Engineered DNA-Binding Proteins for Targeted Genome Editing and Gene Regulation

Engineered DNA-Binding Proteins for Targeted Genome Editing and Gene Regulation
Author: Morgan Lee Maeder
Publisher:
Total Pages:
Release: 2013
Genre:
ISBN:

Engineered DNA-binding proteins enable targeted manipulation of the genome. Zinc fingers are the most well characterized DNA-binding domain and for many years research has focused on understanding and manipulating the sequence-specificities of these proteins. Recently, major advances in the ability to engineer zinc finger proteins, as well as the discovery of a new class of DNA-binding domains - transcription activator-like effectors (TALEs), have made it possible to rapidly and reliably engineer proteins targeted to any sequence of interest. With this capability, focus has shifted to exploring the applications of this powerful technology. In this dissertation I explore three important applications of engineered DNA-binding proteins.

The CRISPR/Cas Tool Kit for Genome Editing

The CRISPR/Cas Tool Kit for Genome Editing
Author: Aftab Ahmad
Publisher: Springer Nature
Total Pages: 342
Release: 2022-01-01
Genre: Medical
ISBN: 981166305X

This book discusses CRISPR/Cas- one of the most powerful tools available to scientists for genome editing. CRISPR/Cas is not only a genome editing tool, but researchers have also engineered it for gene regulation, genome imaging, base editing and epigenome regulations. This book describes the entire toolkit for CRISPR/Cas. The opening section gives an introduction to the technique and compares it with other genome editing tools. Further section gives a historical perspective of the tool, along with its detailed classification. The next chapters describe bioinformatic tools in CRISPR/Cas, and delivery methods for CRISPR/Cas. The book also discusses about the applications of CRISPR/Cas beyond genome editing and use of CRISPR for rewriting genetic codes. The book dedicates a section to the use of CRISPR in plants. The book culminates with a chapter on the current status, challenges and shortcomings of the CRISPR/Cas genome editing tool. The book would be highly interesting to students and researchers in molecular biology, biochemistry, biotechnology, food science, agriculture and plant sciences.

The Paradigm of Understanding, Engineering and Delivering DNA-binding Proteins

The Paradigm of Understanding, Engineering and Delivering DNA-binding Proteins
Author: Joshua Farrell Meckler
Publisher:
Total Pages:
Release: 2015
Genre:
ISBN: 9781339542683

Engineered DNA-binding proteins have put unprecedented power into the hands of molecular biologists. In a blistering five-year span, the field has seen a revolution in technologies, from the hard-to-construct Zinc Fingers, through the extremely effective TAL Effector (TALE) proteins, to the incredibly simple Cas9 platform. These three proteins, co-opted from nature, are entirely distinct in their origins: ZFs are eukaryotic transcription factors, TALEs are invasive bacterial proteins, and Cas9 is part of a prokaryotic immune system. Still, as different as their sources and even their modes of binding, they share a modularity and programmability that has made them ideal for genome engineering. In understanding and then utilizing these tools for biotechnological purposes, investigators have followed a paradigm: understand the binding, build targeted tools upon the framework, and finally, deploy the tools for therapy. If one looks at papers in the genome engineering field, it's not uncommon to see the same study mirrored for these three platforms. Here, we trailblaze our own course along this well-worn pathway. We first biochemically investigate the binding of TAL Effectors, quantifying the relative affinities of their modular repeats and revealing an unexpected polarity of binding. Next, we take a catalytically inactive Cas9 nuclease and we convert it to a targeted gene-regulation tool that is active at endogenous loci in human cells. And finally, we take up the challenge of delivery and demonstrate successful protein-mediated transduction of both TALEs and Cas9.

The CRISPR/Cas System

The CRISPR/Cas System
Author: Muhammad Jamal
Publisher: Caister Academic Press Limited
Total Pages: 0
Release: 2017
Genre: Medical
ISBN: 9781910190630

The use of CRISPR/Cas technology for genome editing suggests many potential applications, including the alteration of the germline of humans, animals and food crops. The speed and efficiency of the CRISPR/Cas system make it a potentially useful system for gene therapy. In this volume expert international authors provide a useful and timely review of the applications of the CRISPR/Cas system across diverse fields and explore further avenues and research directions of this novel and powerful editing technology. The technology and its application are reviewed with respect to reproduction and development, immunity and genetic diseases, system structure and system specificity. Some of the potential problems of the CRISPR/Cas system are also discussed, in particular the specificity of the system: this remains an important topic as improvement could lead to the more direct and efficient use of the CRISPR/Cas system in clinical settings. The authors also debate ethical concerns associated with this powerful new technology. This volume is a rigorous review of the applications and new opportunities for the CRISPR/Cas system and provides a stimulus for current and future research. An invaluable guide for all scientists working in the fields of genome editing and gene therapy the book is also recommended for all life sciences libraries.

