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Author : James Bentley Brown
Publisher :
ISBN 13 :
Total Pages : 170 pages
Book Rating : 4.:/5 (35 download)
Download or read book Mapping the Affinities of Sequence-specific DNA-binding Proteins written by James Bentley Brown and published by . This book was released on 2008 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : M. Michael Gromiha
Publisher : Academic Press
ISBN 13 : 0123884241
Total Pages : 349 pages
Book Rating : 4.1/5 (238 download)
Download or read book Protein Bioinformatics written by M. Michael Gromiha and published by Academic Press. This book was released on 2011-04-21 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the most pressing tasks in biotechnology today is to unlock the function of each of the thousands of new genes identified every day. Scientists do this by analyzing and interpreting proteins, which are considered the task force of a gene. This single source reference covers all aspects of proteins, explaining fundamentals, synthesizing the latest literature, and demonstrating the most important bioinformatics tools available today for protein analysis, interpretation and prediction. Students and researchers of biotechnology, bioinformatics, proteomics, protein engineering, biophysics, computational biology, molecular modeling, and drug design will find this a ready reference for staying current and productive in this fast evolving interdisciplinary field. Explains all aspects of proteins including sequence and structure analysis, prediction of protein structures, protein folding, protein stability, and protein interactions Presents a cohesive and accessible overview of the field, using illustrations to explain key concepts and detailed exercises for students.
Author : Robert C. Blanks
Publisher :
ISBN 13 :
Total Pages : 280 pages
Book Rating : 4.:/5 (225 download)
Download or read book Oligodeoxynucleotide Affinity Column for the Isolation of Sequence Specific DNA Binding Proteins written by Robert C. Blanks and published by . This book was released on 1989 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : A. Travers
Publisher : Springer Science & Business Media
ISBN 13 : 9401114803
Total Pages : 189 pages
Book Rating : 4.4/5 (11 download)
Download or read book DNA-Protein Interactions written by A. Travers and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: Our understanding of the mechanisms regulating gene expression, which determine the patterns of growth and development in all living organisms, ultimately involves the elucidation of the detailed and dy namic interactions of proteins with nucleic acids -both DNA and RNA. Until recently the commonly presented view of the DNA double helix as visualized on the covers of many textbooks and journals - was as a monotonous static straight rod incapable in its own right of directing the processes necessary for the conservation and selective reading of genetic information. This view, although perhaps extreme, was reinforced by the necessary linearity of genetic maps. The reality is that the biological functions of both DNA and RNA are dependent on complex, and sometimes transient, three-dimensional nucleoprotein structures in which genetically distant elements are brought into close spatial proximity. It is in such structures that the enzymatic manipulation of DNA in the essential biological processes as DNA replication, transcription and recombination are effected - the complexes are the mediators of the 'DNA transactions' of Hatch Echols.
Author : Thomas A. Steitz
Publisher : CUP Archive
ISBN 13 : 9780521414890
Total Pages : 108 pages
Book Rating : 4.4/5 (148 download)
Download or read book Structural Studies of Protein-Nucleic Acid Interaction written by Thomas A. Steitz and published by CUP Archive. This book was released on 1993-09-16 with total page 108 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this 1993 text, Nobel Prize winner Professor Steitz reviews the wide-ranging research in structural studies of DNA-binding proteins and their complexes with DNA. The author clearly and concisely describes the uses of techniques in molecular genetics, DNA synthesis, protein crystallography and nuclear magnetic response.
