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Author: Beena Mary Kadakkuzha
Publisher:
ISBN:
Category : RNA.
Languages : en
Pages : 288
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Book Description
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.
Author: Beena Mary Kadakkuzha
Publisher:
ISBN:
Category : RNA.
Languages : en
Pages : 288
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Book Description
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.
Author: Niyati Jain
Publisher:
ISBN:
Category : RNA.
Languages : en
Pages : 248
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Book Description
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.
Author: Jia Lu
Publisher:
ISBN:
Category : Nucleotide sequence
Languages : en
Pages : 208
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Book Description
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.
Author:
Publisher: Academic Press
ISBN: 0080923348
Category : Science
Languages : en
Pages : 403
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Book Description
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
Author:
Publisher:
ISBN:
Category : Dissertations, Academic
Languages : en
Pages : 906
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Book Description
Author:
Publisher:
ISBN:
Category : Chemistry
Languages : en
Pages : 778
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Book Description
Author: Shaul Mukamel
Publisher: Oxford University Press on Demand
ISBN: 9780195132915
Category : Science
Languages : en
Pages : 543
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Book Description
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.
Author: National Research Council
Publisher: National Academies Press
ISBN: 030916463X
Category : Science
Languages : en
Pages : 222
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Book Description
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.
Author: Marcus Wilhelmsson
Publisher: John Wiley & Sons
ISBN: 1118175867
Category : Science
Languages : en
Pages : 474
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Book Description
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.
Author: Abderrazzak Douhal
Publisher: World Scientific
ISBN: 9810248660
Category : Science
Languages : en
Pages : 854
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Book Description
This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological molecules, surfaces and nanostructures. At the same time it stresses the different ways to control the rates and pathways of reactive events in chemistry and biology. Particular emphasis is given to biological processes as an area where femtodynamics is becoming very useful for resolving the structural dynamics from techniques such as electron diffraction, and X-ray and IR spectroscopy. Finally, the latest developments in quantum control (in both theory and experiment) and the experimental pulse-shaping techniques are described.
