scholarly journals The basic building blocks and evolution of CRISPR–Cas systems

2013 ◽  
Vol 41 (6) ◽  
pp. 1392-1400 ◽  
Author(s):  
Kira S. Makarova ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin
Keyword(s):  
Adaptive Immunity ◽  
Purifying Selection ◽  
Building Blocks ◽  
Comparative Sequence Analysis ◽  
Structural Rearrangements ◽  
Recognition Mechanism ◽  
Recent Advances ◽  
Self Recognition ◽  
First Time ◽  
Cas Proteins

CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) is an adaptive immunity system in bacteria and archaea that functions via a distinct self/non-self recognition mechanism that involves unique spacers homologous with viral or plasmid DNA and integrated into the CRISPR loci. Most of the Cas proteins evolve under relaxed purifying selection and some underwent dramatic structural rearrangements during evolution. In many cases, CRISPR–Cas system components are replaced either by homologous or by analogous proteins or domains in some bacterial and archaeal lineages. However, recent advances in comparative sequence analysis, structural studies and experimental data suggest that, despite this remarkable evolutionary plasticity, all CRISPR–Cas systems employ the same architectural and functional principles, and given the conservation of the principal building blocks, share a common ancestry. We review recent advances in the understanding of the evolution and organization of CRISPR–Cas systems. Among other developments, we describe for the first time a group of archaeal cas1 gene homologues that are not associated with CRISPR–Cas loci and are predicted to be involved in functions other than adaptive immunity.

scholarly journals Recent advances in structural studies of the CRISPR-Cas-mediated genome editing tools

2018 ◽  
Vol 6 (3) ◽  
pp. 438-451 ◽  
Author(s):  
Yuwei Zhu ◽  
Zhiwei Huang
Keyword(s):  
Nucleic Acids ◽  
Genome Editing ◽  
Adaptive Immunity ◽  
Structural Biology ◽  
Structural Studies ◽  
Guide Rnas ◽  
Recent Advances ◽  
Cas Proteins

Abstract Clustered regularly interspaced short palindromic repeats (CRISPR) and accompanying CRISPR-associated (Cas) proteins provide RNA-guided adaptive immunity for prokaryotes to defend themselves against viruses. The CRISPR-Cas systems have attracted much attention in recent years for their power in aiding the development of genome editing tools. Based on the composition of the CRISPR RNA-effector complex, the CRISPR-Cas systems can be divided into two classes and six types. In this review, we summarize recent advances in the structural biology of the CRISPR-Cas-mediated genome editing tools, which helps us to understand the mechanism of how the guide RNAs assemble with diverse Cas proteins to cleave target nucleic acids.

Probing the Substrate Promiscuity of Isopentenyl Phosphate Kinase as a Platform for Hemiterpene Analogue Production

2019 ◽  
Author(s):  
Sean Lund ◽  
Taylor Courtney ◽  
Gavin Williams
Keyword(s):  
Synthetic Biology ◽  
Building Blocks ◽  
Isoprenoid Biosynthesis ◽  
Thermoplasma Acidophilum ◽  
Substrate Promiscuity ◽  
Enzymatic Pathways ◽  
First Time ◽  
Rate Limiting ◽  
Alcohol Dependent ◽  
Isopentenyl Phosphate

Isoprenoids are a large class of natural products with wide-ranging applications. Synthetic biology approaches to the manufacture of isoprenoids and their new-to-nature derivatives are limited due to the provision in Nature of just two hemiterpene building blocks for isoprenoid biosynthesis. To address this limitation, artificial chemo-enzymatic pathways such as the alcohol-dependent hemiterpene pathway (ADH) serve to leverage consecutive kinases to convert exogenous alcohols to pyrophosphates that could be coupled to downstream isoprenoid biosynthesis. To be successful, each kinase in this pathway should be permissive of a broad range of substrates. For the first time, we have probed the promiscuity of the second enzyme in the ADH pathway, isopentenyl phosphate kinase from Thermoplasma acidophilum, towards a broad range of acceptor monophosphates. Subsequently, we evaluate the suitability of this enzyme to provide non-natural pyrophosphates and provide a critical first step in characterizing the rate limiting steps in the artificial ADH pathway.<br>

scholarly journals A Sustainable Improvement of ω-Bromoalkylphosphonates Synthesis to Access Novel KuQuinones

