Computational Design of a Circular RNA with Prionlike Behavior

2016 ◽  
Vol 22 (2) ◽  
pp. 172-184 ◽  
Author(s):  
Stefan Badelt ◽  
Christoph Flamm ◽  
Ivo L. Hofacker
Keyword(s):  
Synthetic Biology ◽  
Structure Formation ◽  
Computational Methods ◽  
Computational Design ◽  
Circular Rna ◽  
Equilibrium Thermodynamics ◽  
Rna Molecules ◽  
Rna Design ◽  
Kinetics Of ◽  
Functional Rna

RNA molecules engineered to fold into predefined conformations have enabled the design of a multitude of functional RNA devices in the field of synthetic biology and nanotechnology. More complex designs require efficient computational methods, which need to consider not only equilibrium thermodynamics but also the kinetics of structure formation. Here we present a novel type of RNA design that mimics the behavior of prions, that is, sequences capable of interaction-triggered autocatalytic replication of conformations. Our design was computed with the ViennaRNA package and is based on circular RNA that embeds domains amenable to intermolecular kissing interactions.

scholarly journals Cotranscriptional kinetic folding of RNA secondary structures

2020 ◽  
Author(s):  
Vo Hong Thanh ◽  
Pekka Orponen
Keyword(s):  
Structure Formation ◽  
Rna Structure ◽  
Rna Folding ◽  
Computational Prediction ◽  
Simulation Method ◽  
Rna Structures ◽  
Rna Molecules ◽  
Primitive Operation ◽  
Nucleotide Resolution ◽  
Kinetics Of

Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence, however, has shown that RNA folds concurrently with its elongation. We investigate RNA structure formation, taking into account also the cotranscriptional effects. We propose a single-nucleotide resolution kinetic model of the folding process of RNA molecules, where the polymerase-driven elongation of an RNA strand by a new nucleotide is included as a primitive operation, together with a stochastic simulation method that implements this folding concurrently with the transcriptional synthesis. Numerical case studies show that our cotranscriptional RNA folding model can predict the formation of metastable conformations that are favored in actual biological systems. Our new computational tool can thus provide quantitative predictions and offer useful insights into the kinetics of RNA folding.

Designing Chemically Selective Liquid Crystalline Materials that Respond to Oxidizing Gases

2021 ◽  
Author(s):  
Nanqi Bao ◽  
Jake Gold ◽  
Tibor Szilvasi ◽  
Huaizhe Yu ◽  
Robert Twieg ◽  
...  
Keyword(s):  
Computational Methods ◽  
First Principles ◽  
Liquid Crystalline ◽  
Soft Materials ◽  
Crystalline Materials ◽  
Liquid Crystalline Materials ◽  
Chemically Selective ◽  
Kinetics Of

Computational methods can provide first-principles insights into the thermochemistry and kinetics of reactions at interfaces, but this capability has not been widely leveraged to design soft materials that respond selectively...

scholarly journals Current and Emerging Themes in the Structural Analysis of Viral RNA Genomes: Applications for the Development of Novel Therapeutic Drugs

2015 ◽  
Vol 1 (1) ◽  
pp. 15 ◽  
Author(s):  
Cristina Romero-López ◽  
Alfredo Berzal-Herranz
Keyword(s):  
Rna Folding ◽  
Viral Infections ◽  
Genome Structure ◽  
Rna Molecules ◽  
Molecular Virology ◽  
Viral Genomes ◽  
Viral Propagation ◽  
Bioinformatic Tools ◽  
Rna Domains ◽  
Functional Rna

