Author: Andreas Werner
Publisher:
ISBN:
Category :
Languages : en
Pages : 211
Get Book Here
Book Description
The research in this Ph.D. thesis is part of an ongoing effort to improve our understanding of RNA structure and stability: In the first part, an RNA aptamer is studied in complex with its target, the Sec7 domain of intracellular protein cytohesin-1. Aptamers are in vitro selected RNA molecules that have an affinity rivaling that of monoclonal antibodies, possess interesting pharmacological properties and are a powerful tool for functional analysis in vivo. We also present a systematic structural investigation of how aptamers and their natural counterparts bind their ligands in order to delineate common principles. In the second part, we study the counterion-induced collapse of prokaryotic RNase P RNAs by UV melting, with the goal of optimizing secondary and tertiary structure for crystallization. We demonstrate the utility of this method in two test cases: First, thermodynamic parameters are extracted from the kissing complex, a typical tertiary interaction found in many RNAs. This leads to the discovery that the ionic strength dependence may give clues about the structural transitions observed. Second, we study the effect of mutations on a more complex RNA, the IRES site of hepatitis C virus, and correlate UV melting data to a dynamic equilibrium between alternative structures. The lessons learned from these experiments are then applied to RNase P to disrupt specific tertiary interactions to facilitate crystallization. The effect of these mutations is investigated using both UV melting and a novel, fluorescence-based approach. Finally, crystallization screens are constructed using methods of experimental design, and a new approach for crystallization in gels is developed.
Author: D. S. Eggleston
Publisher: Elsevier
ISBN: 0080542557
Category : Science
Languages : en
Pages : 261
Get Book Here
Book Description
The Many Faces of RNA is the subject for the eighth SmithKline Beecham Pharmaceuticals Research Symposia. It highlights a rapidly developing area of scientific investigation. The style and format are deliberately designed to promote in-depth presentations and discussions and to facilitate the forging of collaborations between academic and industrial partners.This symposium focuses on several of the many fundamental, advancing strategies for exploring RNA and its functions. It emphasizes the interplay between biology, chemistry, genomics, and molecular biology which is leading to exciting new insights and avenues of investigation. The book explores RNA as a therapeutic target, RNA as a tool, RNA and its interactions, along with chemical, computational, and structural investigations.
Author: Jan Barciszewski
Publisher: Springer Science & Business Media
ISBN: 9401144850
Category : Science
Languages : en
Pages : 373
Get Book Here
Book Description
RNA Biochemistry and Biotechnology describes various aspects of nucleic acid and protein structure, mainly RNA structure and proteins, interacting with specific RNA species. Papers deal with DNA protein interactions, telomerase, aminoacyl-tRNA synthetases, elongation factor Tu, DNA repair, RNA structure, NMR technology, RNA aptamer interaction of biological macromolecules with metal ions. Two papers deal with theoretical aspects of RNA structure production and computer modelling. Many papers describe the possibility of commercial application of RNA biotechnology. One article discusses the impact of direct democracy on basic science supporting biotechnology. Readership: Advanced graduate students, Ph.D. students and young scientists as well as specialists in the field.
Author: Daniel Herschlag
Publisher: Academic Press
ISBN: 0123809231
Category : Science
Languages : en
Pages : 567
Get Book Here
Book Description
This MIE volume provides laboratory techniques that aim to predict the structure of a protein which can have tremendous implications ranging from drug design, to cellular pathways and their dynamics, to viral entry into cells. - Expert researchers introduce the most advanced technologies and techniques in protein structure and folding - Includes techniques on tiling assays
Author: Daniel Herschlag
Publisher: Academic Press
ISBN: 0080922139
Category : Science
Languages : en
Pages : 491
Get Book Here
Book Description
This MIE volume provides laboratory techniques that aim to predict the structure of a protein which can have tremendous implications ranging from drug design, to cellular pathways and their dynamics, to viral entry into cells. - Expert researchers introduce the most advanced technologies and techniques in protein structure and folding - Includes techniques on tiling assays
Author: Hsin-Yue Tsai
Publisher:
ISBN:
Category : RNA-protein interactions
Languages : en
Pages : 123
Get Book Here
Book Description
Abstract: Ribonuclease P (RNase P) catalyzes the 5' maturation of tRNAs in all three domains of life and functions as a Mg2+-dependent ribonucleoprotein (RNP) complex. It is composed of one RNA subunit, essential for catalysis, and a varying number of protein cofactors depending on the source. We have now used bacterial and archaeal RNase P to understand how proteins aid RNA catalysis. Bacterial RNase P is composed of one catalytic RNA subunit and one protein cofactor, which is known to facilitate substrate binding and RNA catalysis. Although molecular modeling led to tertiary structure models of the RNA subunits, that were subsequently shown to be correct, and high-resolution studies established the structure of the protein subunit from bacterial RNase P, RNA-protein interactions in the holoenzyme were not established. Here, we have used a hydroxyl radical-mediated footprinting approach to generate this information which, together with results from other biochemical/biophysical studies, have furnished distance constraints for building three-dimensional models of the bacterial RNase P holoenzyme in the absence or presence of its precursor tRNA substrate. The model reveals how the protein subunit facilitates RNA catalysis by directly interacting with both the ptRNA substrate and the catalytic core of the RNA subunit. Unlike bacterial RNase P, both archaeal and eukaryal RNase P contain multiple protein subunits, whose roles are unclear largely due to the failure to reconstitute archaeal/eukaryal RNase P in vitro. Using recombinant subunits, we have now reconstituted functional RNase P from Pyroccocus furiosus, a thermophilic archaeon, and gained insights regarding its assembly pathway(s) and the contribution of its different protein subunits to RNA catalysis. The Pfu RNase P RNA is capable of multiple turnover catalysis with either of two pairs of protein subunits and becomes significantly more active, at lower magnesium concentrations, with addition of the remaining protein pair. These data support a central tenet of the RNA world hypothesis that the evolution of RNA enzymes to RNP complexes involved gradual recruitment of proteins to enhance biological function. Collectively, these two studies highlight the common strategies employed by protein cofactors to enhance RNA catalysis (i.e., enhanced substrate binding and improved affinity for Mg2+).
