Download or read book RNA written by Marlene Belfort and published by Elsevier Publishing Company. This book was released on 1989 with total page 252 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 RNA Catalysis Splicing Evolution written by and published by . This book was released on 1989 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 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 Papers Presented at the Albany Conference on RNA Catalysis Splicing Evolution Rensselaerville NY U S A 22 25 September 1988 written by and published by . This book was released on 1989 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Expanding the Catalytic Potential and Chemical Composition of RNA Through in Vitro Evolution written by Xiaochang Dai and published by . This book was released on 1998 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: In vitro evolution techniques have been used to alter the catalytic function of existing ribozymes and to develop ribozymes with novel catalytic functions. We report the result of using nucleotide analogs in an in vitro evolution system to expand the chemical repertoire of nucleic acids and to further advance their catalytic potential. In the presence of 5-bromo-UTP, five successive rounds of stepwise in vitro evolution were carried out, starting with the Tetrahymena group I ribozyme and selecting for improved phosphoester transfer activity. As the result, a population of highly active, fully bromouridin substituted ribozymes were obtained. Thirty subclones were isolated following the 5th round of selection and were sequenced. Three major mutations were found to be responsible for the improved catalytic activity. Compared to the bromouridine substituted wild-type ribozyme, the evolved subclones showed a 27-fold improvement in catalytic efficiency. In vitro evolution also has been used as a powerful tool to study important issues regarding evolution at the molecular level, such as adaptation and coevolution. A more advanced in vitro evolution system in which RNA catalysis of 3' ,5 ' -regiospecific oligonucleotide ligation is coupled directly with amplification was used to address these issues. This continuous evolution system was challenged by the use of [alpha-S] CTP and [alpha-S] UTP over the native NTPs. The change in chemical composition of the ligase ribozymes was achieved by gradually adjusting the ratio of [alpha-S] NTPs relative to unmodified NTPs throughout the evolution process. A total of 75 rounds of continuous evolution were performed, starting with a ligase ribozyme that was previously evolved with the unmodified NTPs. Approximately 20 point mutations and three insertions arose during the course of evolution. An evolved DNA-cleaving group I ribozyme was tested for its ability to catalyze the cleavage of an amide bond. An unactivated amide bond was presented in the context of an oligonucleotide whose 5' portion was complementary to the substrate binding domain of the ribozyme. A 100-fold rate enhancement of amide bond cleavage compared to the incatalyzed reaction was observed.
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 RNA Catalysis Structure Function and Evolution written by Saurja Dasgupta and published by . This book was released on 2018 with total page 357 pages. Available in PDF, EPUB and Kindle. Book excerpt: However, our understanding of the possible mechanisms for the emergence of distinct endonucleolytic ribozyme function during evolution and the ease of access to distinct catalytic motifs involved in RNA cleavage is limited. We have explored the mutational connections between the VS, hairpin and hammerhead ribozymes and delineated plausible pathways by which these distinct ribonuclease motifs can be accessed via intersection of their neutral networks. Intersections between neutral networks are possible due to the existence of bifunctional sequences that exhibit catalytic functions corresponding to both networks. We have identified two such bifunctional sequences that can support hairpin and VS, and hammerhead and hairpin dual functions. Bifunctional sequences present plausible evolutionary nodes toward increasing complexity in functional RNA as illustrated by the hammerhead, hairpin and VS ribozymes in our study. Our results provide a framework to investigate the evolutionary origins of distinct catalytic function in RNA.
Download or read book RNA Catalysis in Pre mRNA Splicing Revealed by Mechanistic Analysis of Exon Ligation written by and published by . This book was released on 2013 with total page 103 pages. Available in PDF, EPUB and Kindle. Book excerpt: In nuclear pre-messenger RNA splicing, introns are excised by the spliceosome, a multi-megadalton machine composed of both proteins and small nuclear RNAs (snRNAs). Following the discovery of self-splicing group II intron RNAs, the snRNAs were hypothesized to catalyze splicing. However, no definitive evidence for a role of either RNA or protein in catalysis by the spliceosome has been reported to date. By using metal ion rescue strategies, here we identify ligands in the yeast U6 snRNA that position divalent metal ions that function during the two steps of splicing. We then demonstrate a biochemical link between those ligands and the divalent metal ion that stabilizes the leaving group during exon ligation, thus showing for the first time that the U6 snRNA catalyzes exon ligation in the spliceosome. Strikingly, all of the U6 catalytic metal ligands we identified correspond to the ligands observed to position catalytic, divalent metal ions in crystal structures of a group II intron RNA. These findings indicate that group II introns and the spliceosome share common catalytic mechanisms, and likely common evolutionary origins. Our results demonstrate that RNA mediates catalysis within the spliceosome.