Author : Michael J Waring
Publisher : Royal Society of Chemistry
ISBN 13 : 1847555306
Total Pages : 271 pages
Book Rating : 4.8/5 (475 download)
Download or read book Sequence-specific DNA Binding Agents written by Michael J Waring and published by Royal Society of Chemistry. This book was released on 2007-10-31 with total page 271 pages. Available in PDF, EPUB and Kindle. Book excerpt: The binding of antibiotics and drugs to DNA is a fast developing area of research with important applications in medicine, particularly the treatment of cancer. Sequence-specific DNA Binding Agents uniquely discusses key aspects of this topic, providing a novel perspective on the subject. Written by experts in the field, this book discusses diverse modes of binding of antibiotics and drugs to DNA, emphasising matters that are important or promising for cancer treatment. Chapters discuss established agents like actinomycin D but also look at novel drugs with strong potential in chemotherapy such as new topoisomerase inhibitors, telomerase inhibitors, peptide nucleic acids and triple helix-forming oligonucleotides. There are also sections discussing methodological advances including computational methods, slow kinetics, melting curve analysis and approaches to medicinal chemistry. Finally there is a section on RNA structure and its potential as a drug target. The book is ideal for researchers in industry and academia who require a comprehensive source of reference to this rapidly expanding subject.
Author : Bernhard Schölkopf
Publisher : MIT Press
ISBN 13 : 9780262195096
Total Pages : 428 pages
Book Rating : 4.1/5 (95 download)
Download or read book Kernel Methods in Computational Biology written by Bernhard Schölkopf and published by MIT Press. This book was released on 2004 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: A detailed overview of current research in kernel methods and their application to computational biology.
Author : Anandhakumar Chandran
Publisher : Springer
ISBN 13 : 9811065470
Total Pages : 123 pages
Book Rating : 4.8/5 (11 download)
Download or read book Advancing Development of Synthetic Gene Regulators written by Anandhakumar Chandran and published by Springer. This book was released on 2017-09-19 with total page 123 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on an “outside the box” notion by utilizing the powerful applications of next-generation sequencing (NGS) technologies in the interface of chemistry and biology. In personalized medicine, developing small molecules targeting a specific genomic sequence is an attractive goal. N-methylpyrrole (P)–N-methylimidazole (I) polyamides (PIPs) are a class of small molecule that can bind to the DNA minor groove. First, a cost-effective NGS (ion torrent platform)-based Bind-n-Seq was developed to identify the binding specificity of PIP conjugates in a randomized DNA library. Their biological influences rely primarily on selective DNA binding affinity, so it is important to analyze their genome-wide binding preferences. However, it is demanding to enrich specifically the small-molecule-bound DNA without chemical cross-linking or covalent binding in chromatinized genomes. Herein is described a method that was developed using high-throughput sequencing to map the differential binding sites and relative enriched regions of non-cross-linked SAHA-PIPs throughout the complex human genome. SAHA-PIPs binding motifs were identified and the genome-level mapping of SAHA-PIPs-enriched regions provided evidence for the differential activation of the gene network. A method using high-throughput sequencing to map the binding sites and relative enriched regions of alkylating PIP throughout the human genome was also developed. The genome-level mapping of alkylating the PIP-enriched region and the binding sites on the human genome identifies significant genomic targets of breast cancer. It is anticipated that this pioneering low-cost, high through-put investigation at the sequence-specific level will be helpful in understanding the binding specificity of various DNA-binding small molecules, which in turn will be beneficial for the development of small-molecule-based drugs targeting a genome-level sequence.