Organics ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 107-117
Author(s):  
Mattia Forchetta ◽  
Valeria Conte ◽  
Giulia Fiorani ◽  
Pierluca Galloni ◽  
Federica Sabuzi
Keyword(s):  
Metal Oxides ◽  
Phosphonic Acid ◽  
Organic Molecules ◽  
Building Blocks ◽  
Reaction Conditions ◽  
Phosphonic Acids ◽  
Sustainable Improvement ◽  
Phosphonate Esters ◽  
First Time ◽  
Complex Organic

Owing to the attractiveness of organic phosphonic acids and esters in the pharmacological field and in the functionalization of conductive metal-oxides, the research of effective synthetic protocols is pivotal. Among the others, ω-bromoalkylphosphonates are gaining particular attention because they are useful building blocks for the tailored functionalization of complex organic molecules. Hence, in this work, the optimization of Michaelis–Arbuzov reaction conditions for ω-bromoalkylphosphonates has been performed, to improve process sustainability while maintaining good yields. Synthesized ω-bromoalkylphosphonates have been successfully adopted for the synthesis of new KuQuinone phosphonate esters and, by hydrolysis, phosphonic acid KuQuinone derivatives have been obtained for the first time. Considering the high affinity with metal-oxides, KuQuinones bearing phosphonic acid terminal groups are promising candidates for biomedical and photo(electro)chemical applications.

scholarly journals Bacterial cellulose spheroids as building blocks for 3D and patterned living materials and for regeneration

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joaquin Caro-Astorga ◽  
Kenneth T. Walker ◽  
Natalia Herrera ◽  
Koon-Yang Lee ◽  
Tom Ellis
Keyword(s):  
Bacterial Cellulose ◽  
Building Blocks ◽  
Genetically Engineered ◽  
High Yield ◽  
Synthetic Materials ◽  
Chemical Inputs ◽  
First Time ◽  
3D Shapes ◽  
Promising Avenue ◽  
Living Materials

AbstractEngineered living materials (ELMs) based on bacterial cellulose (BC) offer a promising avenue for cheap-to-produce materials that can be programmed with genetically encoded functionalities. Here we explore how ELMs can be fabricated in a modular fashion from millimetre-scale biofilm spheroids grown from shaking cultures of Komagataeibacter rhaeticus. Here we define a reproducible protocol to produce BC spheroids with the high yield bacterial cellulose producer K. rhaeticus and demonstrate for the first time their potential for their use as building blocks to grow ELMs in 3D shapes. Using genetically engineered K. rhaeticus, we produce functionalized BC spheroids and use these to make and grow patterned BC-based ELMs that signal within a material and can sense and report on chemical inputs. We also investigate the use of BC spheroids as a method to regenerate damaged BC materials and as a way to fuse together smaller material sections of cellulose and synthetic materials into a larger piece. This work improves our understanding of BC spheroid formation and showcases their great potential for fabricating, patterning and repairing ELMs based on the promising biomaterial of bacterial cellulose.

scholarly journals Galectins as self/non-self recognition receptors in innate and adaptive immunity: an unresolved paradox

2012 ◽  
Vol 3 ◽  
Author(s):  
Gerardo R. Vasta ◽  
Hafiz Ahmed ◽  
Mihai Nita-Lazar ◽  
Aditi Banerjee ◽  
Marta Pasek ◽  
...  
Keyword(s):  
Adaptive Immunity ◽  
Innate And Adaptive Immunity ◽  
Self Recognition

α-Aminoboronates: recent advances in their preparation and synthetic applications

2021 ◽  
Author(s):  
Wenbo Ming ◽  
Harjeet S. Soor ◽  
Xiaocui Liu ◽  
Alina Trofimova ◽  
Andrei K. Yudin ◽  
...  
Keyword(s):  
Building Blocks ◽  
Synthetic Methods ◽  
Mechanistic Explanations ◽  
Recent Advances

This review summarizes new methodology for the synthesis of α-aminoboronates, including asymmetric synthetic methods and mechanistic explanations of reactivity. Applications of α-aminoboronates as versatile synthetic building blocks are also discussed.

