Download or read book Applications of an Expanded Genetic Code written by Eric M. Brustad and published by ProQuest. This book was released on 2008 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt: With an ever expanding genetic code it is no longer a question of whether an unnatural amino acid can be introduced into a protein sequence, but what can be done with them. This thesis describes the introduction of novel amino acids to the genetic codes of E. coli and yeast and the applications of those amino acids towards novel protein biochemistry and the study of biomolecular structure and function. This includes the development of orthogonal protein labeling strategies that allow the site-specific attachment of biophysical probes and other molecules onto a protein surface. An unnatural ketone containing amino acid is described that allows the general and efficient introduction of fluorophores and spin probes onto a protein surface. This chemistry is exploited for the site-specific double labeling of proteins with fluorophores and the utility of this methodology is demonstrated by the examination of bacteriophage T4 lysozyme folding via single molecule fluorescence energy transfer. To expand the orthogonal chemistry presented by unnatural amino acid mutagenesis, the addition of a boronic acid containing amino acid to the genetic code of E. coli is also described. The unique chemistry of this functionality is exploited for the site-specific labeling of proteins with fluorophores through Suzuki coupling reactions as well as the formation boronic esters with diol containing compounds. This latter chemistry is also useful for the genetic encoding of carbohydrate recognition into a protein sequence as well as the development of a single step scarless protein purification methodology. The evolution of the E. coli leucyl tRNA synthetase for the site-selective introduction of methionine, cysteine and alanine analogs into proteins in yeast is also described. From this work, a single tRNA synthetase that shows promiscuous activity for over ten unnatural amino acid structures is investigated. Finally, a project investigating the role and source of reactive oxygen species in cytokine signaling is also be briefly discussed.
Download or read book Non Natural Amino Acids written by and published by Academic Press. This book was released on 2009-07-24 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: By combining the tools of organic chemistry with those of physical biochemistry and cell biology, Non-Natural Amino Acids aims to provide fundamental insights into how proteins work within the context of complex biological systems of biomedical interest. The critically acclaimed laboratory standard for 40 years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. With more than 400 volumes published, each Methods in Enzymology volume presents material that is relevant in today's labs -- truly an essential publication for researchers in all fields of life sciences. - Demonstrates how the tools and principles of chemistry combined with the molecules and processes of living cells can be combined to create molecules with new properties and functions found neither in nature nor in the test tube - Presents new insights into the molecular mechanisms of complex biological and chemical systems that can be gained by studying the structure and function of non-natural molecules - Provides a "one-stop shop" for tried and tested essential techniques, eliminating the need to wade through untested or unreliable methods
Download or read book Expansion of the Genetic Code Unnatural Amino Acids and Their Applications written by Subhendu Sekhar Bag and published by Frontiers Media SA. This book was released on 2022-08-26 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Engineering the Genetic Code written by Nediljko Budisa and published by John Wiley & Sons. This book was released on 2006-05-12 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ability to introduce non-canonical amino acids in vivo has greatly expanded the repertoire of accessible proteins for basic research and biotechnological application. Here, the different methods and strategies to incorporate new or modified amino acids are explained in detail, including a lot of practical advice for first-time users of this powerful technique. Novel applications in protein biochemistry, genomics, biotechnology and biomedicine made possible by the expansion of the genetic code are discussed and numerous examples are given. Essential reading for all molecular life scientists who want to stay ahead in their research.
Download or read book Directed Evolution of and with Expanded Genetic Codes written by Chang C. Liu and published by . This book was released on 2009 with total page 438 pages. Available in PDF, EPUB and Kindle. Book excerpt: By expanding the genetic code to allow the cotranslational incorporation of unnatural amino acids, one can site-specifically introduce unique chemical functionality into proteins in vivo. By using such expanded genetic codes in directed evolution, one can impose selection for novel protein function wherein variants containing unnatural amino acids will be selected should the unnatural amino acids confer a functional advantage. I first describe the expansion of E. coli 's genetic code for the site-specific incorporation of the unnatural amino acid sulfotyrosine and the subsequent use of this expanded genetic code for the expression and study of several proteins including sulfo-hirudin and sulfated anti-HIV antibodies. I then describe the development of a phage-based system for evolution with expanded genetic codes and the application of this system for directed evolution, through which proteins that use unnatural amino acids for enhanced function can emerge from selection. This work demonstrates the value of genetically encoding more than the 20 natural amino acids for protein engineering applications and shows that these expanded genetic codes can confer a selective advantage.
