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"Chin, Jason"
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Gravity
\"What keeps objects from floating out of your hand? What if your feet drifted away from the ground? What stops everything from floating into space? Gravity ... Jason Chin has taken a complex subject and made it brilliantly accessible to young readers in this unusual, innovative, and very beautiful book.
Book
Expanding and reprogramming the genetic code
Nature uses a limited, conservative set of amino acids to synthesize proteins. The ability to genetically encode an expanded set of building blocks with new chemical and physical properties is transforming the study, manipulation and evolution of proteins, and is enabling diverse applications, including approaches to probe, image and control protein function, and to precisely engineer therapeutics. Underpinning this transformation are strategies to engineer and rewire translation. Emerging strategies aim to reprogram the genetic code so that noncanonical biopolymers can be synthesized and evolved, and to test the limits of our ability to engineer the translational machinery and systematically recode genomes.
A review of the recent developments in reprogramming the genetic code of cells and organisms to include non-canonical amino acids in precisely engineered proteins.
Rewriting genetic guidelines
In living organisms, proteins that are encoded by DNA are composed of 20 canonical amino acids, with some organisms using up to two additional derivatives. Theoretically, other molecules that are related to these amino acids could form a similar protein backbone and might confer new properties on the proteins. Jason Chin reviews the most recent studies on reprogramming the genetic code, where progress is being made in incorporating these non-canonical (that is, not naturally occurring) amino acids into proteins, even using the cell's own machinery to do so, and without disrupting overall protein function.
Journal Article
Redwoods
A young city boy, riding the subway, finds an abandoned book about redwoods. He finds himself in the very forest described in the book. After finishing the book, he leaves it for someone else to read.
Book
Reprogramming the genetic code
The encoded biosynthesis of proteins provides the ultimate paradigm for high-fidelity synthesis of long polymers of defined sequence and composition, but it is limited to polymerizing the canonical amino acids. Recent advances have built on genetic code expansion — which commonly permits the cellular incorporation of one type of non-canonical amino acid into a protein — to enable the encoded incorporation of several distinct non-canonical amino acids. Developments include strategies to read quadruplet codons, use non-natural DNA base pairs, synthesize completely recoded genomes and create orthogonal translational components with reprogrammed specificities. These advances may enable the genetically encoded synthesis of non-canonical biopolymers and provide a platform for transforming the discovery and evolution of new materials and therapeutics.The ability to reprogramme cellular translation and genomes to produce non-canonical biopolymers has wide-ranging applications, including in therapeutics, but has yet to be fully realized. In this Review, de la Torre and Chin discuss recent advances towards achieving this goal.
Journal Article
Island : a story of the Galâapagos
This book is an epic saga of the life of an island--born of fire, rising to greatness, its decline, and finally the emergence of life on new islands.
Book
Designer proteins: applications of genetic code expansion in cell biology
Key Points
A large number of unnatural amino acids can now be incorporated into proteins using 'orthogonal' aminoacyl-tRNA synthetase–tRNA pairs. The pyrrolysyl-tRNA synthetase (PylRS)–tRNA
CUA
pair is currently the most versatile, and it has been used in bacteria, yeast, mammalian cells and
Caenorhabditis elegans
.
Photocrosslinking amino acids allows protein interactions to be defined
in vitro
and in bacteria, yeast and mammalian cells.
Post-translational modifications, including lysine acetylation, monomethylation and dimethylation, and ubiquitylation, can be quantitatively directed into proteins by genetic code expansion.
Photocaged amino acids allow rapid activation of protein function inside living cells. This approach can be used to dissect signalling pathways.
Biophysical probes can be incorporated into proteins. Infrared probes have been used to examine conformational changes in G protein-coupled receptors. Other probes will probably have similar uses.
Bio-orthogonal chemistry provides a promising approach for labelling proteins for a range of applications, including imaging, but more rapid methods are needed for cellular imaging.
