Download or read book Thermodynamic Corrections to RNA Folding Models in Cells written by Jacob Sieg and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA performs numerous functions in cells owing to its capacity to adopt complex, diverse, and functional structures. Genome-wide structure-probing techniques have provided insight into RNA structure and function in vivo. However, most biophysical techniques are not readily amenable to the cellular environment. This has caused a gap in the detailed understanding of RNA thermodynamics artificial buffer conditions in vitro and understanding of RNA thermodynamics inside organisms (in vivo). In vitro studies of RNA in artificial cytoplasm that mimic a cell, so called in vivo-like conditions, provide a link between mechanistically tractable insight in vitro and understanding of RNA structure in vivo. This thesis describes the development and application of a realistic artificial cytoplasm for detailed mechanistic studies of RNA and determines thermodynamic corrections to RNA secondary structure models used in structure prediction algorithms. Chapter 2 examines the biological network of metabolites and metal ions in diverse organisms, using absolute metabolite concentrations and metal ion-binding constants in a multi-component model. This information is applied in Chapter 3 to develop the Eco80 artificial cytoplasm, which contains 80% of Escherichia coli metabolites, and demonstrates that the metabolome weakens RNA helix stability and strengthens RNA chemical stability. Chapter 4 describes folding free energies determined for an expanded helix set in Eco80 and applies in vivo-like thermodynamic corrections to improve RNA secondary structure prediction in E. coli. Chapter 5 provides unique experimental considerations for measuring the thermodynamics of RNA helix formation in artificial cytoplasm and presents the facile data-processing software MeltR. Lastly, Chapter 6 applies LC-MS/MS to RNA studies in biological systems and describes theoretical approaches to combining sequencing-based RNA structure probing with complementary LC-MS/MS analysis, as applied to measuring tRNA structure in cells. Additionally, Chapter 6 also describes unique methods of preparing cell lysates for RNA measurements and the use of LC-MS/MS based metabolite profiling to identify ligands that bind to RNA.

Download or read book Thermodynamics of RNA Structural Changes written by Peter J. Mikulecky and published by . This book was released on 2005 with total page 564 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Physics based Modeling for RNA Folding written by Xiaojun Xu and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA (ribonucleic acid) molecules play a variety of crucial roles in cellular functions at the level of transcription, translation and gene regulation. Many RNAs have also been found to play catalytic and regulatory roles. RNA functions are tied to structures and dynamics. To understand the quantitative relationship between RNA functions and RNA 3D structures, stabilities and kinetics, we need a predictive model for RNA folding. We focus on the development of physics-based models for RNA folding. RNA molecules often undergo multiple conformational switches in order to perform their cellular functions, suggesting that RNA-involved processes can be kinetically controlled. Therefore, a full characterization of RNA folding and function should consider not only the native structure but also the folding kinetics. RNA hairpin is one of the most fundamental motifs in RNA structures. Predicting the physical mechanism of the folding and conformational switch for hairpins has far reaching impact on our understanding of more complex RNA folding problems. In the first project, we used Kinetic Monte Carlo method to explore the detailed kinetic mechanism for the conformational switches between bistable RNA hairpins. We found three types of conformational switch pathways for RNA hairpins: refolding after complete unfolding, folding through basepair-exchange pathways and through pseudoknot-assisted pathways, respectively. The study of this project led to new insights about RNA folding: tertiary structure such as pseudoknots can help secondary structure folding by lowering the kinetic barrier. The problem of RNA structure prediction from the nucleotide sequence is an unsolved problem for both 2D and 3D structures. One of the key issues in the current RNA structure prediction methods is the lack of the knowledge about the tertiary interactions. Tertiary interactions are crucial for RNA functions. Therefore, a model that can predict RNA structures with tertiary interactions is highly needed. In the second project, we developed a statistical mechanical model for the folding of tertiary structures with loop-loop kissing interactions. Based on a coarse-grained RNA conformational model, we developed an algorithm to compute the entropy parameters for the formation of the kissing structures. The model enables computational prediction of the structure and thermodynamic stability of RNA tertiary folds with long-range kissing loop-loop kissing contacts. The validity of the model is supported by the good theory-experiment agreements for the native structures and thermodynamic stabilities for a series of RNA/RNA complex systems. For large RNAs, due to the increased complexity of the structures, the accuracy of computational predictions for RNA folding decreases. For such complex RNA structures, a novel structure determination strategy is to combine computational modeling with experimental data such as the reactivity profile of Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE), an method for chemical probing of RNA structure. Although the SHAPE technology has been widely applied to a broad range of RNA structure probing problems, the quantitative relationship between the structure/dynamics and SHAPE reactivity is not understood. In the third project, we developed a model to quantify the relationship between RNA three-dimensional structure and SHAPE reactivity. We developed an analytical function to rebuild SHAPE profiles from three-dimensional structures. The algorithm starts from RNA structures and combines nucleotide interaction strength and conformational propensity, ligand (SHAPE reagent) accessibility, and base-pairing pattern through a composite function to quantify the correlation between SHAPE reactivity and nucleotide conformational stability. Comparisons between predicted SHAPE profiles and experimental SHAPE data show high correlations, suggesting the validity of the extracted analytical function. The result supports our analysis for the key factors that determine the SHAPE reactivity from structure.

