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Single Molecule Spectroscopy For Studying Conformational Dynamics Of Short Oligonucleotides
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Book Synopsis Single Molecule Spectroscopy for Studying Conformational Dynamics of Short Oligonucleotides by : Ron Reuven Lin
Download or read book Single Molecule Spectroscopy for Studying Conformational Dynamics of Short Oligonucleotides written by Ron Reuven Lin and published by . This book was released on 2012 with total page 66 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding biology at the molecular level has been driving technological advances in biological and medical science for many years. Methods for probing molecular systems are often dependent on sampling the concerted actions of large assemblies of molecules rather than for studying individual molecules operating in isolation. Most methods used in experimental biology are largely insensitive to the activity of a single molecule. Over the past twenty five years, advances in a variety of disciplines have been employed which allow researchers to use single molecule approaches to for examining biomolecules, a development which has had remarkable implications for advancing the understanding of cellular processes. Single molecule techniques have been used to resolve questions about everything from replication, recombination, transcription and translation and protein folding, among other subjects. The structure-function relationship in biology is central to the understanding of cellular processes, and has provided one of the most significant intellectual frameworks for understanding molecular pathways. Its success is validated by numerous studies using X-ray crystallography that now routinely allow researchers to make rational predictions explaining why and how biomolecules interact. The famous "lock and key" model for enzymatic function perhaps best exemplifies this framework. Despite their predictive power, structure-functional relationships often gloss over a basic fact of biological systems--both structure and function may in fact possess a remarkable degree of dynamism. This dissertation summarizes my efforts to develop and refine methods for interrogating the dynamical properties of single molecules, with a particular emphasis on studying structural properties of DNA and examining protein-DNA interactions. I provide an overview of fluorescence, FRET and fluorescence lifetime spectroscopy in Chapter 1, and discuss the methods I developed using fluorescence lifetime to examine conformational fluctuations of sub-persistence length segments of DNA. In Chapter 2, I describe a microfluidic-based platform developed in the Shimon Weiss Lab for conducting single molecule FRET assays, which was used to exploit persistence length changes in DNA upon hybridization to screen context-dependent RNA polymerase transcription. Finally, in Chapter 3, I describe a new detector with improved red spectrum sensitivity, which provides a foundation for further work applying fluorescence lifetime analysis to studying structural perturbations in DNA on nanosecond timescales.
Book Synopsis Single-Molecule Spectroscopy Studies of the Conformational Dynamics of Enzymes by : Maolin Lu
Download or read book Single-Molecule Spectroscopy Studies of the Conformational Dynamics of Enzymes written by Maolin Lu and published by . This book was released on 2014 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: Conformational motions of enzymes are highly dynamic and intrinsically stochastic. Obtaining molecular level insights into conformational dynamics of enzymes is critical for unraveling the complex intimate structure-to-function relationship. This dissertation describes the investigation of conformational dynamics of HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) and T4 lysozyme by single-molecule FRET (Forster/fluorescence resonance energy transfer) spectroscopy and photon stamping spectroscopy. This dissertation also demonstrates the developments of corresponding single-molecule spectroscopic approaches to serve scientifically experimental demands. This dissertation also demonstrates the developments of corresponding single-molecule spectroscopic approaches to serve scientifically experimental demands. Multiple conformational intermediate states and multi-dimensional conformational motions of T4 lysozyme have been observed. The Markov process has successfully reproduced the experimental observations, suggesting that T4 lysozyme hinge-bending open-close conformational changes follow multiple pathways involving multiple intermediate states. The combination of lifetime and anisotropy results presents a whole picture of multi-dimensional conformational dynamics in the process of T4 lysozyme open-close hinge-bending. The non-exponential features of both lifetime and anisotropy autocorrelation functions reveal dynamic and static inhomogeneity/complexity of multi-dimensional conformational fluctuations. The investigations of probing and manipulating HPPK conformational dynamics has been described. The consistency between the decay rate of donor lifetime and rising rate of acceptor lifetime gives a direct observation of FRET dynamic process at single-molecule level. The autocorrelation analysis of donor lifetimes have revealed intermittent conformational coherence of multiple HPPK Loop3-active site conformational states, regulated by substrate-enzyme interactions. Mechanically manipulating a targeted dye-labeled single HPPK in pinpoint nano-scale precision and simultaneously monitoring the conformational changes during the AFM pulling event has been achieved. The observed results of different lifetime fluctuations, distinct anisotropy fluctuations and various dynamic rates have suggested the existence of function-inert and function-active scenarios of HPPK Loop 3-active site conformational dynamic motions. The developments of single-molecule spectroscopic approaches have been demonstrated, including 1) single molecule photon stamping FRET spectroscopy, on the basis of only measuring the donor's lifetime trajectory; 2) single-molecule AFM-FRET nanoscopy, capable of effectively pinpointing and mechanically manipulating a targeted dye-labeled single protein in a large sampling area; and 3) single-molecule multi-parameter photon stamping spectroscopy system, integrating fluorescence anisotropy-FRET-lifetime and capable of observing single-molecule multi-dimensional conformational motions.
