Click Chemistry-based Artificial Metallonucleases

Click Chemistry-based Artificial Metallonucleases
Author: Alex Gibney
Publisher:
Total Pages: 0
Release: 2024
Genre:
ISBN:

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Nucleic acids are essential to all life on earth, with the remarkable stability of the phosphodiester backbone providing the integrity required for faithful storage of genetic information. Evolution has, therefore, resulted in a variety of cellular machinery that monitor and maintain this genetic integrity from deleterious processes such as DNA oxidation, which is an inevitable consequence of aerobic respiration and the resulting production of reactive oxygen species (ROS). These DNA repair processes are energetically expensive and prone to error, with both factors contributing to an upper tolerance of DNA oxidation in the cellular environment, exceedance of which ultimately results in triggering of apoptosis or other cell death processes. DNA oxidation and the resulting over-stimulation of the afore mentioned repair processes is therefore a promising approach for the development of novel anticancer agents. The design of inorganic and organometallic complexes that result in DNA-localised ROS production and cleavage of the phosphodiester backbone has proven to be a key strategy in the development in such potential therapeutics, now known as artificial metallonucleases (AMNs). Here, a series of AMNs have been developed using the Nobel prize-winning "Click" chemistry, incorporating the 1,2,3-triazole, resultant of the Cu(I)-catalysed alkyne/azide click reaction as a key structural motif in both DNA recognition and transition metal binding. This method of AMN development has been coined the "Click and Cut" strategy. Clicking a range of commercially available alkynes with proximal N,O and S donors around a C3 -symmetric mesitylene core that has previously been found to facilitate DNA recognition resulted in a series of structurally diverse and potent Cu(II) AMNs. The activity of these Tri-Click (TC) AMNs were investigated using a range of standard and state-of-the-art techniques such as agarose gel electrophoresis, fluorescence quenching, fluorescence melting, microscale thermophoresis and repair-assisted damage detection (RADD). The Cu(II)-TC AMNs were found to selectively bind to and cleave from the minor groove of the DNA duplex, facilitated by a crescent-shape conformation adopted by two arms of the tripodal structures. Cleavage of native DNA was found to occur via a superoxide and peroxide dependant mechanism, with this mechanism being retained in the intracellular environment. Anticancer screening of the most promising ligands revealed broad spectrum activity against a range of cell lines in the national cancer institute's 60 cell line assay.

The Development of Hybrid Antigene Therapeutics Using Nucleic Acid Click Chemistry

The Development of Hybrid Antigene Therapeutics Using Nucleic Acid Click Chemistry
Author: Teresa Lauria
Publisher:
Total Pages: 0
Release: 2020
Genre:
ISBN:

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Given their ability to break single- and double-strand DNA with high selectivity, the design of restriction endonuclease mimics has become an area of considerable research interest. One class of mimetics are copper artificial metallo-nucleases (AMNs) that prompt direct strand scission by oxidatively damaging duplex DNA. Therefore, the formation of metal-catalysed free radicals in the vicinity of nucleic acids provides a viable route to developing artificial gene editing tools. The aim of this research was to develop new copper-based AMNs for selective knockdown of the green fluorescent protein (GFP) gene. To achieve this, a novel pool of gene-targeted biomaterials was developed by hybridising intercalating azide-modified phenanthrene AMNs to triplex formation oligonucleotides (TFOs) using copper-catalysed alkyne-azide cycloaddition (CuAAC) 'click' chemistry. Upon isolating the family of AMN-TFO hybrids, the project focused on their triplex formation and stabilisation properties. In the presence of coordinated copper(II) ions and a reductant, AMN-TFOs selectively cleaved the GFP gene fragment and site-specific fragmentation patterns were identified using fluorophore-tagged sequences. Building on this first generation of hybrid AMNs, second generation hybrids were developed by clicking di-copper binding bis-phenanthroline ligands to alkyneTFOs. These di-copper(II) AMN-TFOs were prepared using both CuAAC and strainpromoted azide-alkyne cycloaddition (SPAAC) reactions and cleavage reactions with a GFP gene fragment were compared to first generation mononuclear AMN-TFO hybrids. The final aspect of this work focused on extending this technology to develop a novel class of luminescent probes. To achieve this, polypyridyl ruthenium(II) complexes bearing an azide-phenanthroline handle were prepared and conjugated to alkyne TFOs and their preliminary GFP-targeting and luminescence properties were identified.