Download or read book Investigating RNA Folding and Adaptation in Cellular Conditions written by Kathleen Leamy and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA is an essential biomolecule that controls many processes in cells by folding into complex three-dimensional structures. Regulation can happen at the transcriptional or translational levels by RNA self-cleavage, ligand binding, or unfolding, to name a few. The folding and structures of these so called functional RNAs that adopt tertiary structures has been studied for several decades. These studies have revealed that functional RNAs fold in a hierarchical manner where secondary structures form before tertiary structure, RNA folds over broad energetic landscapes, and RNAs become trapped in stable misfolded, non-functional structures that can last for hours. The majority of these studies have been performed on just a few RNA sequences and in classic solution conditions of 1 M Na+. Although these studies have revealed fundamentals of RNA folding, they have been performed in non-biological solutions and on a low range of sequence diversity. This limits our knowledge of how RNA folds in cells.In cells the ionic conditions are much lower than those typically used in vitro. There is ~ 140 mM K+, 10 mM Na+, 0.5-1.0 mM Mg2+ in eukaryotic cells, and 1.5-2.0 mM Mg2+ in prokaryotic cells. There are also numerous small molecules, including free nucleotides, amino acids, and metabolites, and the biomolecule and organelles contribute 20-40% molecular crowding. Recent efforts have shown that mimicking some of these cellular conditions in vitro affect the folding and function of RNAs. In all chapters of the work herein, I describe the effects of cellular mimics on RNA folding processes, including the stability of secondary and tertiary structures, cotranscriptional folding, and RNA adaptation to high temperatures. Several functional RNAs have been shown to fold in a more two-state manner in cellular mimics, but in a multi-state manner in classic in vitro conditions. However, the mechanism behind this two-state folding has been largely uninvestigated. In Chapter Two, I focus on how cooperativity arises in biological crowded and Mg2+ conditions by studying the influence of these conditions on the structure and stability of the secondary and tertiary structures of tRNAphe. I find that cooperativity occurs through both a destabilization of secondary structures and a stabilization of tertiary structure. This is very similar to the folding of proteins, where weak secondary structure and strong tertiary structure drive cooperativity to the native state. Full-length RNAs are typically studied by renaturing a full-length transcript in vitro and watching it fold or unfold. However, in cells the growing transcript folds as it emerges from the polymerase, and the mechanism behind cotranscriptional structure formation is largely unknown. In Chapter Three, I study cotranscriptional structure formation in tRNAphe. I find that in cellular mimics, structures that form cotranscriptionally are weakened compared to in buffer, until a single nucleotide is added and a large increase in transcript stability is observed. This large increase in stability results in cooperative folding to the native state, and only happens when all secondary and tertiary contacts can form. This single nucleotide control of folding is observed both experimentally and computationally, and suggests that nature has selected for minimal structure formation in cotranscriptional intermediates until two-state folding to the functional state can be achieved. Organisms grow at a wide range of temperatures, which range from freezing to boiling, and their RNAs need to adopt to fold and function in those extreme environments. Yet, only a few sequences of a type of RNA are typically studied. In Chapter Four, I investigate how tRNAphe adapts to extreme temperatures, and how model transcripts from thermophiles fold under cellular conditions. The data reveals that tRNA adapts to extreme temperature by altering the stability of secondary structures, while nucleotides in tertiary structures are highly conserved. We also show that model transcripts from thermophiles maintain cooperative folding, but only in the most cellular-like solution conditions. This study showed a novel mechanism for functional RNA adaptation.A challenge in the RNA folding community is that there is not a good method for studying thermodynamics in complex solution conditions, such as cell extracts. This has two main causes: (1) Cosolutes and biomolecules interfere with the signal from an RNA of interest, which is normally UV detected at 260 or 280 nm, and (2) Methods to study thermodynamics typically involve heating the sample to denature the RNA, however this will also denature biomolecules in solution, no longer making it cellular-like. In Chapter Five, I describe efforts to develop a method to study RNA thermodynamics in complex cellular mimics that will overcome the above described challenges. Overall, the work presented in this thesis provides insights into how RNAs fold and adapt in cellular conditions, with implications for understanding how nature selects for RNA structures.

