10.71781/31475

Computational Features Evaluation for RNA Secondary Structure Prediction

Zhao, Y., Ni, Q., & Wang, Z. (2009) · International Conference on Biomedical Engineering and Informatics (BMEI) · doi:10.1109/bmei.2009.5304921

Graph Representations and Algorithms in Computational Biology of RNA Secondary Structure

Stefan Washietl, A., & Gesell, T. (2010) · Birkhäuser Boston eBooks · doi:10.1007/978-0-8176-4789-6_17

Development of oligonucleotide based artificial ribonucleases 2'-O-MeOBAN´s and PNAzymes

Murtola, M. (2009) · Figshare

INSIGHTS INTO ENZYMATIC MANIPULATIONS OF NUCLEIC ACIDS

Alexander, R. C. (2005) · UKnowledge (University of Kentucky)

Studying the importance of 2´OH groups of tRNA in the RNase P mediated cleavage of tRNA precursors

Vetukuri, R. R. (2006)

Master Proof Coupling of Fast and Slow Modes in the Reaction Pathway of the Minimal Hammerhead Ribozyme Cleavage

Radhakrishnan, R. (2007)

and Biological Functions of RNA Hairpins

Bevilacqua, P. C., & Blose, J. M. (2008)

Maximizing Expected Base Pair Accuracy in RNA Secondary Structure Prediction by Joining Stochastic Context-Free Grammars Method

Habashy, S. M. (2012)

Evolving an Enzyme From a Non-Catalytic Sequence

Gysbers, R. (2015) · MacSphere (McMaster University) · doi:10.71548/15737

Efficient methods for matching RNA sequence-structure patterns

Meyer, F. (2015)

Design and synthesis of novel antisense nucleopeptides and their biophysical evaluation

Park, C. (2010) · Washington State University · doi:10.7273/000006170

Exploring RNA and protein 3D structures by geometric algorithms

Wang, X. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/203x-4r65

Characterisation of testis- and ovary- specific long non-coding RNAs

Yang, J. X. (2017) · Figshare · doi:10.4225/03/58b76c29c9268

Modulation unterschiedlicher Formen der Multidrug-Resistenz mittels eines Multitargetmultiribozymes

Kowalski, P. (2006) · doi:10.18452/15511

Metal interactions and activities of truncated and extended hammerhead ribozyme constructs

Osborne, E. M. (2007) · OakTrust (Texas A&M University Libraries)

Monitoring folding pathways for large RNAs using site-directed spin-labeling techniques

Zalma, C. A. (2007) · OakTrust (Texas A&M University Libraries)

A NON-CATALYTIC SEQUENCE

Gysbers, R. (2015)

Structural Characterization of Selected Pdases

Wellington, S. (2012) · CU Scholar (University of Colorado Boulder)

Development and Evaluation of Nano‑scale Systems for Targeted Delivery to Treat Liver Fibrosis

Yang, N. (2011) · doi:10.21007/etd.cghs.2011.0364

LA DUALIDAD ANÁLOGO DIGITAL DE LA INFORMACIÓN SE EJEMPLIFICA EN EL ESTUDIO DE LAS MÓLECULAS DE RNA The Analog Digital Duality of Information is Exemplified by Studying RNA Molecules

Andrade, E. (2011) · DOAJ (DOAJ: Directory of Open Access Journals)

RNA-mediated chemistries: a case of replication and capping

Zaher, H. S. (2007) · Summit (Simon Fraser University)

THREE FUNDAMENTALS OF THE BIOLOGICAL GENETIC ALGORITHM A Biologist's View ofBiological Inspiration vs. Biology Envy

Freeland, S. J. (2003)

Microbial Diversity and Global Environmental Issues

Ogunseitan, O. A. (2004) · Wiley eBooks · doi:10.1002/9780470750490.ch11

The Transcription of Genes

Metzler, D. E., Metzler, C. M., & Sauke, D. J. (2001) · Elsevier eBooks · doi:10.1016/b978-012492543-4/50031-3

Performing Collective Tasks with Flagellated Bacteria Acting as Natural and Hybrid Microrobots

Martel, S. M. (2013) · doi:10.1201/b14908-27

The transposon Galileo in the Drosophila genus.