Download or read book Design and Evolution of Trans Splicing Group I Intron Ribozymes written by Zhaleh N. Amini and published by . This book was released on 2015 with total page 151 pages. Available in PDF, EPUB and Kindle. Book excerpt: Group I introns are catalytic RNAs (ribozymes) capable of catalyzing their self-excision from precursor RNAs through two consecutive transesterification reactions. Although the ribozyme has evolved to perform this cis-splicing reaction in nature, man-made modifications to the 5' end of the ribozyme have allowed it to catalyze a trans-splicing reaction, in which it is able to replace the 3' portion of a substrate RNA with it's own 3' tail. The trans-splicing group I introns used in this thesis were variants of the Tth.L 1925 IC1 group I intron ribozyme found in Tetrahymena thermophila. The work contained in this dissertation aims to both utilize trans-splicing group I introns to further understand principles of RNA evolution, as well as develop and optimize a new trans-splicing variant of the ribozyme for future use in therapy. In the first study of this dissertation, a trans-splicing group I intron was used as a model system to examine the effect of selection pressure and recombination on evolving populations of RNA in a cellular environment. Four parallel evolutions were completed, two employing a low selection pressure, and two employing a high selection pressure. Ribozyme populations with higher efficiency, measured by cellular growth conferred by the ribozyme, resulted from evolutions performed at a low selection pressure. It was found that this increase in fitness was the result of a set of four mutations acting cooperatively. Fitness profiles of evolutionary intermediates revealed that a low selection pressure can increase the accessibility of evolutionary paths leading to the evolution of cooperative mutations. This finding not only adds to the understanding of natural RNA evolution, but also aids in the design of more efficient evolutions of RNA species. In the second study of this dissertation, a new trans-splicing variant of the group I intron was developed, capable of catalyzing the removal of internal sequences from pre-mRNA and joining the two flanking sequences, thereby generating a functional RNA. This group I intron has been termed the `spliceozyme' because its action is analogous to that of the spliceosome. The action performed by the spliceozyme give this system the ability to repair certain types of diseases caused by mis-splicing and therefore, the potential to be used therapeutically. To increase the efficiency and therapeutic potential of this system, the spliceozyme was evolved in E. coli cells, challenging it to more efficiently catalyze the removal of internal sequences. The most efficient variant contained a set of mutations resulting in increased product formation and decreased side product formation. This observed effect was seen in vitro, suggesting that this effect may increase spliceozyme efficiency in a range cell types. Future work will move this system into mammalian cells and optimize the spliceozyme for use in a mammalian system, thus developing it as a therapeutic tool.
Download or read book RNA Catalysis and the Origin of Life written by Thomas Cech and published by . This book was released on 1990 with total page 32 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Handbook of RNA Biochemistry written by Roland K. Hartmann and published by John Wiley & Sons. This book was released on 2015-06-22 with total page 1370 pages. Available in PDF, EPUB and Kindle. Book excerpt: The second edition of a highly acclaimed handbook and ready reference. Unmatched in its breadth and quality, around 100 specialists from all over the world share their up-to-date expertise and experiences, including hundreds of protocols, complete with explanations, and hitherto unpublished troubleshooting hints. They cover all modern techniques for the handling, analysis and modification of RNAs and their complexes with proteins. Throughout, they bear the practising bench scientist in mind, providing quick and reliable access to a plethora of solutions for practical questions of RNA research, ranging from simple to highly complex. This broad scope allows the treatment of specialized methods side by side with basic biochemical techniques, making the book a real treasure trove for every researcher experimenting with 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 In Vivo Selection and in Vivo Evolution of a Trans splicing Ribozyme written by Karen Elizabeth Olson and published by . This book was released on 2012 with total page 199 pages. Available in PDF, EPUB and Kindle. Book excerpt: Group I introns are catalytic RNAs (ribozymes) that are capable of self-splicing out of primary transcripts. Through two consecutive transesterification reactions, the intron is removed and flanking exons are ligated. The group I intron sequence evolved for cis-splicing in nature. However, sequence modifications allow this ribozyme to catalyze a trans-splicing reaction as well. If the 5'-portion of the intron is truncated so that it no longer contains an exon, the ribozyme can then bind in trans at its 5'-end to an RNA substrate, cleave the substrate and replace the 3'-terminal portion of the substrate with its own 3'-exon. When the splice site is upstream of a mutation in a messenger RNA (mRNA) sequence, the transfer of the 3'-exon can replace and repair the downstream portion of the mRNA. Thus, this reaction can be utilized as a type of gene therapy on the mRNA level. Repairing mRNA offers the benefit of maintaining natural gene regulation and the ability to target gain-of-function mutations that gene therapy via gene transfer does not. Although the idea of utilizing a group I intron for gene therapy is not new, to date no gene therapy trials have used this trans-splicing reaction. This is in part due to the low efficiency of the ribozyme under clinically relevant conditions. This thesis represents an effort to increase trans-splicing efficiency of the Tetrahymena thermophila group I intron toward the development of a gene therapy. To find ribozyme variants with increased trans-splicing efficiency an in vivo selection procedure was developed in which the most efficient ribozymes are selected from millions of ribozyme variants. Ribozymes with an improved 5'-terminus were selected from a library with 9 x 106 ribozyme variants. Ribozymes with an improved internal sequence resulted from 21 rounds of evolution, which included mutagenesis and recombination. The in vivo evolution produced a highly efficient repair ribozyme that appears to be recruiting a cellular protein to increase activity. Future experiments that establish an analogous selection strategy in mammalian cells may make it possible to develop trans-splicing ribozymes for treating genetic diseases.
Download or read book Spliceosomal Pre mRNA Splicing written by Klemens J. Hertel and published by Humana. This book was released on 2014-02-21 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing a guide to classical experimental approaches to decipher splicing mechanisms and experimental strategies that rely on novel multi-disciplinary approaches, Spliceosomal Pre-mRNA Splicing: Methods and Protocols describes the theory of alternative pre-mRNA splicing in seven introductory chapters and then introduces protocols and their theoretical background relevant for a variety of experimental research. These protocol chapters cover basic methods to detect splicing events, analyses of alternative pre-mRNA splicing in vitro and in vivo manipulation of splicing events and high-throughput and bioinformatic analyses of alternative splicing. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols and tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, Spliceosomal Pre-mRNA Splicing: Methods and Protocols will aid newcomers and seasoned molecular biologists in understanding the fascinating world of alternative splicing with the ultimate goal of paving the way for many new discoveries to come.
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.