Ribozymes (eBook)

Sabine Müller is Full Professor for Biochemistry/Bioorganic Chemistry at Greifswald University (Germany). Having obtained her academic degrees from Humboldt University Berlin, she spent one and a half years as a postdoc at the MRC in Cambridge (UK) and then took up a group leader position again at Humboldt University. After finishing her Habilitation in 2003, she moved to the Ruhr University Bochum, where she was a Professor for Bioorganic Chemistry, before taking up her present appointment at Greifswald in 2006. Professor Müller has received several scientific awards, including a Heisenbergstipendium of the Deutsche Forschungsgemeinschaft (DFG). She is a member of the Leibniz-Societät der Wissenschaften zu Berlin and of AcademiaNet. Benoît Masquida is a research director at Centre National de la Recherche Scientifique. After graduating from Université Louis Pasteur in Strasbourg (France) working on the rules governing RNA folding, he spent one year at Yale University concentrating on ribosomal RNA structural motifs. After coming back to Strasbourg, he was appointed as a CNRS Research Scientist. He was promoted to Research Director in 2016, acknowledging his important contributions in the RNA structural biology field. Wade Winkler is an Associate Professor of Cell Biology and Molecular Genetics at the University of Maryland (USA). He acquired a graduate degree from The Ohio State University before spending three years as a postdoctoral researcher at Yale University. In 2004, he began his independent scientific career at The University of Texas Southwestern Medical Center in the Department of Biochemistry, and relocated his laboratory to the University of Maryland in 2011. Through the years, Professor Winkler has authored multiple influential publications on the different types of regulatory RNAs in bacteria.

INTRODUCTION
The chemical principles of RNA catalysis

NATURALLY OCCURRING RIBOZYMES
Biological roles of self-cleaving ribozymes
Chemical mechanisms of the nucleolytic ribozymes
The glmS ribozyme and its multifunctional coenzyme glucosamine-6-phosphate
The lariat capping ribozyme
Self-splicing group II introns
The Spliceosome: an RNA-Protein ribozyme derived from ancient mobile genetic elements
The ribosome and protein synthesis
The RNase P ribozyme
Ribozyme Discovery in Bacteria
Small self-cleaving ribozymes in the genomes of vertebrates

ENGINEERED RIBOZYMES
Phosphoryl transfer ribozymes
RNA replication and the RNA polymerase ribozyme
Maintenance of genetic information in the first ribocell
Ribozyme-catalyzed RNA recombination
Engineering of hairpin ribozymes for RNA processing reactions
Engineering of the Neurospora Varkud Satellite ribozyme for cleavage of non-natural stem-loop substrates
Chemical modifications in natural and engineered ribozymes
Ribozymes for regulation of gene expression
Development of flexizyme aminoacylation ribozymes and their applications
In vitro selected (deoxy)ribozymes that catalyze carbon-carbon-bond formation
Nucleic acid catalyzed RNA ligation and labeling

DNAZYMES
The chemical repertoire of DNA enzymes
Light-utilizing DNAzymes
Applications of DNAzymes in computing and nanotechnology.

RIBOZYMES AS TOOLS IN DIAGNOSTICS AND THERAPY
Optimization of antiviral ribozymes
DNAzymes as Biosensors
Compartmentalization-based technologies for in vitro selection and evolution of ribozymes and light-up RNA aptamers

TOOLS AND METHODS TO STUDY RIBOZYMES
Elucidation of ribozyme mechanisms at the example of the Pistol ribozyme
Strategies for crystallization of natural ribozymes
NMR spectroscopic investigation of ribozymes
Studying Ribozymes with Electron Paramagnetic Resonance Spectroscopy
Computational modeling methods for 3D structure prediction of ribozymes