Modern Tools for Genetic Engineering

Modern Tools for Genetic Engineering
Author: Michael Kormann
Publisher: BoD – Books on Demand
Total Pages: 228
Release: 2016-05-18
Genre: Science
ISBN: 9535123920

Site-specific endonucleases create double-strand breaks within the genome and can be targeted to literally any genetic mutation. Together with a repair template, a correction of the defective locus becomes possible. This book offers insight into the modern tools of genome editing, their hurdles and their huge potential. A new era of in vivo genetic engineering has begun.

Targeted Genome Editing Using Site-Specific Nucleases

Targeted Genome Editing Using Site-Specific Nucleases
Author: Takashi Yamamoto
Publisher: Springer
Total Pages: 206
Release: 2015-01-05
Genre: Science
ISBN: 4431552278

This book serves as an introduction to targeted genome editing, beginning with the background of this rapidly developing field and methods for generation of engineered nucleases. Applications of genome editing tools are then described in detail, in iPS cells and diverse organisms such as mice, rats, marine invertebrates, fish, frogs, and plants. Tools that are mentioned include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR/Cas9, all of which have received much attention in recent years as breakthrough technologies. Genome editing with engineered nucleases allows us to precisely change the target genome of living cells and is a powerful way to control functional genes. It is feasible in almost all organisms ranging from bacteria to plants and animals, as well as in cultured cells such as ES and iPS cells. Various genome modifications have proven successful, including gene knockout and knock-in experiments with targeting vectors and chromosomal editing. Genome editing technologies hold great promise for the future, for example in biomedical research, clinical medicine, and generation of crops and livestock with desirable traits. A wide range of readers will find this book interesting, and with its focus on applications in a variety of organisms and cells, the book will be valuable for life scientists in all fields.

Genome Editing and Engineering

Genome Editing and Engineering
Author: Krishnarao Appasani
Publisher: Cambridge University Press
Total Pages: 535
Release: 2018-08-23
Genre: Science
ISBN: 1316762084

Recent advances in genome editing tools using endonucleases such as TALENs, ZFNs, and CRISPRs, combined with genomic engineering technologies, have opened up a wide range of opportunities from applications in the basic sciences and disease biology research, to the potential for clinical applications and the development of new diagnostic tools. This complete guide to endonuclease-based genomic engineering gives readers a thorough understanding of this rapidly expanding field. Chapters cover the discovery, basic science, and application of these techniques, focusing particularly on their potential relevance to the treatment of cancer, and cardiovascular and immunological disease. The final section discusses the legal and ethical issues which accompany the technology. Providing authoritative coverage of the potential that genome editing and engineering have, this is an ideal reference for researchers and graduate students and those working in the biotechnology and pharmaceutical industries, as well as in a clinical setting.

Artificial Nucleases

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

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.

Genome Editing in Plants

Genome Editing in Plants
Author: Om Prakash Gupta
Publisher: CRC Press
Total Pages: 382
Release: 2021-07-25
Genre: Science
ISBN: 1000410196

Genome Editing in Plants: Principles and Applications addresses the information of genome editing starting from principles and historical aspects to the latest advancements in the field. As genome-editing technology has emerged as promising and cutting edge, researchers around the world have started producing original research outputs, which have significantly improved our current understanding and potential of this technology. The initial chapters of this book describe different genome-editing tools as well as their principles and applications. Other chapters are dedicated to the present status and future applications of genome-editing techniques in various crop improvement programmes. Some of the advanced applications of CRISPR/Cas tools, such as base editing and RNA detection, along with regulatory aspects of genome-edited crops are described in detail. This book serves as a valuable resource to researchers in the field of crop improvement; graduate and postgraduate students engaged in plant molecular biology and biotechnology; academicians; and policy makers. Key Features: Addresses topics associated with historical development and principles of genome-editing technology Addresses basic mechanisms operating under each genome-editing technology Addresses its application in plants to design crops as per the current and future demands Addresses the regulatory mechanisms of genome-edited crops

Genome Editing

Genome Editing
Author: Kursad Turksen
Publisher: Springer
Total Pages: 171
Release: 2016-08-09
Genre: Science
ISBN: 3319341480

This timely volume explores the use of CRISPR-Cas9 for genome editing, presenting cutting-edge techniques and their applications in treatment of disease. The chapters describe latest methods such as use of targetable nucleases, investigation of the non-coding genome, mouse genome editing, increasing of knock-in efficiency in mouse zygotes, and generation of reporter stem cells; the text contextualizes these methods in treatment of cardiovascular disease, diabetes mellitus, retinitis pigmentosa, and others. The final chapters round out the book with a discussion of controversies and future directions. Genome Editing is an essential, of-the-moment contribution to this rapidly growing field. Drawing from a wealth of international perspectives, it presents novel techniques and applications for the engineering of the human genome. This book is essential reading for all clinicians and researchers in stem cells, regenerative medicine, genomics, biochemical and biomedical engineering- especially those interested in learning more about genome editing and applying it in a targeted, specific way.