Book Synopsis Photon-counting Single-molecule Spectroscopy for Studying Conformational Dynamics and Macromolecular Interactions by : Ted Alfred Laurence
Download or read book Photon-counting Single-molecule Spectroscopy for Studying Conformational Dynamics and Macromolecular Interactions written by Ted Alfred Laurence and published by . This book was released on 2002 with total page 390 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Single Molecule Spectroscopy by : R. Rigler
Download or read book Single Molecule Spectroscopy written by R. Rigler and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 375 pages. Available in PDF, EPUB and Kindle. Book excerpt: The topics range from single molecule experiments in quantum optics and solid-state physics to analogous investigations in physical chemistry and biophysics.
Book Synopsis Spectroscopy and Dynamics of Single Molecules by :
Download or read book Spectroscopy and Dynamics of Single Molecules written by and published by Elsevier. This book was released on 2019-08-14 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: Spectroscopy and Dynamics of Single Molecules: Methods and Applications reviews the most recent developments in spectroscopic methods and applications. Spectroscopic techniques are the chief experimental methods for testing theoretical models and research in this area plays an important role in stimulating new theoretical developments in physical chemistry. This book provides an authoritative insight into the latest advances in the field, highlighting new techniques, current applications, and potential future developments An ideal reference for chemists and physicists alike, Spectroscopy and Dynamics of Single Molecules: Methods and Applications is a useful guide for all those working in the research, design, or application of spectroscopic tools and techniques across a wide range of fields. Includes the latest research on ultrafast vibrational and electronic dynamics, nonlinear spectroscopies, and single-molecule methods Makes the content accessible to researchers in chemistry, biophysics, and chemical physics through a rigorous multi-disciplinary approach Provides content edited by a world-renowned chemist with more than 30 years of experience in research and instruction
Book Synopsis Single Molecule Spectroscopy in Chemistry, Physics and Biology by : Astrid Graslund
Download or read book Single Molecule Spectroscopy in Chemistry, Physics and Biology written by Astrid Graslund and published by Springer Science & Business Media. This book was released on 2010-04-17 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by the leading experts in the field, this book describes the development and current state of the art in single molecule spectroscopy. The application of this technique, which started 1989, in physics, chemistry and biosciences is displayed.
Book Synopsis Protein Conformational Dynamics by : Ke-li Han
Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.
Book Synopsis Single-Molecule/Entity Spectroscopy by : Anne Myers Kelley
Download or read book Single-Molecule/Entity Spectroscopy written by Anne Myers Kelley and published by American Chemical Society. This book was released on 2023-11-01 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-Molecule/Entity Spectroscopy is an indispensable resource for scientists interested in understanding single-molecule spectroscopy comprehensively. By presenting detailed information on the technique’s principles, discussing its diverse applications, and providing insights into future developments, researchers can acquire a holistic overview of this dynamic field without the need to consult an extensive array of individual papers. This primer bridges the gap between standard undergraduate coursework to practical implementation in the research lab for single-molecule spectroscopy.
Book Synopsis Multimodal Measurements of Single-molecule Conformational Dynamics by : Ivan Enchev Ivanov
Download or read book Multimodal Measurements of Single-molecule Conformational Dynamics written by Ivan Enchev Ivanov and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-molecule methods can monitor the dynamics of biological macromolecules in real time. Here we develop FluoRBT, which provides multimodal measurements of structural transitions in nucleic acids and nucleoprotein complexes by combining magnetic tweezers manipulation, infrared darkfield imaging, and single-molecule FRET. We demonstrate the capabilities of FluoRBT by observing structural transitions in DNA under mechanical strain through concurrent changes in FRET and angle or extension. We also apply FluoRBT to study the dynamics of DNA interrogation by the RNA-guided CRISPR nuclease Cas9. We identify a structural intermediate corresponding to DNA:RNA hybridization within the target "seed" region, and characterize how the interplay between sequence mismatches and DNA superhelicity modulates access to states competent for stable binding and cleavage. FluoRBT can further be used to dissect the mechanism of mechanochemical coupling in DNA gyrase by correlating progress through the supercoiling reaction with rich dynamics of the N-gate ATPase domain observed in single-molecule FRET assays. By combining mechanical measurements of global deformations in nucleic acids with FRET measurements of local conformational changes, FluoRBT enables multidimensional investigations of systems ranging from DNA structures to large molecular machines.
