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Author : Jeffrey Robert Vieregg
Publisher :
ISBN 13 :
Total Pages : 468 pages
Book Rating : 4.:/5 (35 download)
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:
Author : Peter Caton Anthony
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (689 download)
Download or read book Single-molecule Studies of Nucleic Acid Folding written by Peter Caton Anthony and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Nucleic acids--DNA and RNA--are critical to life, involved in the storage and decoding of genetic information in the cell as well as the regulation and catalysis of specific biological processes. The function of a nucleic acid molecule is determined in large part by the structure it adopts, which in turn depends on its sequence. The mechanisms of sequence-directed nucleic acid folding remain incompletely understood, particularly for large RNA molecules. The work presented in this thesis uses single-molecule optical-trapping techniques to study nucleic acid folding, where reversible folding is induced and measured in individual molecules through the application of force. In Chapter 2 we demonstrate direct measurement of the full folding energy landscapes of DNA hairpins, which comprise a model system for studying nucleic acid secondary structure, and show how such landscapes are sensitive to sequence. In Chapter 3 we study the electrostatics of DNA hairpin folding by measuring trends in folding energies under different ionic conditions and comparing these trends with those predicted by Poisson-Boltzmann theory. Finally, in Chapter 4 we examine folding of the TPP riboswitch aptamer, an RNA molecule with complex secondary structure that also adopts tertiary structure upon binding a small-molecule ligand. We measured the folding energy landscape of the aptamer and perturbations of this landscape resulting from mutations and ligand binding, and propose a kinetic model to describe the coupling between aptamer folding and ligand binding. Taken together, the results presented here demonstrate the usefulness of the energy landscape framework for characterizing nucleic acid folding in conjunction with single-molecule measurements.
Author : Kristina Marie Herbert
Publisher :
ISBN 13 :
Total Pages : 205 pages
Book Rating : 4.:/5 (269 download)
Download or read book Sequence Dependent Pausing by RNA Polymerase written by Kristina Marie Herbert and published by . This book was released on 2007 with total page 205 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Andres F. Oberhauser
Publisher : Springer Science & Business Media
ISBN 13 : 1461449219
Total Pages : 283 pages
Book Rating : 4.4/5 (614 download)
Download or read book Single-molecule Studies of Proteins written by Andres F. Oberhauser and published by Springer Science & Business Media. This book was released on 2012-11-09 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Single Molecule Studies of Proteins, expert researchers discuss the successful application of single-molecule techniques to a wide range of biological events, such as the imaging and mapping of cell surface receptors, the analysis of the unfolding and folding pathways of single proteins, the analysis interaction forces between biomolecules, the study of enzyme catalysis or the visualization of molecular motors in action. The chapters are aimed at established investigators and post-doctoral researchers in the life sciences wanting to pursue research in the various areas in which single-molecule approaches are important; this volume also remains accessible to advanced graduate students seeking similar research goals.
Author : Paul R. Selvin
Publisher : CSHL Press
ISBN 13 : 087969775X
Total Pages : 511 pages
Book Rating : 4.8/5 (796 download)
Download or read book Single-molecule Techniques written by Paul R. Selvin and published by CSHL Press. This book was released on 2008 with total page 511 pages. Available in PDF, EPUB and Kindle. Book excerpt: Geared towards research scientists in structural and molecular biology, biochemistry, and biophysics, this manual will be useful to all who are interested in observing, manipulating and elucidating the molecular mechanisms and discrete properties of macromolecules.
Author : Christian Francisco Perez
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (889 download)
Download or read book Combined Optical Trapping and Sm-FRET for Nucleic Acid Folding Studies written by Christian Francisco Perez and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: By studying ancient RNA motifs found in all kingdoms of life, we are also looking back in time to a common evolutionary ancestor. Riboswitches and ribozymes are structured RNAs capable of gene regulation and catalysis. Their surprising catalytic/functional diversity and prevalence across species hints at an "RNA World" that predates our current paradigm which depends on DNA for information and protein for catalysis. The TPP riboswitch is an ancient ligand-binding RNA that regulates vitamin B1 (TPP) synthesis in bacteria, archaea, and even higher organisms like plants. Using single molecule optical trapping (OT) and the judicious application of piconewton forces, we have studied the folding pathways of the riboswitch and its response to TPP and other analogues. Ligand binding appears to form in two steps: TPP must first bind weakly before proceeding to a strongly bound state, as measured by the non-equilibrium work required to unfold it. To probe the physical origin of these states, we use a novel dual-beam optical trap combined with simultaneous FRET that can measure two orthogonal signals of the molecule's conformation. We demonstrate the direct observation of both the unfolding of secondary (base-paired) structures (via OT) and long-range tertiary contacts (via FRET) that form during ligand binding. In time, we anticipate this technique will become a sought-after tool that can expose the intricate folding pathways of complex biomolecules.