More sophisticated methods for incorporating multiple distinct amino acids, including orthogonal ribosome evolution and the generation of new synthetase–tRNA pairs are likely to expand the range of applications that are possible in the future.
The incorporation of unnatural amino acids at defined sites in proteins can now be used to probe protein conformational changes, protein interactions and the role of post-translational modifications in regulating biological function. The use of photocaged amino acids and bio-orthogonal labels for proteins holds great promise for cell biological studies in live cells.
Designer amino acids, beyond the canonical 20 that are normally used by cells, can now be site-specifically encoded into proteins in cells and organisms. This is achieved using 'orthogonal' aminoacyl-tRNA synthetase–tRNA pairs that direct amino acid incorporation in response to an amber stop codon (UAG) placed in a gene of interest. Using this approach, it is now possible to study biology
in vitro
and
in vivo
with an increased level of molecular precision. This has allowed new biological insights into protein conformational changes, protein interactions, elementary processes in signal transduction and the role of post-translational modifications.
Journal Article
Grand Canyon
\"Home to an astonishing variety of plants and animals that have lived and evolved within its walls for millennia, the Grand Canyon is much more than just a hole in the ground. Follow a father and daughter as they make their way through the cavernous wonder, discovering life both present and past\"--Amazon.com.
Book
Mutually orthogonal pyrrolysyl-tRNA synthetase/tRNA pairs
Genetically encoding distinct non-canonical amino acids (ncAAs) into proteins synthesized in cells requires mutually orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pairs. The pyrrolysyl-tRNA synthetase/PyltRNA pair from Methanosarcina mazei (Mm) has been engineered to incorporate diverse ncAAs and is commonly considered an ideal pair for genetic code expansion. However, finding new aaRS/tRNA pairs that share the advantages of the MmPylRS/MmPyltRNA pair and are orthogonal to both endogenous aaRS/tRNA pairs and the MmPylRS/MmPyltRNA pair has proved challenging. Here we demonstrate that several ΔNPylRS/PyltRNACUA pairs, in which PylRS lacks an N-terminal domain, are active, orthogonal and efficiently incorporate ncAAs in Escherichia coli. We create new PylRS/PyltRNA pairs that are mutually orthogonal to the MmPylRS/MmPyltRNA pair and show that transplanting mutations that reprogram the ncAA specificity of MmPylRS into the new PylRS reprograms its substrate specificity. Finally, we show that distinct PylRS/PyltRNA-derived pairs can function in the same cell, decode distinct codons and incorporate distinct ncAAs.
Journal Article
Water is water : a book about the water cycle
\"A spare, poetic picture book exploring the different phases of the water cycle in surprising and engaging ways\"-- Provided by publisher.
Book
Automated orthogonal tRNA generation
The ability to generate orthogonal, active tRNAs—central to genetic code expansion and reprogramming—is still fundamentally limited. In this study, we developed Chi-T, a method for the de novo generation of orthogonal tRNAs. Chi-T segments millions of isoacceptor tRNA sequences into parts and then assembles chimeric tRNAs from these parts. Chi-T fixes the parts, containing identity elements, and combinatorially varies all other parts to generate chimeric sequences. Chi-T also filters the variable parts and chimeric sequences to minimize host identity elements. We show here that experimentally characterized orthogonal tRNAs are more likely to have predicted minimum free energy cloverleaf structures, and Chi-T filters for sequences with a predicted cloverleaf structure. We report RS-ID for the identification of synthetases that may acylate the tRNAs generated by Chi-T. We computationally identified new orthogonal tRNAs and engineered an orthogonal pair generated by Chi-T/RS-ID to direct non-canonical amino acid incorporation, in response to both amber codons and sense codons, with an efficiency similar to benchmark genetic code expansion systems.
Genetic code expansion and reprogramming require orthogonal tRNAs. Methods have now been developed for the automated generation of chimeric orthogonal tRNAs and discovery of their cognate synthetases. These approaches have been used to discover new orthogonal pairs for efficient non-canonical amino acid incorporation.
Journal Article