Download or read book Single Molecule Fluorescence Studies of the RNA Polymerase II Elongation Complex written by Joanna Andrecka and published by . This book was released on 2009 with total page 112 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book RNA Polymerases as Molecular Motors written by Henri C. Buc and published by Royal Society of Chemistry. This book was released on 2009-04-16 with total page 353 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book, written by expert scientists in the field, analyses how these diverse fields of research interact on a specific example - RNA polymerase. The book concentrates on RNA polymerases because they play a central role among all the other machines operating in the cell and are the target of a wide range of regulatory mechanisms. They have also been the subject of spectacular advances in their structural understanding in recent years, as testified by the attribution of the Nobel prize in chemistry in 2006 to Roger Kornberg. The book focuses on two aspects of the transcription cycle that have been more intensively studied thanks to this increased scientific cooperation - the recognition of the promoter by the enzyme, and the achievement of consecutive translocation steps during elongation of the RNA product. Each of these two topics is introduced by an overview, and is then presented by worldwide experts in the field, taking the viewpoint of their specialty. The overview chapters focus on the mechanism-structure interface and the structure-machine interface while the individual chapters within each section concentrate more specifically on particular processes-kinetic analysis, single-molecule spectroscopy, and termination of transcription, amongst others. Specific attention has been paid to the newcomers in the field, with careful descriptions of new emerging techniques and the constitution of an atlas of three-dimensional pictures of the enzymes involved.
Download or read book Single molecule Studies of Different Steps in Human RNA Polymerase II and Bacterial RNA Polymerase Transcription written by Yazan Khalaf Alhadid and published by . This book was released on 2018 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription of genomic DNA of all organisms is carried out by members of the multi-subunit RNA polymerase family. Regulation of RNA polymerase localization and activity underlies cellular homeostasis, division, and response to environmental cues. The catalytic mechanism, overall architecture, and many sequence and structural features of bacterial RNA polymerase are conserved in its Archaeal and Eukaryotic counterparts. The human RNA polymerase II (Pol II) is responsible for transcription of all protein-coding and many non-coding genes. The majority of current knowledge on RNA polymerases and their mechanism at different steps in transcription derives from extensive work done using classical biochemical, genetic and structural biology methods. However, the use of single-molecule approaches addressed crucial questions on the function and mechanism of RNA polymerases during transcription, which were not possible to answer with ensemble-based approaches due to averaging effects. A useful fluorescence-based single-molecule technique to measure distances on the molecular scale and monitor dynamics is F rster resonance energy transfer (FRET). Here, I report on the development of diffusion-based single-molecule FRET (smFRET) methods to investigate different steps in transcription by the in vitro reconstituted human Pol II system. Using an assay that monitors the FRET changes between fluorescent dyes in the unwound region of promoter DNA (transcription bubble), I demonstrated the effect of certain components of the reconstituted system on the relative size of the transcription bubble. I also detail the optimizations done to enhance the affinity of single-stranded DNA (ssDNA) FRET probes to complementary target sequences. These ssDNA FRET probes were used to investigate the effect of certain components of the reconstituted system on Pol II activity by measuring the relative levels of RNA product. In addition to studies on the Pol II system, I report on the effect of the 5'-group of nascent RNA on the stability of the Escherichia coli RNA polymerase (RNAP) transcription bubble. I show how the presence of a 5'-monophosphate appears to destabilize the open bubble while a 5'-hydroxyl has no effect. Finally, I describe the work done on a project I took part in that identified a previously uncharacterized RNAP paused complex in initiation. We demonstrate that RNAP complexes undergoing initial transcription can enter the inactive paused state by backtracking. I also demonstrate how the presence of a 5'-triphosphate rapidly enhances entrance of RNAP complexes undergoing initial transcription into an inactive paused complex.
