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 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 Small Catalytic RNA written by Joseph Albert Monforte and published by . This book was released on 1991 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Ribozymes and RNA Catalysis written by David M J Lilley and published by Royal Society of Chemistry. This book was released on 2007-11-15 with total page 339 pages. Available in PDF, EPUB and Kindle. Book excerpt: The discovery that RNA could act as a macromolecular catalyst in the cell, signified a paradigm shift in molecular biology. Ribozymes and RNA Catalysis 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. There has been a significant coming together in the field of RNA in recent years and this book offers a compelling review of the whole field to date. Written by leading experts in their field, who in turn review the structural and mechanistic data for all known ribozymes this book is well suited for undergraduates, postgraduates and researchers in catalytic chemistry as well as those in related fields who require a unique overview of the subject.

Download or read book Catalytic RNA written by and published by Academic Press. This book was released on 2013-10-21 with total page 255 pages. Available in PDF, EPUB and Kindle. Book excerpt: This special volume of Progress in Molecular Biology and Translational Science focuses on catalytic RNA. Written by experts in the field, the reviews cover a range of topics, from hammerhead ribozymes to spliceosome catalysis to Varkud satellite and hairpin ribozymes. Contributions from leading authorities Informs and updates on all the latest developments in the field

Download or read book Synthesis and Purification of Small Catalytic RNA s written by Hongzhi Wang and published by . This book was released on 1993 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Small Catalytic RNA written by and published by . This book was released on 1991 with total page 106 pages. Available in PDF, EPUB and Kindle. Book excerpt: We have utilized a combination of photochemical cross-linking techniques and site-directed mutagenesis to obtain secondary and tertiary structure information for the self-cleaving, self-ligating subsequence of RNA from the negative strand of Satellite Tobacco Ringspot Virus. We have found that the helical regions fold about a hinge to promoting four different possible tertiary interactions, creating a molecular of similar shape to a paperclip. A model suggesting that the paperclip'' and hammerhead'' RNAs share a similar three dimensional structure is proposed. We have used a self-cleaving RNA molecule related to a subsequence of plant viroids, a hammerhead, '' to study the length-dependent folding of RNA produced during transcription by RNA polymerase. We have used this method to determine the length of RNA sequestered within elongating E. coli and T7 RNA polymerase complexes. The data show that for E. coli RNA polymerase 12{plus minus}1 nucleotides are sequestered within the ternary complex, which is consistent with the presence of an RNA-DNA hybrid within the transcription bubble, as proposed by others. The result for T7 RNA polymerase differs from E. coli RNA polymerase, with only 10{plus minus}1 nucleotides sequestered within the ternary complex, setting a new upper limit for the minimum RNA-DNA required for a stable elongating complex. Comparisons between E. coli and T7 RNA polymerase are made. The relevance of the results to models or transcription termination, abortive initiation, and initiation to elongation mode transitions are discussed.

