Download or read book Exploring the Conformational Dynamics of Functional RNA Molecules by Ultrafast Time resolved Spectroscopy written by Beena Mary Kadakkuzha and published by . This book was released on 2009 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA has the intrinsic property to adopt multiple conformations through very fast independent as well as coupled motions. Resolving the high-resolution structures of dynamically inter-converting states is a major challenge for traditional biophysical techniques such as NMR spectroscopy and X-ray crystallography which provide an averaged structure of well folded conformations. It has been shown that the presence of multiple conformations contributes to the ruggedness of the RNA energy landscape, and the functionally relevant conformations could be less populated or transiently present in the ensemble of structure. In two different RNA molecules; a ribozyme with an asymmetric internal loop and a protein binding RNA with a trinucleotide bulge, the conformational dynamics and the structure-function correlation are explored by time-resolved ultrafast fluorescence spectroscopy. Here, RNAs are labeled with one of the most extensively studied fluorescent nucleic acid probes 2-aminopurine, to probe the base stacking patterns in specific motifs in RNA. Base stacking interactions are the major stabilizing force in RNA and the base stacking motions contribute to the local dynamics in RNA. Chapter 1 reviews the broad picture of RNA beyond the static structures and the role of conformational dynamics in defining structure-function relationships in RNA. Chapter 2 explains the basic principles and experimental set-up of ultrafast spectroscopy approach used in our lab and a brief discussion of other spectroscopic techniques that complement the time-resolved spectroscopy. Chapter 3 discusses the conformational dynamics and heterogeneity of leadzyme. We observed a highly unique asymmetric loop structure in leadzyme that lacks orderliness in the catalytic loop. Chapter 4 reviews the heterogeneity of HIV-1 TAR RNA, where we probe the free and ligand bound TAR to capture any bound conformation in the free state that can lead to the proposal of a possible conformational capture mechanism in TAR-Tat recognition. Chapter 5 summarizes our findings and the future prospects of employing time-resolved approach to study the dynamics of biomolecules. In conclusion, we observed RNA as an ensemble of structures in different structural context rather than a single rigid static structure.

Download or read book Investigating the Conformational Dynamics of RNA Molecules and Their Interaction Modes written by Niyati Jain and published by . This book was released on 2010 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA is a structurally flexible and dynamic molecule, and rapidly interconverts between multiple conformations. Despite the significant advances in traditional biophysical techniques like NMR spectroscopy and X-ray crystallography it is difficult to resolve the structures of dynamically inter-converting states as these methods measure the average property of an ensemble of molecules. It is necessary to resolve and get detailed descriptions of the multiple conformational structures, their quantitative distribution and their related dynamics in order to understand the ruggedness of the energy landscape. The present study attempts to link the conformational dynamics of RNA to its structure and biological function. Ultrafast time-resolved fluorescence spectroscopy is used to probe the distribution of multiple conformations and their dynamics that occur on a very fast timescales. This tool uses the resolution of time domain behavior of 2-aminopurine fluorescence decay on the ultrafast timescale to capture the characteristics of different structures. The RNAs are labeled with the fluorescent base analog 2-aminopurine to probe the base stacking patterns in RNA. Base stacking interactions is a unique feature that defines nucleic acid structures compared to proteins and are the major stabilizing force in RNA. Chapter 1 discusses the RNA folding mechanism and the relationships between sequence, structure, dynamics and function and explains the advantage of using ultrafast time resolved spectroscopy in defining structure-function relationships in RNA. Chapter 2 discusses the conformational heterogeneity and dynamics in purine-sensing riboswitches. We observed multiple conformations where the ligand is significantly stacked with the bases of the binding pocket and shows a dynamic balance between base stacking interactions and hydrogen bonding to achieve specificity and high affinity by the aptamer domain. Chapter 3 explores the conformational heterogeneity of GAAA tetraloop receptor and the impacts of the tertiary interactions between the receptor and the GAAA tetraloop, where we probe the isolated and GAAA-tetraloop bound receptor. The presence of any bound conformation in the free receptor state leads us to propose the conformational capture mechanism in tetraloop-receptor recognition. Chapter 4 summarizes findings of employing the ultrafast spectroscopy approach in studying riboswitches and the GAAA tetraloop-receptor. Overall our research is an effort to understand the role of conformational dynamics in RNA folding, tertiary interactions, recognition and functions.