Download or read book Single molecule Fluorescence Analysis of Opening and Closing of the RNA Polymerase Clamp written by Anirban Chakraborty and published by . This book was released on 2013 with total page 111 pages. Available in PDF, EPUB and Kindle. Book excerpt: Crystal structures of RNA polymerase (RNAP) indicate that the RNAP [beta]' pincer ("clamp") can exist in conformational states, ranging from a fully open conformation that permits entry and exit of DNA, to a fully closed conformation that prevents entry and exit of DNA. It has been hypothesized that the clamp also adopts multiple conformational states in solution and conformational changes in the clamp are important for function. In this work, a single-molecule fluorescence resonance energy transfer (smFRET) approach was developed that enables determination of RNAPclamp conformation in solution. smFRET was measured between a probe at the tip of the RNAP clamp and a probe at a fixed reference point in RNAP. A computational framework was then employed to interpret measured FRET efficiencies in terms of structural changes. Using this approach, RNAP clamp conformation was defined in each step of?70-dependent transcription initiation and elongation and in each step in?54-dependent transcription initiation. Additionally, effects of four RNAP inhibitors, myxopyronin, corallopyronin, ripostatin and Gp2 on RNAP clamp conformation were assessed. It was observed that the clamp is predominantly open in free RNAP and in all steps leading up to the formation of a catalytically-competent-transcription-initiation complex. Upon formation of a catalytically-competent-transcription-initiation complex, the clamp closes, and continues to remain closed during transcription elongation. It was further observed that myxopyronin, corallopyronin, ripostatin and Gp2, prevent opening of the RNAP clamp. The results lead to the proposal that, the open clamp state is important for entry of DNA into, and unwinding of DNA in, the RNAP active center cleft during formation of a catalytically-competent-transcription initiation complex. The results lead to the proposal that, after entry of DNA into the RNAP active-center cleft upon formation of the catalytically competent transcription initiation complex, electrostatic interactions between the negatively charged DNA and the positively charged inner facet of the clamp, induce and/or stabilize clamp closure. The results are in agreement with the proposal that, clamp closure is important for stability of the catalytically competent transcription initiation complex and for stability and processivity of the transcription elongation complex.
Download or read book RNA as Molecular Motors 2E written by Robert Landick and published by Royal Society of Chemistry. This book was released on 2021-12-15 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book, written by expert scientists in the field, analyses how these diverse fields of research interact on a specific example - RNA polymerase.
Download or read book Macromolecular Protein Complexes written by J. Robin Harris and published by Springer. This book was released on 2017-03-07 with total page 571 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume of the established Subcellular Biochemistry series presents 20 chapters dealing with a broad range of interesting protein complexes. It will enable researchers to readily appreciate the major contribution from both X-ray crystallography and cryo-electron microscopy in this field of study. The biological significance of these structural studies is emphasised throughout the book. The diversity of the material included here indicates the breadth of this field and the tremendous progress that has been made in recent years. The book is directed primarily to advanced students and researchers in structural biology, and others in the biochemical sciences. It will be supplemented by other related books within the Subcellular Biochemistry series. One of the Editors (JM-W) is actively involved in structural biology and the other (JRH), as a retired academic and the Series Editor of Subcellular Biochemistry, has long experience at editing multi-author books./div
Download or read book RNA Polymerase and Associated Factors Part D written by Sankar Adhya and published by Elsevier. This book was released on 2003-12-18 with total page 715 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA polymerase is molecule important to gene transcription. Along with associated factors, RNA polymerase is part of the process in which RNA is transcribed to produce a protein.* Models and methods for studying polymerase translocation* Assay for movements of RNA polymerase along DNA* Engineering of elongation complexes of bacterial and yeast RNA polymerases
Download or read book Biochemical and Molecular Genetic Studies of the RNA Polymerase II Elongation Complex written by Wade Powell and published by . This book was released on 1997 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Single molecule Measurements of Transcript Elongation and Termination by RNA Polymerase written by Matthew Herbert Larson and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription by RNAP is highly regulated in both prokaryotic and eukaryotic cells, and the ability of the cell to differentiate and respond to its environment is largely due to this regulation. During elongation, for example, RNAP is known to momentarily halt in response to certain cellular signals, and this pause state has been implicated in the regulation of gene expression in both prokaryotic and eukaryotic organisms. In addition, once RNAP reaches the end of a gene, it must reliably terminate and release the newly-transcribed RNA, providing another potential point of regulation within different cell types. Both of these steps are crucial to ensure proper gene expression. In this dissertation, I focus on transcription elongation by both prokaryotic and eukaryotic RNA polymerases, as well as their regulation through pausing and termination. To probe the role of RNA hairpins in transcriptional pausing, a novel single-molecule "RNA-pulling" assay was used to block the formation of secondary structure in the nascent transcript. Force along the RNA did not significantly affect transcription elongation rates, pause frequencies, or pause lifetimes, indicating that short "ubiquitous" pauses are not a consequence of RNA hairpins. Force-based single-molecule techniques were also used to study the mechanism and energetics of transcription termination in bacteria. The data suggest two separate mechanisms for termination: one that involves hypertranslocation of RNAP along the DNA, and one that involves shearing of the RNA:DNA hybrid within the enzyme. In addition, a quantitative energetic model is presented that successfully predicts the termination efficiency of both wild-type and mutant terminators. Finally, the implementation of a novel optical-trapping assay capable of directly observing transcription by eukaryotic RNA polymerase II (RNAPII) molecules is described. This approach was used to probe the RNAPII nucleotide-addition cycle, as well as the role of the trigger loop (a conserved subdomain) in elongation. The results are consistent with a Brownian ratchet model of elongation which incorporates a secondary NTP binding site, and the trigger loop was found to modulate translocation, NTP binding, and catalysis, as well as substrate selection and mismatch recognition by RNAPII.