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 Structural and Catalytic Roles of Metal Ions in RNA written by Astrid Sigel and published by Walter de Gruyter GmbH & Co KG. This book was released on 2015-07-24 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Influence of Biological Small Molecules on the Twister Ribozyme and Development of Methodologies to Study and Discover Small Ribozymes written by Kyle Messina and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The central dogma of molecular biology describes the distinct roles for the three major biological macromolecules: DNA, RNA and protein. In recent years, it has become increasingly apparent that the roles for DNA, RNA and proteins are more complex and less distinct than previously thought. This is especially true for RNA which has been found to be involved in a plethora of different biological activities. Of particular interest are functional RNAs such as riboswitches, RNA which undergo structural changes upon ligand binding, and ribozymes, RNAs which exhibit catalytic activity. Ribozymes are a relatively recent discovery with the earliest examples identified in the 1980s with the discovery of the self-splicing RNA intron in Tetrahymena thermophila. Since then, a number of ribozymes have been identified among diverse organisms. Ribozymes are divided into two main classes, the large and small ribozymes, with a majority of ribozymes belonging to the small ribozyme class. The small ribozymes are typically 100 nucleotides or fewer in length and catalyze a site-specific phosphodiester cleavage reaction. A total of nine small self-cleaving ribozymes have been identified thus far with nearly half being identified in the last several years. Among the newly identified self-cleaving ribozymes is the twister ribozyme, which has been intensely studied through several structural and mechanistic studies to elucidate its catalytic mechanism. The twister ribozyme is one of the most catalytically active self-cleaving ribozymes as it is purported to use multiple catalytic strategies. The twister ribozyme is hypothesized to utilize two ionizable residues, with pKas of 6.9 and 9.5, thought to be a general acid and general base. The higher pKa of 9.5 has been attributed to a guanine, which is hypothesized to serve as both a general base and electrostatically stabilize the phosphorane intermediate. The lower pKa of 6.9 has been attributed to the conserved A1 which is purported to act as a general acid. While crystallographic evidence supports the role of A1 as a general acid, the available experimental evidence is mixed with no clear answer. As such, one goal of this thesis is to further define the catalytic mechanism of the twister ribozyme. The other goal of this thesis is to develop new methodologies to investigate the structure and biological activity of small self-cleaving ribozymes.Chapter 2 is focused on characterizing and establishing the mechanism by which small biological molecules stimulate the self-cleavage activity of the twister ribozyme. We find that moderate buffer concentrations can stimulate the catalytic activity of the twister ribozyme up to 5-fold. The buffers are a range of small molecules including common laboratory buffers, and biological metabolites such as imidazole, amino acids, and amino sugars. Additionally, Brnsted plot analysis indicates that the small molecules assist in proton transfer, most likely general acid catalysis. Further, we observe that at biological Mg2+ concentrations and low pH, the self-cleavage activity of the twister ribozyme appears largely buffer independent while at biological Mg2+ concentrations and pH or at high Mg2+ concentrations, the self-cleavage activity of the twister ribozyme is buffer dependent. As such, we propose a multi-channel mechanism for the twister ribozyme consisting of a buffer independent and buffer dependent channels. This work establishes a simple way to overcome the limited chemical diversity of RNA and could apply to the catalytic mechanisms of many ribozymes in vivo.Chapter 3 is aimed at characterizing the role that the A1 residue plays in the catalytic mechanism of the twister ribozyme through a combination of chemical rescue and glycosidic conformational analysis experiments. We observe that inhibited twister ribozyme constructs containing an A1 N3 deaza or abasic A1 modification can be rescued over 100-fold using small protonatable molecules such as imidazole and histidine, similar to the chemical rescue effects observed in the antigenomic HDV ribozyme with a C76U mutation. Additionally, Brnsted plot analysis indicates that the small molecules rescue catalytic activity through proton transfer, suggesting that the wild type A1 residue is also involved in proton transfer, likely general acid catalysis. We also determine through glycosidic conformational analysis that an 8BrA1 modified twister ribozyme is up to 10-fold faster than a non-modified A1 residue in an appropriate background suggesting that the catalytic conformation is syn as suggested by multiple crystallographic studies. This study provides functional evidence that A1 is syn while conducting proton transfer.The goal of Chapter 4 is to develop a novel computational and experimental pipeline to identify and assay the in vitro catalytic activity of putative ribozymes en masse. To do this, we developed a computational pipeline, based on RNABOB, to identify ribozyme candidates of known ribozyme motifs with variant secondary structures. Four RNABOB descriptors were written based on the type III hammerhead ribozyme, the human HDV-like CPEB3 ribozyme and the type P1 twister ribozyme, both with and without the P3 stem, with loosened constraints identified nearly 23,500 ribozyme candidates among 18 different organisms. Additionally, we optimized an experimental pipeline to assay thousands of ribozymes at a time for in vitro catalytic activity by taking advantage of massively parallel oligo synthesis (MPOS) to produce the DNA templates. Currently, we have optimized a majority of the experimental pipeline and successfully identified all active ribozymes in a sample set of oligos.The goal of Chapter 5 is to develop a scaffold to artificially increase the size of small nucleic acid structures to a size that is amenable for cryo-EM visualization and single particle reconstruction. Thus far, we have developed a nucleic acid-based scaffold, dubbed a Nanosprout Scaffold, that can multimerize small nucleic acids into a larger structure of an appropriate size for cryo-EM visualization. The Nanosprout Scaffold consists of a DNA oligonucleotide, denoted DNA guide, that multiple nucleic acids of interest with 5-extensions can multimerize to via complementary base pairing interactions. So far, we have designed multiple Nanosprout Constructs based on the env22 twister ribozyme, and the 10MD5/10MD5-AC DNAzymes with moderate success. We observe, in aqueous conditions, that Nanosprout Constructs assemble with moderate to high affinity and with catalytic activity approaching, or on par, with the native constructs. Additionally, we are able to visualize individual env22 twister ribozymes via TEM and cryo-EM, albeit several issues persist as the fully multimerized env22 Nanosprout Constructs either partially disassemble or do not form under these conditions. The Nanosprout Scaffold is a promising start to a scaffold system that can be adapted to small nucleic acids for cryo-EM structure determination.