Download or read book Investigation of Conformational Dynamics in Regulatory RNA written by Jia Lu and published by . This book was released on 2012 with total page 208 pages. Available in PDF, EPUB and Kindle. Book excerpt: It has been hypothesized that the ground state conformational dynamics of RNA can significantly enhance its functional capacity beyond its static structure modeled by traditional biophysical techniques. Therefore, understanding the dynamic aspects of RNA structures is fundamentally important for fully elucidating the sequence-structure-dynamics-function relationship. Time-resolved fluorescence up-conversion spectroscopy allowed us to resolve the heterogeneous nature of RNA molecules and capture the conformational changes upon ligand binding to advance our understanding of detailed mechanism of conformational dynamics for different RNA molecules. The non-specific base stacking interaction makes a major contribution to the RNA ground state rugged energy landscape and is also the main stabilizing force in RNA. The fluorescent base 2-aminopurine, which is an analog to adenine, was used to characterize the heterogeneity of base stacking patterns in RNA, and get a quantitative description of inter-converting states in the ensemble.

Download or read book Fluorescence Spectroscopy written by and published by Academic Press. This book was released on 2011-09-06 with total page 403 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fluorescence spectroscopy is a type of electromagnetic spectroscopy, using a beam of light, which analyzes fluorescence from a sample. Given its extremely high sensitivity and selectivity, it is an important investigational tool in many areas including material sciences, analytical sciences, and across a broad range of chemical, biochemical and medical research. It has become an essential investigational technique allowing detailed, real-time observation of the structure and dynamics of intact biological systems. The pharmaceutical industry uses it heavily and it has become a dominating technique in biochemistry and molecular genetics. - Keeps MIE buyers and online subscribers up-to-date with the latest research with this highly used technique - Provides tried and tested techniques which eliminate searching through many different sources

Download or read book Dissertation Abstracts International written by and published by . This book was released on 2008 with total page 906 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Visualizing Chemistry written by National Research Council and published by National Academies Press. This book was released on 2006-06-01 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientists and engineers have long relied on the power of imaging techniques to help see objects invisible to the naked eye, and thus, to advance scientific knowledge. These experts are constantly pushing the limits of technology in pursuit of chemical imagingâ€"the ability to visualize molecular structures and chemical composition in time and space as actual events unfoldâ€"from the smallest dimension of a biological system to the widest expanse of a distant galaxy. Chemical imaging has a variety of applications for almost every facet of our daily lives, ranging from medical diagnosis and treatment to the study and design of material properties in new products. In addition to highlighting advances in chemical imaging that could have the greatest impact on critical problems in science and technology, Visualizing Chemistry reviews the current state of chemical imaging technology, identifies promising future developments and their applications, and suggests a research and educational agenda to enable breakthrough improvements.

Download or read book Book of Abstracts written by and published by . This book was released on 2000 with total page 778 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Single Molecule Optical Detection Imaging and Spectroscopy written by W. E. Moerner and published by John Wiley & Sons. This book was released on 2008-09-26 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single Molecule Spectroscopy is one of the hottest topics in today's chemistry. It brings us close to the the most exciting vision generations of chemists have been dreaming of: To observe and examine single molecules! While most of chemistry deals with myriads of molecules, this books presents the latest developments for the detection and investigation of single entities. Written by internationally renowned authors, it is a thorough and comprehensive survey of current methods and their applications.

Download or read book Principles of Nonlinear Optical Spectroscopy written by Shaul Mukamel and published by Oxford University Press on Demand. This book was released on 1999 with total page 543 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook presents a systematic and unifying viewpoint for a wide class of nonlinear spectroscopic techniques in time domain and frequency domain. It is directed towards active researchers in physics, optics, chemistry, and materials science, as well as graduate students who enter this complex and rapidly developing field. Nonlinear optical interactions of laser fields with matter provide powerful spectroscopic tools for the understanding of microscopic interactions and dynamic processes. One of the major obstacles facing researchers in this field, however, is the flood of experimental techniques and terminologies, which create a serious language barrier. The general microscopic correlation function approach to the nonlinear optical response developed in this book is essential for understanding the relationships among different techniques and a comparison of their information content, the design of new measurements, and for a systematic comparison of the optical response of different systems such as dyes in solutions, atoms and molecules in the gas phase, liquids, molecular aggregates and superlatives, and semiconductor nanostructures. The approach is based on formulating the nonlinear response by representing the state of matter by the density matrix and following its evolution on Liouville space. Current active research areas such as femtosecond time-domain techniques, semi-classical and wave-packet dynamics, pulse shaping, pulse locking, exciton confinement, and the interplay of electronic, nuclear and field coherence are emphasized. The material has been developed from the author's highly successful interdisciplinary course at the University of Rochester attended by science and engineering graduate students.