Book Synopsis Theory and Evaluation of Single-molecule Signals by : Eli Barkai
Download or read book Theory and Evaluation of Single-molecule Signals written by Eli Barkai and published by World Scientific. This book was released on 2008 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews recently developed theoretical and numerical approaches to deal with optical and mechanical signals from individual molecules. The character of data generated by single molecules, and more generally by single nano-objects, qualitatively differs from those obtained in conventional experiments on large ensembles of molecules. Fluctuations, randomness and irreproducibility are central to single-molecule measurements, and the specific methods required to extract reliable and statistically relevant information from them are presented here. With contributions mainly from participants of the ?Theory, Modeling and Evaluation of Single-Molecule Measurements? workshop held in Leiden, the Netherlands, on April 16-20, 2007, this book is an authoritative compendium on the subject.
Book Synopsis Dynamic Studies of Single Molecule Spectroscopy by : Liangquan Li
Download or read book Dynamic Studies of Single Molecule Spectroscopy written by Liangquan Li and published by . This book was released on 1998 with total page 124 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Selective Spectroscopy of Single Molecules by : Igor Osad'ko
Download or read book Selective Spectroscopy of Single Molecules written by Igor Osad'ko and published by Springer. This book was released on 2010-10-19 with total page 382 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the first detailed and comprehensive guide to the theory of optical band shape of guest-molecule-doped crystals, polymers and glasses. Its main focus is on the dynamics of a single molecule, measured with the help of a train of photons emitted at random time moments.
Book Synopsis Handbook of Fluorescence Spectroscopy and Imaging by : Markus Sauer
Download or read book Handbook of Fluorescence Spectroscopy and Imaging written by Markus Sauer and published by John Wiley & Sons. This book was released on 2010-12-23 with total page 425 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing much-needed information on fluorescence spectroscopy and microscopy, this ready reference covers detection techniques, data registration, and the use of spectroscopic tools, as well as new techniques for improving the resolution of optical microscopy below the resolution gap. Starting with the basic principles, the book goes on to treat fluorophores and labeling, single-molecule fluorescence spectroscopy and enzymatics, as well as excited state energy transfer, and super-resolution fluorescence imaging. Examples show how each technique can help in obtaining detailed and refined information from individual molecular systems.
Book Synopsis Frontiers of Molecular Spectroscopy by : Jaan Laane
Download or read book Frontiers of Molecular Spectroscopy written by Jaan Laane and published by Elsevier. This book was released on 2011-08-11 with total page 741 pages. Available in PDF, EPUB and Kindle. Book excerpt: Much of what we know about atoms, molecules, and the nature of matter has been obtained using spectroscopy over the last one hundred years or so. In this book we have collected together twenty chapters by eminent scientists from around the world to describe their work at the cutting edge of molecular spectroscopy. These chapters describe new methodology and applications, instrumental developments, and theory which is taking spectroscopy into new frontiers. The range of topics is broad. Lasers are utilized in much of the research, but their applications range from sub-femtosecond spectroscopy to the study of viruses and also to the investigation of art and archeological artifacts. Three chapters discuss work on biological systems and three others represent laser physics. The recent advances in cavity ringdown spectroscopy (CRDS), surface enhanced Raman spectroscopy (SERS), two-dimensional correlation spectroscopy (2D-COS), and microwave techniques are all covered. Chapters on electronic excited states, molecular dynamics, symmetry applications, and neutron scattering are also included and demonstrate the wide utility of spectroscopic techniques. Provides comprehensive coverage of present spectroscopic investigations Features 20 chapters written by leading researchers in the field Covers the important role of molecular spectroscopy in research concerned with chemistry, physics, and biology
Download or read book Cumulated Index Medicus written by and published by . This book was released on 2000 with total page 1840 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Bioelectrochemistry by : Richard C. Alkire
Download or read book Bioelectrochemistry written by Richard C. Alkire and published by John Wiley & Sons. This book was released on 2013-09-25 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioelectrochemistry is a fast growing field at the interface between electrochemistry and other sciences such as biochemistry, analytical chemistry and medicinal chemistry. In the recent years, the methods and the understanding of the fundamentals have seen significant progress, which has led to rapid development in the field. Here, the expert editors have carefully selected contributions to best reflect the latest developments in this hot and rapidly growing interdisciplinary topic. The resulting excellent and timely overview of this multifaceted field covers recent methodological advances, as well as a range of new applications for analytical detection, drug screening, tumor therapy, and for energy conversion in biofuel cells. This book is a must-have for all Electrochemists, Biochemists, Analytical Chemists, and Medicinal Chemists.
Book Synopsis Fluorescent Analogs of Biomolecular Building Blocks by : Marcus Wilhelmsson
Download or read book Fluorescent Analogs of Biomolecular Building Blocks written by Marcus Wilhelmsson and published by John Wiley & Sons. This book was released on 2016-04-04 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fluorescent Analogs of Biomolecular Building Blocks focuses on the design of fluorescent probes for the four major families of macromolecular building blocks. Compiling the expertise of multiple authors, this book moves from introductory chapters to an exploration of the design, synthesis, and implementation of new fluorescent analogues of biomolecular building blocks, including examples of small-molecule fluorophores and sensors that are part of biomolecular assemblies.
