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The discovery of ribozymes nearly 30 years ago triggered a huge interest in the chemistry and biology of RNAs. Much of the recently made progress focusing on metal ions is addressed in MILS 9. This book, written by 28 internationally recognized experts from 8 nations, provides a most up-to-date view and is thus of special relevance for colleagues teaching courses in biological inorganic chemistry and for researchers dealing, e.g., with nucleic acids, gene expression, and enzymology, but also for those in analytical and bioinorganic chemistry or biophysics. Structural and Catalytic Roles of Metal Ions in RNA describes in an authoritative and timely manner in 12 stimulating chapters, supported by nearly 1600 references, 13 tables, and 75 illustrations, mostly in color, metal ion-binding motifs, methods to detect and characterize metal ion-binding sites, and the role of metal ions in folding and catalysis. It deals with diffuse metal ion binding, RNA quadruplexes, the regulation of riboswitches, metal ions and ribozymes, including artificial ribozymes. The spliceosome, the ribosome, ribozymes involving redox cofactors as well as the binding of kinetically inert metal ions to RNA are also covered.
Catalytic RNA. --- Ribonucleic acid enzymes --- Ribozymes --- RNA enzymes --- Non-coding RNA --- Nucleases
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This volume of Methods in Enzymology aims to provide a reference for the diverse, powerful tools used to analyze RNA helicases. The contributions in this volume cover the broad scope of methods in the research on these enzymes. Several chapters describe quantitative biophysical and biochemical approaches to study molecular mechanisms and conformational changes of RNA helicases. Further chapters cover structural analysis, examination of co-factor effects on several representative examples, and the analysis of cellular functions of select enzymes. Two chapters outline approaches to the analys
Catalytic RNA. --- RNA Helicases. --- RNA Nucleotidyltransferases --- RNA --- Nucleotidyltransferases --- Nucleic Acids --- Phosphotransferases --- Nucleic Acids, Nucleotides, and Nucleosides --- Chemicals and Drugs --- Transferases --- Enzymes --- Enzymes and Coenzymes --- RNA, Messenger --- RNA Helicases --- Human Anatomy & Physiology --- Health & Biological Sciences --- Animal Biochemistry --- Messenger RNA --- Physiological transport. --- Metabolism. --- analysis. --- Catalytic rna. --- Messenger rna --- Rna helicases --- Analysis. --- Ribonucleic acid enzymes --- Ribozymes --- RNA enzymes --- Non-coding RNA --- Nucleases
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Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications explores various molecular modelling techniques and their applications in providing an understanding of the detailed mechanisms at play during biocatalysis in enzyme and ribozyme systems. These areas are reviewed by an international team of experts in theoretical, computational chemistry, and biophysics. This book has three sections that group together different aspects of multi-scale quantum simulations. The first section consists of four chapters that describe strategies for multi-scale quantum models and present an overview of the current state-of-the-art molecular modelling methodologies most relevant to handling these complex systems with quantum mechanics and molecular simulation. With five chapters, the second section mainly focuses on the current efforts to improve the accuracy of quantum calculations using simplified empirical model forms. The last section consists of five chapters focused on the applications of important biological systems using multi-scale quantum models. This book presents detailed reviews concerning the development of various techniques, including ab initio molecular dynamics, density functional theory, combined QM/MM methods, solvation models, force field methods, and free-energy estimation techniques, as well as successful applications of multi-scale methods in the biocatalysis systems including several protein enzymes and ribozymes. Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications is an excellent source of information for research professionals involved in computational chemistry and physics, material science, nanotechnology, rational drug design and molecular biology. It is also likely to be of interest to graduate and undergraduate students exposed to these research areas.