Llorca, M.-E. (2011) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.10755532

RNA Secondary Structure Prediction Using Neural Machine Translation

Zhang, L. (2016)

GPU-Optimized Molecular Dynamics Simulations

Lipscomb, T. J. (2012) · WakeSpace Scholarship (Wake Forest University)

Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

Zuniga, M. C. (2017)

RNA Rings in the Origin of Life

Moreira, A. (2003) · ResearchSpace (University of Auckland)

Development and application of liquid chromatography-mass spectrometry for the analysis of nucleic acids

Kung, A. (2018)

Prebiological Organization of Molecules in Models and in the Matter of the Origin of Life

Zhogol, R. A., & . (2018) · International Journal of Engineering & Technology · doi:10.14419/ijet.v7i3.14.17044

Chemical and Pharmacological Modulation of Telomerase

Soares, J. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/fgzz-7e09

Enzymes: Characteristics and Mechanisms

Price, N. C., & Lapthorn, A. J. (2004) · CRC Press eBooks · doi:10.1081/e-esmc-120012683

How does Mg 2+ modulate the RNA folding mechanism — a case study of G:C W:W Trans base pairPreprint

Halder, A., Roy, R., Bhattacharyya, D., & Mitra, A. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/098079

Improving Coupled Enzyme Assays With Capillary Electrophoresis

Nguyen, T. (2019) · Louisiana State University · doi:10.31390/gradschool_dissertations.4888

Discovery and Characterization of Non-coding RNA Through Modern Genomics

Zhang, C., Yu, B., & Sun, X. (2019) · Elsevier eBooks · doi:10.1016/b978-0-08-100596-5.22711-x

DNA/RNA as catalyst

Brück, T. (2020) · Catalysis from A to Z · doi:10.1002/9783527809080.cataz05723

Protein Biosynthesis

Litwack, G. (2021) · Elsevier eBooks · doi:10.1016/b978-0-323-85718-5.00015-7

Proteins

Litwack, G. (2021) · Elsevier eBooks · doi:10.1016/b978-0-323-85718-5.00005-4

References

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Genomics

Semizarov, D., & Blomme, E. A. G. (2010) · Wiley eBooks · doi:10.1002/9780470571224.pse090

Bibliography

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Faculty Opinions recommendation of Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation.

Unrau, P. J. (2005) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.1008763.341205

Faculty Opinions recommendation of Site-specific RNA methylation by a methyltransferase ribozyme.

Müller, S. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.738912864.793582213

Functional characterization and application of 2',5'- branched RNA forming deoxyribozymes using lanthanides as cofactors

Javadi‐Zarnaghi, F. (2013) · doi:10.53846/goediss-4284

Faculty Opinions recommendation of Next-level riboswitch development-implementation of Capture-SELEX facilitates identification of a new synthetic riboswitch.

Narberhaus, F. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.735506129.793558911

Ribozyme

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Faculty Opinions recommendation of Site-specific RNA methylation by a methyltransferase ribozyme.

Kath‐Schorr, S. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.738912864.793580589

Biological Supermolecules — Learning from Nature

(2006) · Springer eBooks · doi:10.1007/3-540-26185-0_6

Faculty Opinions recommendation of DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides.

Silverman, S. K. (2009) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.1147336.604494

Design vs. Iterative Methods – Mimicking the Way Nature Generates Catalysts

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References

Weiss, K. M., & Buchanan, A. V. (2004) · Wiley eBooks · doi:10.1002/0471532657.refs

Introduction

Reidys, C. M. (2010) · Springer eBooks · doi:10.1007/978-0-387-76731-4_1

References

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General Introduction

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RNA structure probing using long-read nanopore sequencing technology

Aw, A. J. G. (2022) · doi:10.32657/10356/158914

Theories of the Origin of Biomolecular Homochirality

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Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA

Feyrer, H., Schlagnitweit, J., & Petzold, K. (2021) · Journal of Visualized Experiments · doi:10.3791/62470-v

Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentialsPreprint

Gong, T., Ju, F., & Bu, D. (2022) · Research Square · doi:10.21203/rs.3.rs-2074610/v1

Decision: Computational drug discovery under RNA times — R1/PR4

Bernetti, M., Aguti, R., Bosio, S., et al. (2022) · QRB Discovery · doi:10.1017/qrd.2022.20.pr4

The chemical versatility of RNA

Hiller, D. A., & Strobel, S. A. (2011) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2011.0143 · Cited by 30

Introduction

Westhof, É. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-545-9_1 · Cited by 5

RNA catalysis: More than a messenger

Lilley, D. M. J. (2006) · The Biochemist · doi:10.1042/bio02802007

Ribozymes: ancient and modern

Lilley, D. M. J. (2015) · The Biochemist · doi:10.1042/bio03702004 · Cited by 1

5 Catalytic Strategies of Self-Cleaving Ribozymes: Relics of an RNA World?Preprint

Ke, A., & Doudna, J. A. (2006) · Cold Spring Harbor Monograph Archive · doi:10.1101/087969739.43.109 · Cited by 4