Author: Brian Charles Thomas
Publisher:
ISBN:
Category :
Languages : en
Pages : 284
Get Book Here
Book Description
Author: Sven Klussmann
Publisher: John Wiley & Sons
ISBN: 3527607919
Category : Science
Languages : en
Pages : 518
Get Book Here
Book Description
In The Aptamer Handbook, leading scientists from academia as well as biotech and pharma companies introduce the revolutionary concept of designing RNA and DNA oligonucleotides with novel functions by in vitro selection. These functions comprise high affinity binding (aptamers), catalytic activity (ribozymes and deoxyribozymes) or combinations of binding and catalytic properties (aptazymes). Basic concepts and technologies describing in detail how these functional oligonucleotides can be identified are presented. Numerous examples demonstrate the versatility of in vitro selected oligonucleotides. Special emphasis has been put on a section that shows the broad applicability of aptamers, e. g. in target validation, for analytics, or as new therapeutics. This first overview in the field is of prime interest for a broad audience of scientists both in academia and in industry who wish to expand their knowledge on the potential of new oligonucleotide functions and their applications.
Author: Atsushi Ogawa
Publisher: Humana
ISBN: 9781493963300
Category : Science
Languages : en
Pages : 0
Get Book Here
Book Description
Artificial riboswitches and other ligand-responsive gene regulators make it possible to switch protein synthesis ON or OFF with arbitrary ligand molecules. Artificial Riboswitches: Methods and Protocols focuses on the state-of-the-art methods developed in recent years for creating artificial riboswitches, therefore this volume could be regarded as a collection of recipes for the gene circuit elements in synthetic biology and metabolic engineering. Chapters cover topics such as screening or rational design methods for obtaining artificial riboswitches that function in either bacterial or eukaryotic translational systems, protocols for evaluating the activities of the resultant riboswitches, as well as protocols for construction of ligand-dependent, trans-acting gene regulators. Written in the 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 notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Artificial Riboswitches: Methods and Protocols seeks to serve not only bioengineers who aim to reprogram cell behaviors and molecular biologists who leverage these regulators for genetic studies, but to all researchers interested in this fascinating field.
Author: Bin Wang
Publisher: CRC Press
ISBN: 9814411647
Category : Medical
Languages : en
Pages : 468
Get Book Here
Book Description
In the past few decades there has been incredible growth in "bionano"-related research, which has been accompanied by numerous publications in this field. Although various compilations address topics related to deoxyribonucleic acid (DNA) and protein, there are few books that focus on determining the structure of ribonucleic acid (RNA) and using RNA as building blocks to construct nanoarchitectures for biomedical and healthcare applications. RNA Nanotechnology is a comprehensive volume that details both the traditional approaches and the latest developments in the field of RNA-related technology. This book targets a wide audience: a broad introduction provides a solid academic background for students, researchers, and scientists who are unfamiliar with the subject, while the in-depth descriptions and discussions are useful for advanced professionals. The book opens with reviews on the basic aspects of RNA biology, computational approaches for predicting RNA structures, and traditional and emerging experimental approaches for probing RNA structures. This section is followed by explorations of the latest research and discoveries in RNA nanotechnology, including the design and construction of RNA-based nanostructures. The final segment of the book includes descriptions and discussions of the potential biological and therapeutic applications of small RNA molecules, such as small/short interfering RNAs (siRNAs), microRNAs (miRNAs), RNA aptamers, and ribozymes.
