Download or read book Catalytic RNAs for a RNA World written by Janina E. Moretti and published by . This book was released on 2013 with total page 121 pages. Available in PDF, EPUB and Kindle. Book excerpt: At some point in the origin of life, life likely went through a stage where RNA acted as genome and catalyst--the RNA world. Eventually, life evolved into the form we observe today, with DNA acting as genome and proteins acting as the main catalysts. Although there is no known direct evidence of RNA world organisms, we can gain understanding of life's early ancestors by creating catalytic RNAs in the lab that could have existed in an RNA world. This dissertation aims to develop and improve two of these catalytic RNAs (ribozymes). The first is a triphosphorylation ribozyme, a catalytic RNA that triphosphorylates the 5' hydroxyl groups of RNA using trimetaphosphate. In a RNA world, this activity could have been useful for chemically activating RNAs for ligation or polymerization. The second is a polymerase ribozyme, a catalytic RNA that catalyzes RNA polymerization. This activity could have been important for replication in a RNA world organism. In order to identify catalytic RNAs that can triphosphorylate their own 5' hydroxyl groups, an in vitro selection method was established. From a library of ~1014 random sequences, several active sequences were identified and one was analyzed in greater detail. This triphosphorylation ribozyme was modified to act in trans and had a reaction rate of 0.16 min−1 under optimal conditions. Preliminary analysis of its secondary structure suggests that it forms a four helical junction motif. A catalytic RNA that catalyzes the polymerization of RNA was previously developed, but it is too inefficient to replicate itself. Its limitation is weak substrate binding. Here efforts were made to improve the polymerase ribozyme by reducing charge repulsion between the negatively charged ribozyme and its substrate using positively charged amino acids as cofactors. However, these cofactors did not improve ribozyme polymerization. An in vitro selection method that puts selection pressure on the ribozyme to bind its substrate in trans was developed to try to find improved polymerase ribozymes. Although no active ribozymes were found, several steps of a technically challenging in vitro selection method were established. In summary, this thesis presents work to develop two catalytic RNAs for a RNA world. An existing polymerase ribozyme was tested with amino acid cofactors and progress was made towards developing an in vitro selection that could be used to find novel polymerase ribozymes. Also, a novel catalytic RNA that can triphoshphorylate RNAs was created. This opens up new avenues that will deepen our understanding of the RNA world.
Download or read book Ribozymes and RNA Catalysis written by David Malcolm James Lilley and published by Royal Society of Chemistry. This book was released on 2008 with total page 339 pages. Available in PDF, EPUB and Kindle. Book excerpt: Takes the reader through the origins of catalysis in RNA and necessarily includes significant discussion of structure and folding. The main focus of the book concerns chemical mechanism with extensive comment on how, despite the importance of RNA catalysis in the cell, its origins are still poorly understood and often controversial. The reader is given an outline of the important role of RNA catalysis in many aspects of cell function, including RNA processing and translation.
Download or read book The RNA World written by Raymond F. Gesteland and published by CSHL Press. This book was released on 2006 with total page 774 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent studies on the activities of RNA in the cell have revolutionized our understanding of the many roles played by this molecule. The first two editions of The RNA World(1993, 1999) shed light on the pre–biotic era dominated by this versatile molecule, and provided an overview of the state of RNA research at the time. The new third edition of The RNA Worldupdates this perspective, describing the vast array of newly discovered roles for RNA in the modern world. The updated original chapters are supplemented with new chapters on RNA–protein complexes, snRNPs and snoRNPs, telomerase RNA, RNAi, microRNAs, noncoding RNA, and many other subjects. This book is essential reading for anyone interested in the biology of nucleic acids and gene regulation and a valuable resource for teaching these concepts.
Download or read book Catalytic RNA written by Fritz Eckstein and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, unprecedented advances in many aspects of the molecular biology of nucleic acids have been witnessed. The area of RNA chemistry has undergone a kind of explosion, with a huge interest in RNA-mediated catalysis. At the same time, our structural understanding of DNA-protein interactions has increased enormously, and the related area of RNA-protein interactions is beginning to gather pace. This softcover edition from the successful series Nucleic Acids and Molecular Biology is devoted to the structure and mechanism of ribozymes, and their potential exploitation. The subject has both important evolutionary implications and potential practical application in the development of therapeutic agents for diseases such as AIDS.