Click and Cut

Click and Cut
Author: Bríonna McGorman
Publisher:
Total Pages: 0
Release: 2022
Genre:
ISBN:

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Triplex forming oligonucleotides (TFOs) are short strands of nucleotides that can hybridise to duplex DNA and form triple helical structures. As triplex formation is sequence selective, there is significant interest in applying this technology for antigene therapy. In this work, primer extension (PEX) protocols were designed and utilised to enzymatically synthesise TFOs bearing artificial metallo-nucleases (AMNs). Initially, single nucleotide incorporation-primer extension (SNI-PEX) was employed to generate TFOs bearing a single modification. This was then expanded to the novel multiple nucleotide incorporation-primer extension (MNIPEX) protocol, which enabled multiple different modified bases to be incorporated at specific sites in the TFO sequence. Click chemistry was employed to generate a library of functionalised nucleotides, which were then enzymatically incorporated into the TFO strand by a DNA polymerase. These AMN-TFO hybrids can recognise and damage specific DNA sequences, and therefore are capable of targeting a gene of interest. Real-time PCR (qPCR) and polyacrylamide gel electrophoresis (PAGE) protocols were then developed to analyse and compare the activity of these sequence-selective hybrids. PAGE was employed to visualise the sequence specificity of the TFO-drug hybrids and to identify 'on' and 'off' targeting effects. Next, the DNA damaging capabilities of three distinct TFO-hybrids, each bearing a unique AMN ligand (5N3 -TPMA, 6N3 -TPMA and 4N3 benzyl-DPA), were quantified by a specifically developed qPCR protocol. Here, target DNA post treatment with the AMN-TFO hybrid, was amplified in the presence of SYBR Green I and the resulting fluorescent signal was compared to that of the untreated controls. Results show the AMN-TFOs can discriminate between target and off-target DNA, and differences in the DNA damaging capabilities of each AMN ligand were recorded. These results indicate that TFO-drug hybrids may have the ability to overcome problems associated with non-molecularly targeted DNA damaging agents, and represent a new class of gene knockout agent.

Nanozymes: Next Wave of Artificial Enzymes

Nanozymes: Next Wave of Artificial Enzymes
Author: Xiaoyu Wang
Publisher: Springer
Total Pages: 134
Release: 2016-07-27
Genre: Technology & Engineering
ISBN: 3662530686

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This book describes the fundamental concepts, the latest developments and the outlook of the field of nanozymes (i.e., the catalytic nanomaterials with enzymatic characteristics). As one of today’s most exciting fields, nanozyme research lies at the interface of chemistry, biology, materials science and nanotechnology. Each of the book’s six chapters explores advances in nanozymes. Following an introduction to the rise of nanozymes research in the course of research on natural enzymes and artificial enzymes in Chapter 1, Chapters 2 through 5 discuss different nanomaterials used to mimic various natural enzymes, from carbon-based and metal-based nanomaterials to metal oxide-based nanomaterials and other nanomaterials. In each of these chapters, the nanomaterials’ enzyme mimetic activities, catalytic mechanisms and key applications are covered. In closing, Chapter 6 addresses the current challenges and outlines further directions for nanozymes. Presenting extensive information on nanozymes and supplemented with a wealth of color illustrations and tables, the book offers an ideal guide for readers from disparate areas, including analytical chemistry, materials science, nanoscience and nanotechnology, biomedical and clinical engineering, environmental science and engineering, green chemistry, and novel catalysis.

Modified Nucleic Acids

Modified Nucleic Acids
Author: Kazuhiko Nakatani
Publisher: Springer
Total Pages: 280
Release: 2016-04-04
Genre: Science
ISBN: 3319271113

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This book spans diverse aspects of modified nucleic acids, from chemical synthesis and spectroscopy to in vivo applications, and highlights studies on chemical modifications of the backbone and nucleobases. Topics discussed include fluorescent pyrimidine and purine analogs, enzymatic approaches to the preparation of modified nucleic acids, emission and electron paramagnetic resonance (EPR) spectroscopy for studying nucleic acid structure and dynamics, non-covalent binding of low- and high-MW ligands to nucleic acids and the design of unnatural base pairs. This unique book addresses new developments and is designed for graduate level and professional research purposes.

Metal-based Anticancer Agents

Metal-based Anticancer Agents
Author: Angela Casini
Publisher: Royal Society of Chemistry
Total Pages: 370
Release: 2019-04-05
Genre: Science
ISBN: 1788017676

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Metal-based anticancer drugs are among the most successful therapeutic agents, as evidenced by the frequent prescription of selected platinum and arsenic compounds to patients. Metal-based Anticancer Agents covers the interdisciplinary world of inorganic drug discovery and development by introducing the most prominent compound classes based on different transition metals, discussing emerging concepts and enabling methods, as well as presenting key pre-clinical and clinical aspects. Recent progress on the unique features of next-generation targeted metal-based anticancer agents, including supramolecular coordination complexes used for both therapy and drug delivery, promise a bright future beyond the benefits of pure cytotoxic activity. With contributions from global leaders in the field, this book will serve as a useful reference to established researchers as well as a practical guide to those new to metallodrugs, and postgraduate students of medicinal chemistry and metallobiology.

