Download or read book Expanding the Genetic Code of Escherichia Coli written by Lei Wang and published by . This book was released on 2002 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Pathway Engineering of the Expanding Genetic Code written by John Christopher Anderson and published by . This book was released on 2003 with total page 546 pages. Available in PDF, EPUB and Kindle. Book excerpt: Several projects focused on expanding the genetic code of Escherichia coli to include amino acids beyond the common twenty are described. These include the identification of extended codons, orthogonal pairs, and the engineering of amino acid metabolic pathways in E. coli . To incorporate multiple unnatural amino acids at distinct sites in a polypeptide, multiple noncoding codons are required. To this end efficiently-suppressed 4- and 5-base codons were identified using a selection strategy. To make use of these extended codons, three orthogonal aminoacyl-tRNA synthetase/suppressor tRNA pairs were engineered from archaebacteria. These systems do not cross-react with their E. coli homologs, but efficiently suppress UAG, AGGA, or UGA codons. Using a combination of saturation mutagenesis and genetic selection, several variants of the Pyrococcus horikoshii lysyl-tRNA synthetase were identified that permit the genetic encoding of homoglutamine in response to the codon AGGA in E. coli . In addition to adding new components to the translational machinery of E. coli , we have also added a biosynthetic pathways for p-aminophenylalanine providing the first example of an autonomous 21-amino acid organism that can biosynthesize an unnatural amino acid and incorporate it into protein with no media supplement. Finally, in an effort to incorporate [alpha]-hydroxy acids genetically into proteins we have identified strains deficient in their biotransformation to [alpha]-amino acids in E. coli . In combination with extended codons and orthogonal pairs, these strains set the stage for the evolution of a system that genetically encodes polyesters. The work described here not only allows us to generate proteins and possibly entire organisms with novel properties not restricted by the common twenty amino acids, it also provides an opportunity to explore basic mechanisms of translation.

Download or read book Expanding the Genetic Code of E Coli to Include the 22nd Genetically Encoded Amino Acid written by Edward Chang and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

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 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 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 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 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 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 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 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 Engineering the Genetic Code of Escherichia Coli with Methionine Analogues and Bioorthogonal Amino Acids for Protein Immobilization written by Alessandro De Simone and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Recoding Expansion of Decoding Rules Enriches Gene Expression written by John F. Atkins and published by Springer Science & Business Media. This book was released on 2010-03-10 with total page 473 pages. Available in PDF, EPUB and Kindle. Book excerpt: The literature on recoding is scattered, so this superb book ?lls a need by prov- ing up-to-date, comprehensive, authoritative reviews of the many kinds of recoding phenomena. Between 1961 and 1966 my colleagues and I deciphered the genetic code in Escherichia coli and showed that the genetic code is the same in E. coli, Xenopus laevis, and guinea pig tissues. These results showed that the code has been c- served during evolution and strongly suggested that the code appeared very early during biological evolution, that all forms of life on earth descended from a c- mon ancestor, and thus that all forms of life on this planet are related to one another. The problem of biological time was solved by encoding information in DNA and retrieving the information for each new generation, for it is easier to make a new organism than it is to repair an aging, malfunctioning one. Subsequently, small modi?cations of the standard genetic code were found in certain organisms and in mitochondria. Mitochondrial DNA only encodes about 10–13 proteins, so some modi?cations of the genetic code are tolerated that pr- ably would be lethal if applied to the thousands of kinds of proteins encoded by genomic DNA.