Download or read book Looking at Ribozymes written by Benoît Masquida and published by John Wiley & Sons. This book was released on 2024-04-02 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: Behind the neologism “ribozymes” lies a family of fascinating molecules, ribo-enzymes, which have been relatively little studied. These catalytically active RNAs are found in all strata of life, from viruses to the human genome. At the end of the 1970s, the discovery of a catalytic RNA nestled in an intron, followed by another involved in the maturation of transfer RNAs, led to the discovery of new ribozymes and the transition from a strictly “proteocentric” vision, inherited from the dogma of molecular biology, to a more “nucleocentric” one. Since then, a variety of ribozymes have been identified in genomes, where their functions often remain mysterious. Looking at Ribozymes traces the discovery of these molecules and presents a picture of their functional diversity, catalytic mechanisms and distribution within the tree of life.
Download or read book Ribozymes written by Sabine Müller and published by John Wiley & Sons. This book was released on 2021-07-09 with total page 81 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ribozymes Provides comprehensive coverage of a core field in the molecular biosciences, bringing together decades of knowledge from the world’s top professionals in the field Timely and unique in its breadth of content, this all-encompassing and authoritative reference on ribozymes documents the great diversity of nucleic acid-based catalysis. It integrates the knowledge gained over the past 35 years in the field and features contributions from virtually every leading expert on the subject. Ribozymes is organized into six major parts. It starts by describing general principles and strategies of nucleic acid catalysis. It then introduces naturally occurring ribozymes and includes the search for new catalytic motifs or novel genomic locations of known motifs. Next, it covers the development and design of engineered ribozymes, before moving on to DNAzymes as a close relative of ribozymes. The next part examines the use of ribozymes for medicinal and environmental diagnostics, as well as for therapeutic tools. It finishes with a look at the tools and methods in ribozyme research, including the techniques and assays for structural and functional characterization of nucleic acid catalysts. The first reference to tie together all aspects of the multi-faceted field of ribozymes Features more than 30 comprehensive chapters in two volumes Covers the chemical principles of RNA catalysis; naturally occurring ribozymes, engineered ribozymes; DNAzymes; ribozymes as tools in diagnostics and therapy, and tools and methods to study ribozymes Includes first-hand accounts of concepts, techniques, and applications by a team of top international experts from leading academic institutions Dedicates half of its content to methods and practical applications, ranging from bioanalytical tools to medical diagnostics to therapeutics Ribozymes is an unmatched resource for all biochemists, biotechnologists, molecular biologists, and bioengineers interested in the topic.
Download or read book Ribozymes and Aptamers in the RNA World and in Synthetic Biology written by Raghav Raj Poudyal and published by . This book was released on 2016 with total page 178 pages. Available in PDF, EPUB and Kindle. Book excerpt: The RNA world hypothesis postulates that Ribonucleic Acids (RNA) may have provided functions of catalysis and genetic information storage during the origin of life on earth. An RNA based life is hypothesized to have undergone Darwinian evolution to ultimately lead into extant biology, where DNA is used as the repository for genetic information and proteins are used as biological catalysts. The discovery of functional RNAs such as catalytic RNAs, regulatory RNAs, and ligand-binding RNA aptamers further strengthen this hypothesis. These functional RNAs are also used as tools for synthetic biology and therapeutics. This work highlights strategies used by RNA enzymes (Ribozymes) for catalysis of chemical reactions, and explores new chemistries catalyzed by ribozymes. We also engineered an in vitro evolved ribozyme to control activities of other functional RNA molecules. Finally, this work explores innovative approaches to discover new RNA enzymes that catalyze biologically relevant reactions. Findings from these studies have revealed potential roles of RNA enzymes during the primordial earth, and also opened doors to build RNA-based tools that regulate biological processes.