Download or read book RNA Folding written by Ronny Lorenz and published by Springer Nature. This book was released on with total page 407 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book The Rna World Third Edition written by Gesteland and published by . This book was released on 2006-01-01 with total page 768 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent studies on the activities of RNA in the cell have revolutionized our understanding of the many roles played by this molecule. The first two editions of The RNA World (1993, 1999) shed light on the pre biotic era dominated by this versatile molecule, and provided an overview of the state of RNA research at the time. The new third edition of The RNA World updates this perspective, describing the vast array of newly discovered roles for RNA in the modern world. The updated original chapters are supplemented with new chapters on RNA protein complexes, snRNPs and snoRNPs, telomerase RNA, RNAi, microRNAs, noncoding RNA, and many other subjects. This book is essential reading for anyone interested in the biology of nucleic acids and gene regulation and a valuable resource for teaching these concepts

Download or read book Nucleic Acids written by Victor A. Bloomfield and published by Sterling Publishing Company. This book was released on 2000-04-17 with total page 854 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text has been organized to meet the needs of those who have only a basic understanding of physical chemistry and molecular biology.

Download or read book Circular Dichroism and the Conformational Analysis of Biomolecules written by G.D. Fasman and published by Springer Science & Business Media. This book was released on 2013-11-11 with total page 739 pages. Available in PDF, EPUB and Kindle. Book excerpt: ''Excellent and very timely....It will undoubtedly become a standard reference for the application of circular dichroism (CD) to biomolecules.'' --- Quarterly Review of Biology, March 1997 ''[T]estament to the book's utility is the fact that during the course of my review I had to 'rescue' it from the desks of graduate students on an almost daily basis. In summary, this is a great book.'' --- American Scientist ''Well documented chapters provide a very good insight into the problems surrounding the conformation of biomacromolecules...An indispensible source of information.'' --- Nahrung, 42(2), 1998 Renowned experts present the first state-of-the-art description of circular dichroism spectroscopy (CD). Chapters present in-depth discussions of the history of the field, the theory of CD for application to globular proteins, membrane proteins, peptides, nucleic acids and their interactions, carbohydrates, and instrumentation. Discussions also feature new techniques using synchrotron radiation, vibrational Raman optical activity, and vibrational CD. More than 250 illustrations supplement the text.

Download or read book Kinetics and Thermodynamics of Protein RNA Interactions and Protein Folding in Vitro and in Cells written by 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 Unifying Evolutionary and Thermodynamic Information for RNA Folding of Multiple Alignments written by Stefan E Seemann and published by . This book was released on 2008 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Computational methods for determining the secondary structure of RNA sequences from given alignments are currently either based on thermodynamic folding, compensatory base pair substitutions or both. However, there is currently no approach that combines both sources of information in a single optimization problem. Here, we present a model that formally integrates both the energy-based and evolution-based approaches to predict the folding of multiple aligned RNA sequences. We have implemented an extended version of Pfold that identifies base pairs that have high probabilities of being conserved and of being energetically favorable. The consensus structure is predicted using a maximum expected accuracy scoring scheme to smoothen the effect of incorrectly predicted base pairs. Parameter tuning revealed that the probability of base pairing has a higher impact on the RNA structure prediction than the corresponding probability of being single stranded. Furthermore, we found that structurally conserved RNA motifs are mostly supported by folding energies. Other problems (e.g. RNA-folding kinetics) may also benefit from employing the principles of the model we introduce. Our implementation, PETfold, was tested on a set of 46 well-curated Rfam families and its performance compared favorably to that of Pfold and RNAalifold