Author : Krishnarao Appasani
Publisher :
ISBN 13 : 110853449X
Total Pages : 172 pages
Book Rating : 4.1/5 (85 download)
Download or read book Single-Molecule Science written by Krishnarao Appasani and published by . This book was released on 2022-05-11 with total page 172 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive volume that brings together authoritative overviews of single molecule science techniques from a biological perspective.
Author : Dagmar Klostermeier
Publisher : Walter de Gruyter
ISBN 13 : 3110284952
Total Pages : 432 pages
Book Rating : 4.1/5 (12 download)
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.
Author : William James Greenleaf
Publisher :
ISBN 13 :
Total Pages : 296 pages
Book Rating : 4.F/5 ( download)
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:
Author : Iddo Heller
Publisher : Springer Nature
ISBN 13 : 1071633775
Total Pages : 511 pages
Book Rating : 4.0/5 (716 download)
Download or read book Single Molecule Analysis written by Iddo Heller and published by Springer Nature. This book was released on 2023-11-13 with total page 511 pages. Available in PDF, EPUB and Kindle. Book excerpt: This third edition volume expands on the previous editions with new discussions on the latest techniques and developments in the field. The chapters in this book are organized into four parts, and cover topics such as optical tweezers; single-molecule fluorescence tools; atomic force microscopy; magnetic tweezers; applications to virus protein shells, unfolding of proteins, nucleic acids, motor proteins, in vivo and in vitro; and protocols to establish specific surface interactions and perform force calibration. Written in the highly successful Methods in Molecular Biology series format, 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. Cutting-edge and thorough, Single Molecule Analysis: Methods and Protocols, Third Edition is a valuable resource for all researchers who want to learn more about this exciting and still expanding field. Chapters 2, 7, 8, 9, 12, 18, and 19 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Author : Arthur Ashkin
Publisher : World Scientific
ISBN 13 : 9814494348
Total Pages : 941 pages
Book Rating : 4.8/5 (144 download)
Download or read book Optical Trapping And Manipulation Of Neutral Particles Using Lasers: A Reprint Volume With Commentaries written by Arthur Ashkin and published by World Scientific. This book was released on 2006-12-29 with total page 941 pages. Available in PDF, EPUB and Kindle. Book excerpt: This important volume contains selected papers and extensive commentaries on laser trapping and manipulation of neutral particles using radiation pressure forces. Such techniques apply to a variety of small particles, such as atoms, molecules, macroscopic dielectric particles, living cells, and organelles within cells. These optical methods have had a revolutionary impact on the fields of atomic and molecular physics, biophysics, and many aspects of nanotechnology.In atomic physics, the trapping and cooling of atoms down to nanokelvins and even picokelvin temperatures are possible. These are the lowest temperatures in the universe. This made possible the first demonstration of Bose-Einstein condensation of atomic and molecular vapors. Some of the applications are high precision atomic clocks, gyroscopes, the measurement of gravity, cryptology, atomic computers, cavity quantum electrodynamics and coherent atom lasers.A major application in biophysics is the study of the mechanical properties of the many types of motor molecules, mechanoenzymes, and other macromolecules responsible for the motion of organelles within cells and the locomotion of entire cells. Unique in vitro and in vivo assays study the driving forces, stepping motion, kinetics, and efficiency of these motors as they move along the cell's cytoskeleton. Positional and temporal resolutions have been achieved, making possible the study of RNA and DNA polymerases, as they undergo their various copying, backtracking, and error correcting functions on a single base pair basis.Many applications in nanotechnology involve particle and cell sorting, particle rotation, microfabrication of simple machines, microfluidics, and other micrometer devices. The number of applications continues to grow at a rapid rate.The author is the discoverer of optical trapping and optical tweezers. With his colleagues, he first demonstrated optical levitation, the trapping of atoms, and tweezer trapping and manipulation of living cells and biological particles.This is the only review volume covering the many fields of optical trapping and manipulation. The intention is to provide a selective guide to the literature and to teach how optical traps really work.
Author : Daniel Foster
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (52 download)
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:
Author : Arne Gennerich
Publisher : Humana
ISBN 13 : 9781493964192
Total Pages : 0 pages
Book Rating : 4.9/5 (641 download)
Download or read book Optical Tweezers written by Arne Gennerich and published by Humana. This book was released on 2016-11-15 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this volume is to provide a comprehensive overview of optical tweezers setups, both in practical and theoretical terms, to help biophysicists, biochemists, and cell biologists to build and calibrate their own instruments and to perform force measurements on mechanoenzymes both in isolation in vitro and in living cells. Chapters have been divided in three parts focusing on theory and practical design of optical tweezers, detailed protocols for performing force measurements on single DNA- and microtubule/actin-associated mechanoenzymes in isolation, and describing recent advances that have opened up quantitative force measurements in living cells. Written in the highly successful Methods in Molecular Biology series format, 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 cutting-edge, Optical Tweezers: Methods and Protocols aims help to further expand the accessibility and use of optical traps by scientists of diverse disciplines.