Download or read book Why Does Evolution Matter written by Gabriel Trueba and published by Cambridge Scholars Publishing. This book was released on 2014 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Evolution is not merely a chapter in biology textbooks; rather, it is the mesh that embraces and connects every biological phenomenon; indeed, as Dobzhansky pointed out, nothing in biology could be understood without the evolutionary logic. The contents of this book highlight the importance of evolution in applied biological sciences such as agricultural, medical, environmental and the social sciences. Evolutionary science provides renewed ideas which can result in practical applications and tools that deal with current problems concerning humanity, such as disease, food production, and environmental destruction. Most of the topics in this book were discussed during the III Summit on Evolution which took place in the Galapagos Islands in June 2013, hosted by the Galapagos Institute for the Arts and Sciences and the Galapagos Science Institute, Universidad San Francisco de Quito.
Download or read book Life from an RNA World written by Michael Yarus and published by Harvard University Press. This book was released on 2010 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: A majority of evolutionary biologists believe that we now can envision our biological predecessors--not the first, but nearly the first, living beings on Earth. This book is about these vanished forebears. The era between the first rudimentary life on Earth and the appearance of more complex beings is called the RNA world. It is RNA (ribonucleic acid) long believed to be a mere biologic copier and messenger, that offers a glimpse into our ancient predecessors. To describe early RNA creatures, here called "ribocytes" or RNA cells, the author uses basics of molecular biology. He reviews our current understanding of the tree of life, examines the structure of RNA itself, explains the operation of the genetic code, and more. Courting controversy among those who question the role of ribocytes -- citing the chemical fragility of RNA and the uncertainty about the origin of an RNA synthetic apparatus -- he offers a vision of early life on Earth.
Download or read book In Vitro Selection of Catalytic RNAs in Emulsion written by Arvin Akoopie and published by . This book was released on 2019 with total page 138 pages. Available in PDF, EPUB and Kindle. Book excerpt: The RNA world hypothesis describes an early stage of life when RNA fulfilled both genomic and catalytic roles. One great effort to support this model is by generating catalytic RNAs (ribozymes) that can catalyze essential RNA world functions. One of these RNA world functions is establishing an energy metabolism in the form of chemically activated nucleotides. Trimetaphosphate has been shown to be a prebiotically plausible activating source that generates nucleoside triphosphates from nucleosides. A main goal of the Muller lab is to generate ribozymes that can establish an energy pathway by using trimetaphosphate. Such a ribozyme could utilize trimetaphosphate and nucleosides to generated chemically activated NTPs. NTPs have an essential role in modern life (as cofactors and monomers for genetic polymerization), and having a prebiotically plausible pathway for its generation would greatly support the RNA world hypothesis. Previous projects from the Muller lab have established a ribozyme that can triphosphorylate its own 5' end. Although this was significant in establishing that triphosphorylation can be catalyzed by ribozymes, it did not generate freely diffusing NTPs. Here I describe a selection for a nucleoside triphosphorylation ribozyme as well as additional RNA evolutions and engineering to accomplish this goal. The main efforts taken were the evolution of a polymerase ribozyme towards a thio-modified nucleotide and characterizing the emulsion environment necessary for the selection to work.
Download or read book Ribonuclease P written by Fenyong Liu and published by Springer Science & Business Media. This book was released on 2009-12-03 with total page 293 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Discovery of Ribonuclease P and Enzymatic Activity of Its RNA Subunit Sydney Brenner and Francis H. C. Crick had a specific project in mind when they offered Sidney Altman a position in their group in 1969 to conduct postdoctoral research at the Medical Research Council Laboratory of Molecular Biology (LMB) in Cambridge, England. At the time, an intense international competition was on- ing in as many as a dozen labs to determine the three-dimensional structure of tRNA. At the LMB, Aaron Klug was attacking the structure by crystallographic analysis with Brian F. C. Clark providing large amounts of purified phenylalanine tRNA. (Eventually, Aaron announced his empirically determined 3-D structure of yeast phenylalanine tRNA, a structure that is generally common to tRNAs, due in part to several conserved, novel three-way nucleotide interactions. ) Concurrently, Michael Levitt, a Ph. D. student of Francis, was visually scrutinizing the cloverleaf secondary structure of the 14 tRNA sequences known at the time. Levitt was searching for nucleotide covariation in different parts of the molecules that were conserved in the 14 sequences known at the time. He identified a possible covariation of an apparent Watson-Crick pairing type between the residues at position 15 from the 5’ end of the tRNA and residue 48. This association implied these parts of the tRNA, namely the D loop containing residue 15 and the 5’ end of the T stem-adjoining residue 48, folded on one another in a tertiary structure shared by different tRNAs.