Author : P. Christine Ackroyd
Publisher :
ISBN 13 :
Total Pages : 502 pages
Book Rating : 4.3/5 (91 download)
Download or read book The Thermodynamic Sources of Affinity and Sequence-specificity written by P. Christine Ackroyd and published by . This book was released on 2001 with total page 502 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Arnold Revzin
Publisher : CRC Press
ISBN 13 : 9780849361777
Total Pages : 278 pages
Book Rating : 4.3/5 (617 download)
Download or read book The Biology of Nonspecific DNA Protein Interactions written by Arnold Revzin and published by CRC Press. This book was released on 1990-08-27 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: This important publication addresses the interactions of proteins with nonspecific binding sites on DNA as they play critical roles in fundamental cellular processes such as transcription, DNA replication, and recombination. The book presents current reviews of the biochemistry of representative nonspecific DNA-protein systems, and of their physiological functions. It includes chapters on the techniques used to characterize the complexes, on their thermodynamic properties, and on the role of nonspecific binding as gene regulatory proteins search for specific target sites on the chromosome. Systems considered include the effects of nonspecific binding in regulation of the lactose operon of Escherichia coli, the T4 bacteriophage gene 32 protein, the E. coli single strand binding (SSB) protein and recA protein, eukaryotic SSB's and histone-DNA complexes. The book presents those proteins displaying multiple modes of DNA binding as participants in more than one cellular process. This monograph combines rigorous descriptions of new findings for these important systems with provocative interpretations of the biological significance of the results. It is of great value to researchers ranging from graduate students to senior scientists in the areas of biochemistry, microbiology and molecular/cell biology.
Author : Chaitanya Rastogi
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (1 download)
Download or read book Accurate and Sensitive Quantification of Protein-DNA Binding Affinity written by Chaitanya Rastogi and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription factors control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in transcription factor binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here we developed a versatile maximum likelihood framework, named No Read Left Behind (NRLB), that fits a biophysical model of protein-DNA recognition to all in vitro selected DNA binding sites across the full affinity range. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. The model captures the specificity of p53 tetrameric binding sites and discovers multiple binding modes in a single sample. Additionally, we confirm that newly-identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes.
Author : Shiro Iuchi
Publisher : Springer Science & Business Media
ISBN 13 : 0387274219
Total Pages : 291 pages
Book Rating : 4.3/5 (872 download)
Download or read book Zinc Finger Proteins written by Shiro Iuchi and published by Springer Science & Business Media. This book was released on 2007-03-06 with total page 291 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the early 1980s, a few scientists started working on a Xenopus transcription factor, TFIIIA. They soon discovered a novel domain associated with zinc, and named this domain "zinc finger. " Th e number of proteins with similar zinc fingers grew quickly and these proteins are now called C2H2, Cys2His2 or classical zinc finger proteins. To date, about 24,000 C2H2 zinc finger proteins have been recognized. Approximately 700 human genes, or more than 2% of the genome, have been estimated to encode C2H2 finger proteins. From the beginning these proteins were thought to be numerous, but no one could have predicted such a huge number. Perhaps thousands of scientists are now working on C2H2 zinc finger proteins fi-om variou s viewpoints. This field is a good example of how a new science begins with the insight of a few scientists and how it develops by efforts of numerous independent scientists, in contrast to a policy-driven scientific project, such as the Human Genome Project, with goals clearly set at its inception and with work performed by a huge collaboration throughout the world. As more zinc finger proteins were discovered, several subfamilies, such as C2C2, CCHC, CCCH, LIM, RING, TAZ, and FYVE emerged, increasing our understanding of zinc fingers. The knowledge was overwhelming. Moreover, scientists began defining the term "zinc finger" differently and using various names for identical zinc fingers. These complications may explain why no single comprehensive resource of zinc finger proteins was available before this publication.
Author : Timothy R. Hughes
Publisher : Springer Science & Business Media
ISBN 13 : 904819069X
Total Pages : 310 pages
Book Rating : 4.0/5 (481 download)
Download or read book A Handbook of Transcription Factors written by Timothy R. Hughes and published by Springer Science & Business Media. This book was released on 2011-05-10 with total page 310 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription factors are the molecules that the cell uses to interpret the genome: they possess sequence-specific DNA-binding activity, and either directly or indirectly influence the transcription of genes. In aggregate, transcription factors control gene expression and genome organization, and play a pivotal role in many aspects of physiology and evolution. This book provides a reference for major aspects of transcription factor function, encompassing a general catalogue of known transcription factor classes, origins and evolution of specific transcription factor types, methods for studying transcription factor binding sites in vitro, in vivo, and in silico, and mechanisms of interaction with chromatin and RNA polymerase.