Download or read book Synthetic DNA and RNA Programming written by Patrick O’Donoghue and published by MDPI. This book was released on 2019-11-19 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dear Colleagues, Synthetic biology is a broad and emerging discipline that capitalizes on recent advances in molecular biology, genetics, protein and RNA engineering and omics technologies. These technologies have transformed our ability to reveal the biology of the cell and the molecular basis of disease. This Special Issue on “Synthetic RNA and DNA Programming” features original research articles and reviews, highlighting novel aspects of basic molecular biology and the molecular mechanisms of disease that were uncovered by the application and development of novel synthetic biology-driven approaches.
Download or read book Advances in Synthetic Biology written by Vijai Singh and published by Springer Nature. This book was released on 2020-04-13 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Genetically Incorporated Non Canonical Amino Acids written by Yu-Hsuan Tsai and published by Springer Nature. This book was released on 2023-06-05 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume explores non-canonical amino acids (ncAAs) through their site-specific incorporation by genetic code expansion (GCE). The collection provides a broad resource of methods for implementing GCE in E. coli, mammalian cells, and animals, highlighting specific applications ranging from fluorescence labeling to photocontrol and the study of protein post-translational modification. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Genetically Incorporated Non-Canonical Amino Acids: Methods and Protocols serves as an ideal source of methodologies that can be adapted and extended, migrated to different model systems, and combined in new ways to help explore a wide range of biological questions and to augment industrial and pharmaceutical protein engineering.
Download or read book Genetic Code Expansion in Biochemical Investigations and Biomedical Applications written by Nanxi Wang and published by . This book was released on 2017 with total page 165 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetic code expansion provides a powerful tool for site-specific incorporation of unnatural amino acids (unAAs) with novel biochemical and physiological properties into proteins in live cells and organisms. To achieve this, a nonsense codon suppression system, which consists of an orthogonal aminoacyl-tRNA synthetase (aaRS) and tRNA pair that specifically decodes a nonsense codon (e.g., amber codon and quadruplet codon) with an unAA but do not "cross talk" with their endogenous counterparts, was established. This Ph.D. thesis presents our efforts on evolution and application of nonsense codon suppression systems for biochemical and biomedical investigations.
Download or read book Molecular Biology of the Cell written by 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 Evolution of the Genetic Code written by Shōzō Ōsawa and published by . This book was released on 1995 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: The genetic code was deciphered experimentally around 1966 and for a number of years scientists considered it to be "universal" for all forms of life. In 1981 researchers shocked the scientific community with the discovery that the code differed in mitochondria and certain other organisms, evidence that the genetic code was still evolving. This book discusses the distribution and origin of the non-universal codes and examines the possible mechanisms of code changes, making it essential reading for all those interested in evolutionary genetics.
Download or read book Noncanonical Amino Acids written by Edward A. Lemke and published by . This book was released on 2018 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book In Vitro Genetic Code Expansion and Selected Applications written by Emil S. Iqbal and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The ability of incorporation non-canonical amino acids (ncAAs) using translation offers researchers the ability of extend the functionality of proteins and peptides for many applications including synthetic biology, biophysical and structural studies, and discovery of novel ligands. Here we describe the three projects where the addition of ncAAs to in vitro translation systems creates useful chemical biology techniques. In the first, a fluorinated histidine derivative is used to create a novel affinity tag that allows for the selective purification of peptides from a complex mixture of proteins. In the second, the high promiscuity of an editing-deficient valine-tRNA synthetase (ValRS T222P) is used to demonstrate ribosomal translation of 13 ncAAs including those with novel side chains [alpha], [alpha] disubstitutions, and cyclic[beta]amino acids. Lastly, a couple of these amino acids are integrated into the powerful ligand discovery tool of mRNA display for the discovery of helical peptide ligands.