Download or read book Prebiotic Chemistry written by Peter Walde and published by Springer Science & Business Media. This book was released on 2005-10-13 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Pyridine Nucleotide Coenzymes written by Johannes Everse and published by Elsevier. This book was released on 2012-12-02 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Pyridine Nucleotide Coenzymes provides a comprehensive discussion of the evolution, properties, and reactions of pyridine nucleotide coenzymes. The pyridine nucleotide coenzymes, NAD and NADP, appear to be among the most versatile of molecules with respect to their biological functions. In addition to their well-documented roles in a large number of oxidation-reduction reactions, these coenzymes are involved in many aspects of metabolic regulation. The book begins by tracing the evolution of coenzymes and pyridine nucleotide coenzymes. This is followed by separate chapters that deal with the static and dynamic properties of the pyridine nucleotide coenzymes; chemistry and solution conformation of the pyridine coenzymes; pyridine nucleotide analogs; and the three-dimensional structures of pyridine nucleotide binding enzymes. Subsequent chapters cover the synthesis and characterization of immobilized coenzymes and derivatives and their applications in affinity chromatography and enzyme reactors; the pathways to quinolinate, a major precursor of pyridine nucleotides; the role of pyridine nucleotides in phagocytosis; and non-oxidation-reduction reactions of pyridine nucleotides.
Download or read book RNA Catalysis Splicing Evolution written by M. Belfort and published by Elsevier. This book was released on 2012-12-02 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: The conference on "RNA: Catalysis, Splicing, Evolution" brought together a unique assembly of scientific leaders in this currently very important field. Two participants of this Conference, Drs. T.R. Cech and S. Altman, were just awarded the 1989 Nobel prize in chemistry, which attests to the timeliness of this volume. The critical reviews authored by these two prominent scientists are included. For those scientists with roots in this field, who do not subscribe to GENE, this is an excellent opportunity to obtain a masterly collection of papers. All the original papers and reviews have undergone the rigorous peer review of the journal "Gene".
Download or read book Recombinant and In Vitro RNA Synthesis written by Graeme L. Conn and published by Humana Press. This book was released on 2016-08-23 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: The discovery of catalytic RNAs in the mid-1980s marked the beginning of a new era in RNA biology and an ever increasing appreciation of the diverse and critical roles played by this fascinating molecule. In Recombinant and In Vitro RNA Synthesis: Methods and Protocols, expert researchers in the field detail approaches from the inception of a new RNA project to the final sample ready for analysis. These experimental protocols combine established work-horse approaches with some of the latest innovative methods for RNA synthesis and purification. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Recombinant and In Vitro RNA Synthesis: Methods and Protocols aids scientists in continuing to study the fascinating world of RNA.
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Biology A Very Short Introduction written by Aysha Divan and published by Oxford University Press. This book was released on 2016-08-18 with total page 195 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Biology is the story of the molecules of life, their relationships, and how these interactions are controlled. It is an expanding field in life sciences, and its applications are wide and growing. We can now harness the power of molecular biology to treat diseases, solve crimes, map human history, and produce genetically modified organisms and crops, and these applications have sparked a multitude of fascinating legal and ethical debates. In this Very Short Introduction, Aysha Divan and Janice Royds examine the history, present, and future of Molecular Biology. Starting with the building blocks established by Darwin, Wallace and Mendel, and the discovery of the structure of DNA in 1953, they consider the wide range of applications for Molecular Biology today, including the development of new drugs, and forensic science. They also look forward to two key areas of evolving research such as personalised medicine and synthetic biology. ABOUT THE SERIES: The Very Short Introductions series from Oxford University Press contains hundreds of titles in almost every subject area. These pocket-sized books are the perfect way to get ahead in a new subject quickly. Our expert authors combine facts, analysis, perspective, new ideas, and enthusiasm to make interesting and challenging topics highly readable.