Download or read book RNA Structure and Folding written by Dagmar Klostermeier and published by Walter de Gruyter. This book was released on 2013-10-14 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: While structure-function relationships of proteins have been studied for a long time, structural studies of RNA face additional challenges. Nevertheless, with the continuous discovery of novel RNA molecules with key cellular functions and of novel pathways and interaction networks, the need for structural information of RNA is still increasing. This volume provides an introduction into techniques to assess structure and folding of RNA. Each chapter explains the theoretical background of one technique, and illustrates possibilities and limitations in selected application examples.
Download or read book Single Particle Tracking and Single Molecule Energy Transfer written by Christoph Bräuchle and published by John Wiley & Sons. This book was released on 2009-10-30 with total page 359 pages. Available in PDF, EPUB and Kindle. Book excerpt: Closing a gap in the literature, this handbook gathers all the information on single particle tracking and single molecule energy transfer. It covers all aspects of this hot and modern topic, from detecting virus entry to membrane diffusion, and from protein folding using spFRET to coupled dye systems, as well recent achievements in the field. Throughout, the first-class editors and top international authors present content of the highest quality, making this a must-have for physical chemists, spectroscopists, molecular physicists and biochemists.
Download or read book The Mechanics of Transcription by RNA Polymerase written by Elio Aaron Abbondanzieri and published by . This book was released on 2005 with total page 164 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Lewin s GENES X written by Jocelyn E. Krebs and published by Jones & Bartlett Publishers. This book was released on 2009-12-07 with total page 958 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lewin's GENES X features informative new chapters, as well as a reorganization of material, provides a more logical flow of topics and many chapters have been renamed to better indicate their contents. Lewin's GENES X also contains new pedagogical features to help students learn as they read and an online student study guide allows students to test themselves on key material. Important Notice: The digital edition of this book is missing some of the images or content found in the physical edition.
Download or read book Mechanisms of Transcription written by Kirill Konovalov and published by . This book was released on 2021 with total page 96 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Biophysics of RNA Protein Interactions written by Chirlmin Joo and published by Springer Nature. This book was released on 2019-09-19 with total page 249 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA molecules play key roles in all aspects of cellular life, but to do so efficiently, they must work in synergism with proteins. This book addresses how proteins and RNA interact to carry out biological functions such as protein synthesis, regulation of gene expression, genome defense, liquid phase separation and more. The topics addressed in this volume will appeal to researchers in biophysics, biochemistry and structural biology. The book is a useful resource for anybody interested in elucidating the molecular mechanisms and discrete properties of RNA-protein complexes. Included are reviews of key systems such as microRNA and CRISPR/Cas that exemplify how RNA and proteins work together to perform their biological function. Also covered are techniques ranging from single molecule fluorescence and force spectroscopy to crystallography, cryo-EM microscopy, and kinetic modeling.
Download or read book Single Molecule Studies of Bacterial RNA Polymerase Dynamics written by Timothy T. Harden and published by . This book was released on 2016 with total page 107 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Machines in Biology written by Joachim Frank and published by Cambridge University Press. This book was released on 2011-12-19 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: The concept of molecular machines in biology has transformed the medical field in a profound way. Many essential processes that occur in the cell, including transcription, translation, protein folding and protein degradation, are all carried out by molecular machines. This volume focuses on important molecular machines whose architecture is known and whose functional principles have been established by tools of biophysical imaging (X-ray crystallography and cryo-electron microscopy) and fluorescence probing (single-molecule FRET). This edited volume includes contributions from prominent scientists and researchers who understand and have explored the structure and functions of these machines. This book is essential for students and professionals in the medical field who want to learn more about molecular machines.