Author : Peixuan Guo
Publisher : CRC Press
ISBN 13 : 1466505664
Total Pages : 614 pages
Book Rating : 4.4/5 (665 download)
Download or read book RNA Nanotechnology and Therapeutics written by Peixuan Guo and published by CRC Press. This book was released on 2013-07-09 with total page 614 pages. Available in PDF, EPUB and Kindle. Book excerpt: Interest in RNA nanotechnology has increased in recent years as recognition of its potential for applications in nanomedicine has grown. Edited by the world's foremost experts in nanomedicine, this comprehensive, state-of-the-art reference details the latest research developments and challenges in the biophysical and single molecule approaches in RNA nanotechnology. In addition, the text also provides in-depth discussions of RNA structure for nanoparticle construction, RNA computation and modeling, single molecule imaging of RNA, RNA nanoparticle assembly, RNA nanoparticles in therapeutics, RNA chemistry for nanoparticle synthesis, and conjugation and labeling.
Author : Kirsten Linnea Frieda
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (86 download)
Download or read book Single-molecule Studies of RNA Conformations and Cotranscriptional Folding in Adenine Riboswitches written by Kirsten Linnea Frieda and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA--a ubiquitous and versatile type of biopolymer that is critically involved in many of life's molecular processes--is produced sequentially in single-stranded form during transcription by RNA polymerase and has the propensity to fold back on itself into interesting structures of functional import. In nature, riboswitches are elegant examples of structured RNA that adopt alternate conformations in response to ligand binding and thereby affect gene expression. We have been able to probe riboswitch conformations in novel detail using single-molecule optical-trapping techniques. These experimental approaches supply a unique perspective on folding since the ability to apply force provides an effective handle on the real-time state of individual RNA molecules and a means of modulating that state. In this dissertation, I focus on three studies that explore adenine riboswitch conformations and mechanisms. Specifically, in the first, we dissect the folding landscape of the aptamer (ligand-binding domain) of an adenine riboswitch. Extending this endeavor to full riboswitch sequences, we probe the interplay of a riboswitch aptamer with its downstream expression platform (which executes the switch's regulatory role), and develop methods to do so both during and after transcription. The second study takes full advantage of the latter ability: In a complete adenine riboswitch controlling transcription, we directly observe cotranscriptional folding of the nascent RNA in which the adopted conformation dictates whether or not to terminate transcription. Finally, in a different adenine riboswitch controlling translation, we investigate switch conformational changes and identify a series of competing structural elements that kinetically trap the riboswitch conformation, implying that the initial, cotranscriptional fold of the riboswitch may determine its gene regulatory state. These efforts enhance our understanding of folding architectures in riboswitches, specifically, and in RNA, more broadly. They further highlight the importance of cotranscriptional folding, providing a novel window into the nascent development of RNA conformations.
Author : Miles J. Padgett
Publisher : CRC Press
ISBN 13 : 1420074148
Total Pages : 510 pages
Book Rating : 4.4/5 (2 download)
Download or read book Optical Tweezers written by Miles J. Padgett and published by CRC Press. This book was released on 2010-06-02 with total page 510 pages. Available in PDF, EPUB and Kindle. Book excerpt: The technical development of optical tweezers, along with their application in the biological and physical sciences, has progressed significantly since the demonstration of an optical trap for micron-sized particles based on a single, tightly focused laser beam was first reported more than twenty years ago. Bringing together many landmark papers on
Author : Shuo Huang
Publisher : CRC Press
ISBN 13 : 100040921X
Total Pages : 238 pages
Book Rating : 4.0/5 (4 download)
Download or read book Single-Molecule Tools for Bioanalysis written by Shuo Huang and published by CRC Press. This book was released on 2022-05-25 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last three decades, the fast development of single-molecule techniques has revolutionized the way we observe and understand biological processes. Some of these techniques have been further adapted as tools for bioanalysis. This book summarizes and details the frontiers of the development of these tools as well as their applications. The contributors are young and established researchers in their respective fields. The main content originates from the lecture notes of a chemistry graduate course taught by the book editor at Nanjing University. This book is suitable to be used as a textbook for a high-level undergraduate or an entry-level graduate course. The systematically written content provides a thorough illustration of the mechanisms of each methodology presented.
