Download or read book High resolution Single molecule Measurements of Transcription and RNA Folding written by William James Greenleaf and published by . This book was released on 2007 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Biophysics of RNA Folding written by Rick Russell and published by Springer Science & Business Media. This book was released on 2012-12-09 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume, written by experts in the field, discusses the current understanding of the biophysical principles that govern RNA folding, with featured RNAs including the ribosomal RNAs, viral RNAs, and self-splicing introns. In addition to the fundamental features of RNA folding, the central experimental and computational approaches in the field are presented with an emphasis on their individual strengths and limitations, and how they can be combined to be more powerful than any method alone; these approaches include NMR, single molecule fluorescence, site-directed spin labeling, structure mapping, comparative sequence analysis, graph theory, course-grained 3D modeling, and more. This volume will be of interest to professional researchers and advanced students entering the field of RNA folding.
Download or read book Visualising RNA Folding Dynamics in Crowded Environments and with Single molecule Resolution written by Bishnu Paudel and published by . This book was released on 2015 with total page 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 An Introduction to Single Molecule Biophysics written by Yuri L. Lyubchenko and published by CRC Press. This book was released on 2017-11-22 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book gives an accessible, detailed overview on techniques of single molecule biophysics (SMB), showing how they are applied to numerous biological problems associated with understanding the molecular mechanisms of DNA replication, transcription, and translation, as well as functioning of molecular machines. It covers major single molecule imaging and probing techniques, highlighting key strengths and limitations of each method using recent examples. The chapters begin with a discussion of single molecule fluorescence techniques followed by an overview of the atomic force microscope and its use for direct time-lapse visualization of dynamics of molecular complexes at the nanoscale, as well as applications in measurements of interactions between molecules and mechanical properties of isolated molecules and their complexes. The next chapters address magnetic tweezers and optical tweezers, including instrumentation, fundamentals of operation, and applications. A final chapter turns to nanopore transport and nanopore-based DNA sequencing technology that will play a major role in next-generation genomics and healthcare applications.
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 Protein and RNA Folding from Bulk Towards High Throughput Single Molecule Experiments written by Krishnarjun Sarkar and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Single Molecule RNA Folding Studied with Optical Trapping written by Jeffrey Robert Vieregg and published by . This book was released on 2007 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Handbook of Single Molecule Biophysics written by Peter Hinterdorfer and published by Springer Science & Business Media. This book was released on 2009-12-24 with total page 634 pages. Available in PDF, EPUB and Kindle. Book excerpt: This handbook describes experimental techniques to monitor and manipulate individual biomolecules, including fluorescence detection, atomic force microscopy, and optical and magnetic trapping. It includes single-molecule studies of physical properties of biomolecules such as folding, polymer physics of protein and DNA, enzymology and biochemistry, single molecules in the membrane, and single-molecule techniques in living cells.
Download or read book Single Molecule Enzymology Fluorescence Based and High Throughput Methods written by and published by Academic Press. This book was released on 2016-10-28 with total page 618 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-Molecule Enzymology, Part A, the latest volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in single-molecule enzymology, and includes sections on such topics as force-based and hybrid approaches, fluorescence, high-throughput sm enzymology, nanopores, and tethered particle motion. - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers research methods in single-molecule enzymology - Contains sections on such topics as force-based and hybrid approaches, fluorescence, high-throughput sm enzymology, nanopores, and tethered particle motion
Download or read book High Resolution Optical Tweezers for Single Molecule Studies of Hierarchical Folding in the PbuE Riboswitch Aptamer written by Daniel Foster and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Imaging Life written by Gary C. Howard and published by Oxford University Press, USA. This book was released on 2014 with total page 505 pages. Available in PDF, EPUB and Kindle. Book excerpt: An overview to the many types of modern biological image analysis.
Download or read book Single molecule Fluorescence Studies of RNA Folding and Protein nucleic Acid Assembly written by Gregory Edward Bokinsky and published by . This book was released on 2007 with total page 136 pages. Available in PDF, EPUB and Kindle. Book excerpt: Our studies of RNA folding examined the minimal hairpin ribozyme, a system that exhibits a simple two-state behavior. By monitoring the folding and unfolding rates of several mutants and with metal ion titrations, we have developed a coarse-grained picture of an elementary RNA folding transition state. We found that the transition state structure is very compact and stabilized by electrostatic interactions, though native tertiary contacts are either lacking entirely or only partially formed.
Download or read book Integrating Timescales from Molecules Up written by Rene A. Nome and published by Frontiers Media SA. This book was released on 2021-06-04 with total page 83 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book RNA Chaperones written by Tilman Heise and published by . This book was released on 2020 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a wide spectrum of methods to study RNA chaperones in vitro, at the single molecule level, and protocols useful for cell-based assays. Beginning with a section on a number of bacterial proteins for study, the volume also explores proteins from eukaryotic cells and how to delve into the complex interactions between RNA chaperones and the folding and unfolding of proteins. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, RNA Chaperones: Methods and Protocols serves as an ideal guide for scientists and students interested in RNA biology and RNA chaperones. Chapter 3 is available Open Access under a CC-BY 4.0 license via link.springer.com.
Download or read book Mechanisms of Transcription written by Bruce Stillman and published by CSHL Press. This book was released on 1998 with total page 724 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proceedings of a summer 1998 meeting, presenting results of recent studies in gene transcription. Covers events ranging from activation, through promoter recognition, repression, chromosome structure, chromatin remodeling, initiation and elongation, and regulatory complexes and pathways. Subjects include targeting sir proteins to sites of action, the yeast RNA polymerase III transcription machinery, nuclear matrix attachment regions to confer long-range function on immunoglobulin, ATP-dependent remodeling of chromatin, and the transcriptional basis of steroid physiology. Annotation copyrighted by Book News, Inc., Portland, OR.
Download or read book Single molecule Studies on Transcriptional Elongation in Prokaryotes and Eukaryotes written by Jing Zhou and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription, the process of copying genetic information stored in DNA into RNA, is fundamental to life. It is carried out by an extraordinary nano-machine called RNA polymerase (RNAP). Transcriptional elongation, during which RNAP moves along the DNA, adding one nucleotide at a time to the RNA transcript, is highly dynamic and regulated. The motion of RNAP is discontinuous and interrupted by pauses that play an essential role in gene regulation. Fundamental questions regarding the mechanisms of elongation and its modulation by transcription factors, however, remain unclear. In this dissertation, I focus on using high-resolution, optical trapping techniques to study the mechanisms of transcriptional elongation by both prokaryotic and eukaryotic RNA polymerases at the single-molecule level. First, I describe the studies on how the motion of single E.coli RNAP molecules is modulated by two universally conserved, essential transcription factors (NusA and NusG). From individual transcriptional elongation records, the rates of entering pause states, the pause state lifetimes, and the pause-free elongation speeds can all be extracted. By studying the effects of NusA (and NusG) on these kinetic rates as a function of the applied load, we were able to develop a quantitative kinetic scheme for elongation and pausing. This model not only explains the functions of NusA/NusG, but also provides insight into the mechanism of transcriptional pausing, which had previously been controversial. Second, a novel optical-trapping assay capable of directly probing elongation by individual eukaryotic RNA polymerase II (RNAPII) molecules will be described. We find that the RNAPII trigger loop, an evolutionarily conserved protein subdomain, not only affects each of the three main phases of elongation, namely: substrate binding, translocation, and catalysis; but also plays a critical role in controlling the fidelity of transcription. Our data also support a Brownian ratchet model for elongation which incorporates a secondary nucleotide binding site.