Download or read book Hepatitis Delta Virus written by John L. Casey and published by Springer Science & Business Media. This book was released on 2006-09-02 with total page 231 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hepatitis delta virus (HDV), which causes severe acute and chronic liver disease, was discovered nearly 30 years ago following the detection of a novel antigen-antibody system in hepatitis B virus carriers. HDV has continued to surprise and fascinate medical science ever since. This volume reviews recent developments in HDV research, from molecular virology to genetics to experimental investigation of new therapeutic and vaccine candidates.

Download or read book Structural and Catalytic Roles of Metal Ions in RNA written by Astrid Sigel and published by Royal Society of Chemistry. This book was released on 2011 with total page 425 pages. Available in PDF, EPUB and Kindle. Book excerpt: The discovery of ribozymes triggered a huge interest in the chemistry and biology of RNAs. Much of the recently made progress focusing on metal ions is addressed in Volume 9. This book, written by 28 internationally recognized experts, provides a most up-to-date view and it 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 metal ion-binding motives, 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 ribosome, ribozymes and redox cofactors, as well as the binding of kinetically inert metal ions to RNA are also considered.

Download or read book Catalytic RNA written by Fritz Eckstein and published by Springer. This book was released on 1997-04-09 with total page 418 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 Therapeutic Applications of Ribozymes written by Kevin J. Scanlon and published by Springer Science & Business Media. This book was released on 1998-06-23 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Therapeutic Applications of Ribozymes, expert laboratory scientists describe in detail their methodologies for constructing ribozymes designed to elucidate the role of specific genes as key routes to the development of novel therapies for a wide variety of diseases. The authors review the many sites targeted with ribozymes in various diseases and provide specific accounts of the practical techniques required for the proper use of ribozymes in these systems. Their cutting-edge protocols demonstrate how to achieve ribozyme expression in distinct cellular systems, the preparation and use of high-efficiency ribozyme DNA or RNA delivery, and the studies required to prove the efficacy of ribozyme-mediated inhibition, with its concomitant effect on phenotypic parameters. Therapeutic Applications of Ribozymes contains all the practical detail necessary to realize the high promise of ribozyme technology as a significant, widely used methodology. Focused on ribozyme targets and the novel associated technology, the book immediately becomes the leading resource for all those seeking to transform this new category of therapeutic agent into efficacious clinical practice.

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 Catalysis of Organic Reactions written by Frank E. Herkes and published by CRC Press. This book was released on 1998-08-21 with total page 676 pages. Available in PDF, EPUB and Kindle. Book excerpt: Documents up-to-date developments in the study of catalysis and its applications to organic synthesis and industrial processes. The text examines the area of homogenous and heterogenous catalysis for industrial and pharmaceutical chemicals, focusing on recent advances in asymmetric synthesis, environmental uses, acid-based synthesis, hydrogenation, oxidation, alkylation, isomerization, amination, hydroformlyation, and more.

Download or read book Combinatorial Chemistry in Biology written by Michael Famulok and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 199 pages. Available in PDF, EPUB and Kindle. Book excerpt: The essence of combinatorial chemistry or techniques involving "molecular diversity" is to generate enormous populations of molecules and to exploit appropriate screening techniques to isolate active components contained in these libraries. This idea has been the focus of research both in academia and in the pharmaceutical or biotechnology industry. Its developments go hand in hand with an exploding number of potential drug targets emerging from genomics and proteomics research. When the editors of Current Topics in Microbiology and Immunology encouraged us to assemble the present volume on Combinatorial Chemistry in Biology, we immediately felt that this might prove quite beneficial for the audience of this series. The field of combinatorial chemistry extends over a broad range of disciplines, from synthetic organic chemistry to biochemistry, from material sciences to cell biology. Each of these fields may have its own view on this topic, something which is reflected in a growing number of monographs and "special editions" of jour nals devoted to this issue or aspects thereof. The title of the present volume of Springer-Verlag's series suggests that it also has its own special focus. And, generally speaking, this is not wrong: we would even claim the special focus of this volume is on the immunologically relevant aspects of combinatorial chemistry.