Author : Bruce Alberts
Publisher :
ISBN 13 : 9780815332183
Total Pages : 0 pages
Book Rating : 4.3/5 (321 download)
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Richard R. Sinden
Publisher : Elsevier
ISBN 13 : 0080571735
Total Pages : 423 pages
Book Rating : 4.0/5 (85 download)
Download or read book DNA Structure and Function written by Richard R. Sinden and published by Elsevier. This book was released on 2012-12-02 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA Structure and Function, a timely and comprehensive resource, is intended for any student or scientist interested in DNA structure and its biological implications. The book provides a simple yet comprehensive introduction to nearly all aspects of DNA structure. It also explains current ideas on the biological significance of classic and alternative DNA conformations. Suitable for graduate courses on DNA structure and nucleic acids, the text is also excellent supplemental reading for courses in general biochemistry, molecular biology, and genetics. Explains basic DNA Structure and function clearly and simply Contains up-to-date coverage of cruciforms, Z-DNA, triplex DNA, and other DNA conformations Discusses DNA-protein interactions, chromosomal organization, and biological implications of structure Highlights key experiments and ideas within boxed sections Illustrated with 150 diagrams and figures that convey structural and experimental concepts
Author : Victor A. Bloomfield
Publisher : Sterling Publishing Company
ISBN 13 : 9780935702491
Total Pages : 854 pages
Book Rating : 4.7/5 (24 download)
Download or read book Nucleic Acids written by Victor A. Bloomfield and published by Sterling Publishing Company. This book was released on 2000-04-17 with total page 854 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text has been organized to meet the needs of those who have only a basic understanding of physical chemistry and molecular biology.
Author : John Andrew Hawkins
Publisher :
ISBN 13 :
Total Pages : 282 pages
Book Rating : 4.:/5 (119 download)
Download or read book Investigations in Integrative and Molecular Bioscience written by John Andrew Hawkins and published by . This book was released on 2018 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern biology is going through a revolution of new methods and insights resulting from the new availability of high-throughput DNA sequencing technology. I here present work contributing mathematical and computational methods for gaining insight from large DNA sequencing data sets at three distinct levels. First, I present a method for improving the accuracy and efficiency of DNA barcodes, short sequences of DNA used to label individual molecules in pooled samples. Many DNA sequencing applications depend on the use of DNA barcodes. However, errors in DNA synthesis and sequencing--substitutions, insertions, and deletions--confound the correct interpretation of these barcodes. I here present Filled/truncated Right End Edit (FREE) barcodes designed for barcode error-correction in the context of a downstream sequence. Second, I present the Chip-Hybridized Affinity Mapping Platform (CHAMP), a novel technology for repurposing used DNA sequencing chips to study the mechanism and sequence preferences of DNA-binding proteins. Since 2012, the CRISPR family of proteins have gained wide application for their efficiency and ease of use in editing genomes in vivo. Using CHAMP, I, in collaboration with experimentalists in Ilya Finkelstein's lab, investigated the mechanism and sequence preference of the CRISPR Cascade complex, and discovered a novel periodic lack of sequence specificity in DNA binding. I further determined specific nucleotides important for recruitment of and processing by the nuclease domain, Cas3. Third, I present a meta-analysis of the order Chiroptera, the order of bats, using the new wealth of DNA sequence information of eighteen bat species. The transcriptome sequencing data for two of these bats--Hypsignathus monstrosus and Rousettus aegyptiacus, bats associated with studies of the Ebola and Marburg viruses respectively-- is novel to this study. Using all this DNA sequence information, I reconstructed a high- confidence Chiropteran phylogeny and found 299 genes with signatures of positive selection, a signature associated with viral antagonism. Further study of these genes may shed light on the mechanism through which several bat viruses relevant to human health hijack the cell, including SARS, Ebola, Hendra, and Nipah