Download or read book Fluorescence Correlation Spectroscopy written by R. Rigler and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 503 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first book-length treatment of both the theoretical background to fluorescence correlation spectroscopy (FCS) and a variety of applications in various fields of science. The high spatial and temporal resolution of FCS has made it a powerful tool for the analysis of molecular interactions and kinetics, transport properties due to thermal motion, and flow. It contains an essential contribution from Nobel Prize winner M. Eigen, who is credited with inventing FCS.

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.

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 New Trends in Fluorescence Spectroscopy written by Bernard Valeur and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 496 pages. Available in PDF, EPUB and Kindle. Book excerpt: This first volume in the new Springer Series on Fluorescence brings together fundamental and applied research from this highly interdisciplinary and field, ranging from chemistry and physics to biology and medicine. Special attention is given to supramolecular systems, sensor applications, confocal microscopy and protein-protein interactions. This carefully edited collection of articles is an invaluable tool for practitioners and novices.

Download or read book Experimental Approaches of NMR Spectroscopy written by The Nuclear Magnetic Resonance Society of Japan and published by Springer. This book was released on 2017-11-23 with total page 634 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the advanced developments in methodology and applications of NMR spectroscopy to life science and materials science. Experts who are leaders in the development of new methods and applications of life and material sciences have contributed an exciting range of topics that cover recent advances in structural determination of biological and material molecules, dynamic aspects of biological and material molecules, and development of novel NMR techniques, including resolution and sensitivity enhancement. First, this book particularly emphasizes the experimental details for new researchers to use NMR spectroscopy and pick up the potentials of NMR spectroscopy. Second, the book is designed for those who are involved in either developing the technique or expanding the NMR application fields by applying them to specific samples. Third, the Nuclear Magnetic Resonance Society of Japan has organized this book not only for NMR members of Japan but also for readers worldwide who are interested in using NMR spectroscopy extensively.

Download or read book Cell Biology by the Numbers written by Ron Milo and published by Garland Science. This book was released on 2015-12-07 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: A Top 25 CHOICE 2016 Title, and recipient of the CHOICE Outstanding Academic Title (OAT) Award. How much energy is released in ATP hydrolysis? How many mRNAs are in a cell? How genetically similar are two random people? What is faster, transcription or translation?Cell Biology by the Numbers explores these questions and dozens of others provid

Download or read book Conical Intersections Electronic Structure Dynamics Spectroscopy written by Wolfgang Domcke and published by World Scientific. This book was released on 2004-07-14 with total page 857 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is widely recognized nowadays that conical intersections of molecular potential-energy surfaces play a key mechanistic role in the spectroscopy of polyatomic molecules, photochemistry and chemical kinetics. This invaluable book presents a systematic exposition of the current state of knowledge about conical intersections, which has been elaborated in research papers scattered throughout the chemical physics literature.Section I of the book provides a comprehensive analysis of the electronic-structure aspects of conical intersections. Section II shows the importance of conical intersections in chemical reaction dynamics and gives an overview of the computational techniques employed to describe the dynamics at conical intersections. Finally, Section III deals with the role of conical intersections in the fields of molecular spectroscopy and laser control of chemical reaction dynamics.This book has been selected for coverage in:• CC / Physical, Chemical & Earth Sciences• Chemistry Citation Index(tm)• Index to Scientific Book Contents® (ISBC)

Download or read book Principles of Fluorescence Spectroscopy written by Joseph R. Lakowicz and published by Springer Science & Business Media. This book was released on 2013-11-11 with total page 487 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fluorescence methods are being used increasingly in biochemical, medical, and chemical research. This is because of the inherent sensitivity of this technique. and the favorable time scale of the phenomenon of fluorescence. 8 Fluorescence emission occurs about 10- sec (10 nsec) after light absorp tion. During this period of time a wide range of molecular processes can occur, and these can effect the spectral characteristics of the fluorescent compound. This combination of sensitivity and a favorable time scale allows fluorescence methods to be generally useful for studies of proteins and membranes and their interactions with other macromolecules. This book describes the fundamental aspects of fluorescence. and the biochemical applications of this methodology. Each chapter starts with the -theoreticalbasis of each phenomenon of fluorescence, followed by examples which illustrate the use of the phenomenon in the study of biochemical problems. The book contains numerous figures. It is felt that such graphical presentations contribute to pleasurable reading and increased understand ing. Separate chapters are devoted to fluorescence polarization, lifetimes, quenching, energy transfer, solvent effects, and excited state reactions. To enhance the usefulness of this work as a textbook, problems are included which illustrate the concepts described in each chapter. Furthermore, a separate chapter is devoted to the instrumentation used in fluorescence spectroscopy. This chapter will be especially valuable for those perform ing or contemplating fluorescence measurements. Such measurements are easily compromised by failure to consider a number of simple principles.