Design, synthesis and evaluation of structurally diverse ortho-acylphenol-diindolylmethane hybrids as anticancer agents

2022 ◽  
Author(s):  
Zhi-Gang Yin ◽  
Xiong-Wei Liu ◽  
Hui-Juan Wang ◽  
Min Zhang ◽  
Xiong-Li Liu ◽  
...  
Keyword(s):  
Carboxylic Acid ◽  
Anticancer Agents ◽  
Nucleophilic Addition ◽  
Ring Opening ◽  
Building Blocks ◽  
Efficient Synthesis ◽  
Design Synthesis ◽  
Pyrone Ring ◽  
Ring Opening Reaction ◽  
First Time

A highly efficient synthesis of structurally diverse ortho-acylphenol–diindolylmethane hybrids 3 using carboxylic acid-activated chromones as versatile synthetic building blocks is reported here for the first time, through 1,4-nucleophilic addition and followed by a decarboxylation and pyrone ring opening reaction process.

scholarly journals Straightforward Preparation of Supramolecular Janus Nanorods by Hydrogen Bonding of End-Functionalized Polymers

2020 ◽  
Author(s):  
Shuaiyuan Han ◽  
Sandrine Pensec ◽  
Cédric Lorthioir ◽  
Jacques Jestin ◽  
Jean-Michel Guigner ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Self Assembly ◽  
Functional Materials ◽  
Phase Segregation ◽  
Building Blocks ◽  
Functionalized Polymers ◽  
Nanometer Range ◽  
One Dimensional ◽  
Oil In Water ◽  
First Time

Janus cylinders are one-dimensional colloids that have two faces with different compositions and functionalities and are useful as building blocks for advanced functional materials. Such anisotropic objects are difficult to prepare with nanometric dimensions. Here we describe a robust and versatile strategy to form micrometer long Janus nanorods with diameters in the 10-nanometer range, by self-assembly in water of end-functionalized polymers. For the first time, the Janus topology is not a result of the phase segregation of incompatible polymer arms, but is driven by the interactions between unsymmetrical and complementary hydrogen bonded stickers. It is therefore independent of the actual polymers used and works even for compatible polymers. To illustrate their applicative potential, we show that these Janus nanorods can efficiently stabilize oil-in-water emulsions.

scholarly journals Recent Advances in Palladium-Catalyzed Isocyanide Insertions

Molecules ◽  
2020 ◽  
Vol 25 (21) ◽  
pp. 4906
Author(s):  
Jurriën W. Collet ◽  
Thomas R. Roose ◽  
Bram Weijers ◽  
Bert U. W. Maes ◽  
Eelco Ruijter ◽  
...  
Keyword(s):  
Organic Synthesis ◽  
Building Blocks ◽  
Insertion Reactions ◽  
Chemical Reagents ◽  
The Past ◽  
Recent Advances ◽  
Recent Developments ◽  
Palladium Catalyzed ◽  
Made In ◽  
Rapid Incorporation

Isocyanides have long been known as versatile chemical reagents in organic synthesis. Their ambivalent nature also allows them to function as a CO-substitute in palladium-catalyzed cross couplings. Over the past decades, isocyanides have emerged as practical and versatile C1 building blocks, whose inherent N-substitution allows for the rapid incorporation of nitrogeneous fragments in a wide variety of products. Recent developments in palladium catalyzed isocyanide insertion reactions have significantly expanded the scope and applicability of these imidoylative cross-couplings. This review highlights the advances made in this field over the past eight years.

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