Download or read book Physical Biology of the Cell written by Rob Phillips and published by Garland Science. This book was released on 2012-10-29 with total page 1351 pages. Available in PDF, EPUB and Kindle. Book excerpt: Physical Biology of the Cell is a textbook for a first course in physical biology or biophysics for undergraduate or graduate students. It maps the huge and complex landscape of cell and molecular biology from the distinct perspective of physical biology. As a key organizing principle, the proximity of topics is based on the physical concepts that

Download or read book Fundamentals of RNA Structure and Function written by Neena Grover and published by Springer Nature. This book was released on 2022-05-09 with total page 257 pages. Available in PDF, EPUB and Kindle. Book excerpt: This highly illustrated textbook provides an essential overview on RNA architecture and function, it offers insights into the RNA basics and also explains novel RNA technologies, such as CRISPR-Cas and their applications. In addition, the mRNA based vaccine technology, which has long been tested, also before the COVID-19 pandemic, is discussed and students receive a basic understanding of this important medical application. The textbook is written by Prof. Grover in collaboration with her students and has an easily accessible style. The book provides a great tool for young researchers and students in biology, biomedical engineering or biochemistry, looking for a compact introduction or refresher work on RNA, including the newest findings and technologies. It is an ideal starter to learn about several RNA specific topics and to research them further.

Download or read book RNA 3D Structure Analysis and Prediction written by Neocles Leontis and published by Springer Science & Business Media. This book was released on 2012-06-05 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.

Download or read book RNA Folding written by Christina Waldsich and published by Humana. This book was released on 2016-08-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Focusing on in vitro and intracellular RNA structure formation, RNA Folding: Methods and Protocols provides a comprehensive collection of experimental protocols which are suitable to dissect RNA folding pathways and to characterize the structure of RNA folding intermediates at nucleotide or even atomic resolution. The presented techniques include powerful tools with a long tradition in RNA research as well as more advanced, novel methods, thus the methods span multiple disciplines, including molecular biology, biochemistry, biophysics, and computational biology. 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. Practical and authoritative, RNA Folding: Methods and Protocols serves as a vital reference for researchers attempting to gain insights into the secrets of this astounding macromolecule.

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 Gibbs Energy and Helmholtz Energy written by Emmerich Wilhelm and published by Royal Society of Chemistry. This book was released on 2021-09-08 with total page 449 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book contains the latest information on all aspects of the most important chemical thermodynamic properties of Gibbs energy and Helmholtz energy, as related to fluids. Both the Gibbs energy and Helmholtz energy are very important in the fields of thermodynamics and material properties as many other properties are obtained from the temperature or pressure dependence. Bringing all the information into one authoritative survey, the book is written by acknowledged world experts in their respective fields. Each of the chapters will cover theory, experimental methods and techniques and results for all types of liquids and vapours. This book is the fourth in the series of Thermodynamic Properties related to liquids, solutions and vapours, edited by Emmerich Wilhelm and Trevor Letcher. The previous books were: Heat Capacities (2010), Volume Properties (2015), and Enthalpy (2017). This book fills the gap in fundamental thermodynamic properties and is the last in the series.

Download or read book Non Protein Coding RNAs written by Nils Walter and published by Springer Science & Business Media. This book was released on 2008-11-18 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, Andrew Fire and Craig Mello. This prize, which follows “RNA” Nobels for splicing and RNA catalysis, highlights just one class of recently discovered non-protein coding RNAs. Remarkably, non-coding RNAs are thought to outnumber protein coding genes in mammals by perhaps as much as four-fold. In fact, it appears that the complexity of an organism correlates with the fraction of its genome devoted to non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic tra- posons, higher-level organization of eukaryotic chromosomes, and gene expression are found to be largely directed by non-protein coding RNAs. Currently, bioinformatic, high-throughput sequencing, and biochemical approaches are identifying an increasing number of these RNAs. Unfortunately, our ability to characterize the molecular details of these RNAs is significantly lacking. The biophysical study of these RNAs is an emergent field that is unraveling the molecular underpinnings of how RNA fulfills its multitude of roles in sustaining cellular life. The resulting understanding of the physical and chemical processes at the molecular level is critical to our ability to harness RNA for use in biotechnology and human therapy, a prospect that has recently spawned a multi-billion dollar industry.