Download or read book Enabling Evolution with Expanded Genetic Codes written by Drew Scott Tack and published by . This book was released on 2016 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: The natural genetic code is largely shared amongst all terrestrial life, though variations do exist that provide evidence of genetic code evolution. The field of synthetic biology has developed methods to augment and modify the genetic code, by reassigning codons and genetically incorporating noncanonical amino acids (NCAAs). Most commonly, amino-acyl tRNA synthetases and their cognate tRNAs are engineered to recognize (NCAAs), the tRNA charged with an NCAA is then used during translation to decode the amber stop codon. Using this method, over 200 unique NCAAs have been added to the genetic code, allowing for the site-specific incorporation of useful chemistries, including covalent bond formation and fluorescence. NCAAs have been implemented in biological research and protein engineering. The second chapter of this dissertation explores the biophysical parameters that allow efficient crosslinking with a NCAA. We investigated several environmental factors which could impact crosslinking between two interacting proteins. We define a set of parameters that permit efficient crosslinking. Noncanonical amino acids are a potentially powerful tool in understanding genetic code evolution. Evolutionary experiments using NCAAs have already been used to explore proposed theories on codon evolution, including codon capture and ambiguous intermediate theories. Though several studies have explored the implications of NCAAs in evolution, significant obstacles have prevented the long-term evolution of wild-type organisms with expanded genetic codes. In chapter three of this dissertation we demonstrate that a single essential enzyme can be engineered to be structurally dependent on a genetically encoded NCAA. This confers a functional addiction to the NCAA and the addiction can be transferred to new bacterial hosts using a DNA plasmid. Chapter four expands on this idea, attempting to use the chemistries bestowed by the NCAA for active site chemistry. Finally, in chapter five we demonstrate that a protein-conferred cellular NCAA addiction is sufficient for the long-term evolution of bacteria with a recoded amber codon. We investigated the genetic and phenotypic impact of evolution with an expanded genetic code.
Download or read book Protein Engineering written by Huimin Zhao and published by John Wiley & Sons. This book was released on 2021-08-23 with total page 41 pages. Available in PDF, EPUB and Kindle. Book excerpt: A one-stop reference that reviews protein design strategies to applications in industrial and medical biotechnology Protein Engineering: Tools and Applications is a comprehensive resource that offers a systematic and comprehensive review of the most recent advances in the field, and contains detailed information on the methodologies and strategies behind these approaches. The authors—noted experts on the topic—explore the distinctive advantages and disadvantages of the presented methodologies and strategies in a targeted and focused manner that allows for the adaptation and implementation of the strategies for new applications. The book contains information on the directed evolution, rational design, and semi-rational design of proteins and offers a review of the most recent applications in industrial and medical biotechnology. This important book: Covers technologies and methodologies used in protein engineering Includes the strategies behind the approaches, designed to help with the adaptation and implementation of these strategies for new applications Offers a comprehensive and thorough treatment of protein engineering from primary strategies to applications in industrial and medical biotechnology Presents cutting edge advances in the continuously evolving field of protein engineering Written for students and professionals of bioengineering, biotechnology, biochemistry, Protein Engineering: Tools and Applications offers an essential resource to the design strategies in protein engineering and reviews recent applications.
Download or read book The Origin and Evolution of the Genetic Code 100th Anniversary Year of the Birth of Francis Crick written by Koji Tamura and published by MDPI. This book was released on 2018-03-23 with total page 203 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a printed edition of the Special Issue "The Origin and Evolution of the Genetic Code: 100th Anniversary Year of the Birth of Francis Crick" that was published in 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.
