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.

This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers computational prediction RNA structure and dynamics, including such topics as computational modeling of RNA secondary and tertiary structures, riboswitch dynamics, and ion-RNA, ligand-RNA and DNA-RNA interactions. - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers computational methods and applications in RNA structure and dynamics - Contains chapters with emerging topics such as RNA structure prediction, riboswitch dynamics and thermodynamics, and effects of ions and ligands.

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.

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.

Synthetic biology encompasses a variety of different approaches, methodologies and disciplines, and many different definitions exist. This Volume of Methods in Enzymology has been split into 2 Parts and covers topics such as Measuring and Engineering Central Dogma Processes, Mathematical and Computational Methods and Next-Generation DNA Assembly and Manipulation. - Encompasses a variety of different approaches, methodologies and disciplines - Split into 2 parts and covers topics such as measuring and engineering central dogma processes, mathematical and computational methods and next-generation DNA assembly and manipulation

Unites a biological and a biotechnological perspective on cyanobacteria, and includes the industrial aspects and applications of cyanobacteria Cyanobacteria Biotechnology offers a guide to the interesting and useful features of cyanobacteria metabolism that keeps true to a biotechnology vision. In one volume the book brings together both biology and biotechnology to illuminate the core acpects and principles of cyanobacteria metabolism. Designed to offer a practical approach to the metabolic engineering of cyanobacteria, the book contains relevant examples of how this metabolic "module" is currently being engineered and how it could be engineered in the future. The author includes information on the requirements and real-world experiences of the industrial applications of cyanobacteria. This important book: Brings together biology and biotechnology in order to gain insight into the industrial relevant topic of cyanobacteria Introduces the key aspects of the metabolism of cyanobacteria Presents a grounded, practical approach to the metabolic engineering of cyanobacteria Offers an analysis of the requirements and experiences for industrial cyanobacteria Provides a framework for readers to design their own processes Written for biotechnologists, microbiologists, biologists, biochemists, Cyanobacteria Biotechnology provides a systematic and clear volume that brings together the biological and biotechnological perspective on cyanobacteria.

This handbook is an interdisciplinary and comprehensive reference covering all aspects of cell biosensors. It is divided into four main sections which are led and organized by numerous international experts. The scope of coverage includes: Fundamentals and genetics for biosensor applications Transducers, Materials and Systems Markets, innovation and education Application of biosensors in business Biosensor research is an exciting hybrid world where biologists, chemists, physicists, engineers and computer engineers come together. This handbook will serve as an invaluable living resource for all researchers in academia and industry working with cell biosensors.

Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.

This book addresses the design of emerging conceptual tools, technologies and systems including novel synthetic parts, devices, circuits, oscillators, biological gates, and small regulatory RNAs (riboregulators and riboswitches), which serve as versatile control elements for regulating gene expression. Synthetic biology, a rapidly growing field that involves the application of engineering principles in biology, is now being used to develop novel systems for a wide range of applications including diagnostics, cell reprogramming, therapeutics, enzymes, vaccines, biomaterials, biofuels, fine chemicals and many more. The book subsequently summarizes recent developments in technologies for assembling synthetic genomes, minimal genomes, synthetic biology toolboxes, CRISPR-Cas systems, cell-free protein synthesis systems and microfluidics. Accordingly, it offers a valuable resource not only for beginners in synthetic biology, but also for researchers, students, scientists, clinicians, stakeholders and policymakers interested in the potential held by synthetic biology.

This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in riboswitches as targets and tools and contains sections on such topics as constructing and optimizing artificial riboswitches, live cell imaging and intracellular sensors with artificial riboswitches, conditional control of gene expression with artificial riboswitches, using artificial riboswitches for protein evolution and pathway optimization, and anti-riboswitch drug screens. - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers research methods in riboswitches as targets and tools - Contains sections on such topics as constructing and optimizing artificial riboswitches, synthetic biology: live cell imaging and intracellular sensors with artificial riboswitches, synthetic biology: conditional control of gene expression with artificial riboswitches, synthetic biology: using artificial riboswitches for protein evolution and pathway optimization, anti-riboswitches drug screens