Artificial Nucleases

Artificial Nucleases
Author: Marina A. Zenkova
Publisher: Springer Science & Business Media
Total Pages: 330
Release: 2004-01-07
Genre: Medical
ISBN: 9783540201120

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The development of agents capable of cleaving RNA and DNA has attracted considerable attention from researchers in the last few years, because of the immediate and very important applications they can find in the emerging fields of biotechnology and pharmacology. There are essentially two classes of these agents - nucleases that occur naturally inside cells and synthetically produced artificial nucleases. The first class includes protein enzyme nucle ases and catalytic RNA structured ribozymes that perform cleavage of the phosphodiester bonds in nucleic acids according to a hydrolytic pathway in the course of different biochemical processes in the cell. A different pathway is used by some antibiotics which cleave DNA via redox-based mechanisms resulting in oxidative damage of nucleotide units and breakage of the DNA backbone. The above molecules are indispensable tools for manipulating nucleic acids and processing RNA; DNA-cleaving antibiotics and cytotoxic ribonucleases have demonstrated utility as chemotherapeutic agents. The second class, artificial nucleases, are rationally designed to imitate the active centers of natural enzymes by simple structures possessing minimal sets of the most important characteristics that are essential for catalysis. A dif ferent approach, in vitro selection, was also used to create artificial RNA and DNA enzymes capable of cleaving RNA. Being less efficient and specific as compared to the natural enzymes, the primitive mimics are smaller and robust and can function in a broad range of conditions.

Nucleic Acids in Chemistry and Biology

Nucleic Acids in Chemistry and Biology
Author: G Michael Blackburn
Publisher: Royal Society of Chemistry
Total Pages: 503
Release: 2015-11-09
Genre: Science
ISBN: 1782625771

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The structure, function and reactions of nucleic acids are central to molecular biology and are crucial for the understanding of complex biological processes involved. Revised and updated Nucleic Acids in Chemistry and Biology 3rd Edition discusses in detail, both the chemistry and biology of nucleic acids and brings RNA into parity with DNA. Written by leading experts, with extensive teaching experience, this new edition provides some updated and expanded coverage of nucleic acid chemistry, reactions and interactions with proteins and drugs. A brief history of the discovery of nucleic acids is followed by a molecularly based introduction to the structure and biological roles of DNA and RNA. Key chapters are devoted to the chemical synthesis of nucleosides and nucleotides, oligonucleotides and their analogues and to analytical techniques applied to nucleic acids. The text is supported by an extensive list of references, making it a definitive reference source. This authoritative book presents topics in an integrated manner and readable style. It is ideal for graduate and undergraduates students of chemistry and biochemistry, as well as new researchers to the field.

New-Generation Bioinorganic Complexes

New-Generation Bioinorganic Complexes
Author: Renata Jastrzab
Publisher: Walter de Gruyter GmbH & Co KG
Total Pages: 325
Release: 2016-03-21
Genre: Technology & Engineering
ISBN: 3110386445

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Bio-Inorganic compounds are successfully applied as therapeutic agents since decades. Thus, scientist designed new metal complexes bearing biomolecules as ligands, investigating their potential as bioactive and therapeutic agents. This book presents a comprehensive overview on materials design, substance classes and their characterization. This book is compiled for scientists interested in medical application of bioinspired materials.

Biomedical Applications of Acridines

Biomedical Applications of Acridines
Author: Jan Ježek
Publisher: Springer
Total Pages: 243
Release: 2017-08-15
Genre: Science
ISBN: 3319639536

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This book describes applications of acridines for the treatment of various neurodegenerative diseases, such as Alzheimer’s disease, Parkinson’s disease, and various prion diseases, and discusses the potential of acridines in neuro-regenerative medicine. Using modern data-mining software, it presents structures of acridines with nucleic acids and proteins and compares them with the native structures. Furthermore, the book presents modern methods of acridine synthesis, comparing them with the most useful conventional methods. Acridines interact with both nucleic acids and proteins, and due to their direct interactions with various enzymes, they can be suitable for the treatment of neurodegenerative diseases, inflammation, immunological disorders, and protozoal diseases. The characteristic spectral properties of acridines can be employed in labeling proteins, nucleic acids, lipids, and even cells and their compartments. Moreover, they can be applied in photodynamic therapy.