Enzymes --Biotechnology. --- Molecules --Models. --- Enzymes --- Biocatalysis --- Molecules --- Animal Biochemistry --- Physical & Theoretical Chemistry --- Chemistry --- Human Anatomy & Physiology --- Physical Sciences & Mathematics --- Health & Biological Sciences --- Biotechnology --- Models --- Enzymology. --- Catalytic RNA. --- Quantum chemistry. --- Mathematical models. --- Biophysics. --- Biological physics --- Models, Mathematical --- Chemistry, Quantum --- Ribonucleic acid enzymes --- Ribozymes --- RNA enzymes --- Chemistry. --- Chemistry, Physical and theoretical. --- Catalysis. --- Materials science. --- Nanotechnology. --- Theoretical and Computational Chemistry. --- Materials Science, general. --- Biology --- Medical sciences --- Physics --- Non-coding RNA --- Nucleases --- Biochemistry --- Simulation methods --- Chemistry, Physical and theoretical --- Quantum theory --- Excited state chemistry --- Materials. --- Molecular technology --- Nanoscale technology --- High technology --- Engineering --- Engineering materials --- Industrial materials --- Engineering design --- Manufacturing processes --- Activation (Chemistry) --- Surface chemistry --- Physical sciences --- Materials --- Material science --- Chemistry, Theoretical --- Physical chemistry --- Theoretical chemistry
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Ribozyme Protocols brings together a broad spectrum of essential and easily reproducible techniques currently used by leading researchers to manipulate RNA molecules and to inactivate gene expression in vivo. The methods collected here range from theoretical design to clinical application and include the synthesis and assay of ribozymes, as well as their use both in vitro and in vivo. Each method is presented by an expert with substantial hands-on experience and in far greater detail than is generally to be found in the research literature. Ribozyme Protocols will help all investigators perform meaningful and successful experiments using ribozymes in both clinical and basic research, as well as launch fresh application initiatives. It is certain to be found indispensable not only by those workers new to the field, but also by experienced researchers who wish to expand their range of expertise.
Catalytic RNA -- Laboratory manuals. --- Electronic books. -- local. --- Nucleic acids -- Laboratory manuals. --- Catalytic RNA --- Genetic Techniques --- RNA, Catalytic --- RNA, Untranslated --- Investigative Techniques --- Enzymes --- Analytical, Diagnostic and Therapeutic Techniques and Equipment --- Enzymes and Coenzymes --- RNA --- Chemicals and Drugs --- Nucleic Acids --- Nucleic Acids, Nucleotides, and Nucleosides --- Animal Biochemistry --- Human Anatomy & Physiology --- Health & Biological Sciences --- Laboratory manuals --- RNA, Catalytic. --- Genetic Techniques. --- Laboratory manuals. --- Catalytic rna --- Genetic techniques. --- Rna, catalytic. --- Nucleic acids --- Polynucleotides --- Biomolecules --- Ribonucleic acid enzymes --- Ribozymes --- RNA enzymes --- Non-coding RNA --- Nucleases --- Biochemistry. --- Biochemistry, general. --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Biology --- Chemistry --- Medical sciences --- Composition
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In this book, seven chapters describe studies aimed at understanding and exploiting the key features of such molecular RNA and DNA devices. In the first section of the book, four chapters are devoted to artificial nucleic acid switches and sensors. These chapters introduce the concept of allosteric ribozymes as molecular switches and sensors; describe nucleic acid enzymes that are switched by oligonucleotides and other nucleic acid enzymes that are switched by proteins; and illustrate how switching elements can be integrated ration-ally into fluorescently signaling molecular sensors made out of nucleic acids. In the second section of the book, three chapters show that nature has been as crafty a molecular-scale engineer as any modern scientist via evolution of natural nucleic acid switches and sensors. RNAs have been found whose activities are modulated either by proteins or by small-molecule metabolites, and both kinds of system are described. Finally, the notion of exploiting naturally occurring RNA switches for drug development is discussed.
Biomedicine. --- Human Genetics. --- Medical Microbiology. --- Medicine. --- Human genetics. --- Microbiology. --- Médecine --- Génétique humaine --- Microbiologie --- Biosensors. --- Catalytic RNA. --- RNA -- Biotechnology. --- Catalytic RNA --- Biosensors --- RNA --- Enzymes --- Nucleic Acids, Nucleotides, and Nucleosides --- RNA, Untranslated --- Genes, Regulator --- Molecular Probe Techniques --- Metabolic Phenomena --- RNA, Catalytic --- Biosensing Techniques --- Metabolism --- Genes, Switch --- Nucleic Acids --- Investigative Techniques --- Genes --- Chemicals and Drugs --- Enzymes and Coenzymes --- Phenomena and Processes --- Analytical, Diagnostic and Therapeutic Techniques and Equipment --- Genome Components --- Genome --- Genetic Structures --- Genetic Phenomena --- Human Anatomy & Physiology --- Biology --- Medicine --- Pathology --- Animal Biochemistry --- Genetics --- Health & Biological Sciences --- Biotechnology --- Biotechnology. --- Biodetectors --- Biological detectors --- Biological sensors --- Biomedical detectors --- Biomedical sensors --- Ribonucleic acid enzymes --- Ribozymes --- RNA enzymes --- Medical microbiology. --- Detectors --- Medical instruments and apparatus --- Physiological apparatus --- Non-coding RNA --- Nucleases
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