Download or read book Adding Unnatural Amino Acids to the Genetic Repertoire written by Jianming Xie and published by . This book was released on 2006 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis focuses on expanding the genetic code of E. coli to include unnatural amino acids beyond the common 20. By means of an orthogonal pair of amber suppressor tRNA[Special characters omitted.] /tyrosyl-tRNA synthetase (TyrRS) imported from an archaea M. jannaschii, several novel amino acids were site-specifically incorporated into proteins in response to an amber codon in E. coli, with high fidelity and efficiency. Typically, large libraries of M. jannaschii TyrRS (Mj TyrRS) mutants were first generated by randomizing 6 residues in the amino acid binding pocket. The libraries were then subjected to alternating positive and negative selections, which may afford synthetase variants that could charge the cognate tRNA[Special characters omitted.] with the unnatural amino acid but not any of the 20 natural amino acids. In one project, a heavy-atom-containing amino acid, p -iodo-L-phenylalanine, was site-specifically incorporated into proteins. The anomalously scattering iodine atom could be used to facilitate X-ray structure determination by SAD phasing. In the second project, a phosphotyrosine analogue, p -carboxymethyl-L-phenylalanine, was cotranslationally incorporated into proteins. When this unnatural amino acid was used to replace Tyr701 in human STAT1, the resulting protein dimerized and bound the same DNA sequence as Tyr701-phosphorylated STAT1. Because this amino acid is resistant to protein tyrosine phosphatase, it should be useful in the generation of stable phosphoprotein analogues, or peptide-based inhibitors to SH2 domains. In another project, a metal-chelating amino acid, bipyridylalanine, was selectively incorporated into proteins. Genetically encoding bipyridylalanine and other metal-chelating amino acids should be useful for the generation of proteins with novel or enhanced properties, such as artificial enzymes, proteins that undergo metal-ion-assisted dimerization/trimerization or folding, proteins that contain redox-active metal-ligand complexes on their surface for use in the artificial electron transfer system, and proteins that bind fluorescent or luminescent metal ions as imaging agents, or bind radionuclides for therapeutic use. A final series of experiments involved attempts to incorporate N-methyl amino acids into proteins, which could be useful in generating protease-resistant proteins. While the N-methyl amino acid was N-demethylated by metabolic enzymes in E. coli, recent experiments suggest that such amino acids are stable in yeast, presenting a possible solution to this problem.

Download or read book Expanding the Genetic Code of Caenorhabditis Elegans by Incorporating Unnatural Amino Acids written by Angela Rose Parrish and published by . This book was released on 2011 with total page 114 pages. Available in PDF, EPUB and Kindle. Book excerpt: The genetic code specifies 20 common amino acids and is largely preserved in both single and multicellular organisms. Unnatural amino acids have been genetically incorporated into proteins by using engineered tRNA/aminoacyl-tRNA synthetase pairs in single cells, enabling new research capabilities and precision inaccessible with common amino acids. Here I show that unnatural amino acids can be genetically incorporated into the coding region of proteins in Caenorhabditis elegans, a multicellular model organism extensively used to study basic biology and human diseases. I established that Escherichia coli tyrosyl and leucyl amber suppressor tRNA/synthetase pairs can be evolved to incorporate different unnatural amino acids in response to the amber stop codon (UAG) into various proteins in worms. To accurately report unnatural amino acid incorporation, I found that it is crucial to integrate the UAG-containing reporter gene into the genome rather than to express it on an extrachromosomal array, where expression can be variable. Unnatural amino acid incorporation is greatly affected by bioavailability, which can be improved by delivering in a dipeptide form. Incorporation levels also depend on dosage, exposure time, and tRNA copy number. Unnatural amino acid incorporation can be improved by stabilizing UAG-containing mRNA by RNAi knockdown of smg-1. I have generated stable transgenic worms capable of genetically encoding unnatural amino acids, enabling exploitation of new functional groups to address complex biological problems in a metazoan. I anticipate my strategies will be generally applicable to other multicellular organisms.

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 The Aminoacyl tRNA Synthetases written by Michael Ibba and published by CRC Press. This book was released on 2005-04-01 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: By virtue of their role as catalysts of the aminoacylation reaction, the aminoacyl-tRNA synthetases ensure that the first step of translation is performed quickly and accurately. In this volume of 36 separate chapters, the many facets of this ancient and ubiquitous family are reviewed, including their surprising structural diversity, enzymology, tRNA interaction properties, and curious alternative functions. These chapters illustrate the degree to which the aminoacyl-tRNA synthetases employ a variety of mechanisms to carry out both the standard functions related to the synthesis of aminoacylated tRNA for protein synthesis, as well as the surprising functions associated with amino acid biosynthesis, cytokine function, and even the processivity of DNA replication. Other chapters explore the regulation of their synthesis, their role in disease, and their prospects as targets for antibacterial therapeutics. This monograph will be a valuable resource for all scientists interested in the fundamentals of protein synthesis from both a basic research and clinical perspective, as well as the relation of translational components to the evolution of the genetic code.