RNA molecules assume different roles in many different biological processes. This functional diversity is intimately related to RNA folding. In recent years, advances in the field of structure analysis by high-throughput methodologies and the development of novel potent bioinformatic tools have enabled the first structural maps of the eukaryotic transcriptome and the further establishment of novel function-structure relationships. This important progress has been of special relevance in the field of molecular virology. Viral genomes are compact entities that require overlapping coding levels to bear all the genetic information required for viral propagation. This is achieved by the acquisition of functional RNA domains, structurally conserved encoding units that perform essential roles for the consecution of the viral cycle. Interfering with the activity of these structural elements offers a potential means of treating viral infections, such as that caused by the hepatitis C virus, HCV. This review summarizes major achievements in the development of emerging methodologies for the analysis of RNA folding and their application to the study of the HCV genome structure. It will also examine the progress toward the design of novel antiviral compounds based in nucleic acids able to interfere with the folding of functional RNA domains.

scholarly journals Circularization restores signal recognition particle RNA functionality in Thermoproteus

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
André Plagens ◽  
Michael Daume ◽  
Julia Wiegel ◽  
Lennart Randau
Keyword(s):  
Genome Rearrangement ◽  
Signal Recognition Particle ◽  
Circular Rna ◽  
Signal Recognition ◽  
Rna Molecules ◽  
Trna Splicing ◽  
Ribonucleoprotein Complexes ◽  
Domains Of Life ◽  
Thermoproteus Tenax ◽  
Srp Rna

Signal recognition particles (SRPs) are universal ribonucleoprotein complexes found in all three domains of life that direct the cellular traffic and secretion of proteins. These complexes consist of SRP proteins and a single, highly structured SRP RNA. Canonical SRP RNA genes have not been identified for some Thermoproteus species even though they contain SRP19 and SRP54 proteins. Here, we show that genome rearrangement events in Thermoproteus tenax created a permuted SRP RNA gene. The 5'- and 3'-termini of this SRP RNA are located close to a functionally important loop present in all known SRP RNAs. RNA-Seq analyses revealed that these termini are ligated together to generate circular SRP RNA molecules that can bind to SRP19 and SRP54. The circularization site is processed by the tRNA splicing endonuclease. This moonlighting activity of the tRNA splicing machinery permits the permutation of the SRP RNA and creates highly stable and functional circular RNA molecules.

scholarly journals FEATURES OF QUANTITATIVE MEASUREMENTS OF THE DYNAMIC MODULE OF ELASTICITY OF BINDERS IN OPTIMIZATION OF PRODUCTION TECHNOLOGY SEROGYPSUM COMPOSITE

2021 ◽  
pp. 86-92
Author(s):  
V.I. Tarasevych ◽  
◽  
Yu.G. Gasan ◽  
V.B. Dolgoshey ◽  
◽  
...  
Keyword(s):  
Time Dependence ◽  
Structure Formation ◽  
Elastic Properties ◽  
Physicochemical Characteristic ◽  
Resonance Method ◽  
Acoustic Resonance ◽  
Mechanical Action ◽  
Bending Vibrations ◽  
Damping Decrement ◽  
Kinetics Of

The paper considers the issues of studying the structure formation of binders during hardening to determine the optimal moments of mechanical action on gypsum concrete specimens, which makes it possible to optimize the technology of their impregnation with sulfur melt. The time dependence of the elastic modulus of a hardening, binder is its important physicochemical characteristic, since it is used to objectively identify the stages of structure formation, to simulate the processes occurring at each of the stages. It is noted that the method of acoustic resonance of bending vibrations, in the case of hardening binders, needs correction with respect to the measurement technique and interpretation of the results obtained. The kinetics of the resonance frequency of a sample consisting of a rigid cell and a dispersion poured into it is a function of the elastic properties of the cell, the dispersion itself, the contact zone of the dispersion with cell and therefore cannot be used for either qualitative or quantitative analysis of the kinetics of hardening. Taking into account the elasticity of cuvette is necessary to obtain reliable information. It has been established that in the presence of shrinkage or significant expansion of the binder, the study of structure formation by the resonance method should be carried out in plastic cuvettes. Regardless of shrinkage, the use of a cuvette requires compulsory consideration of its elastic properties. It is advisable to objectively distinguish the stages of structure formation on the basis of the kinetics of not the dynamic modulus of elasticity itself, but the rate of its change. The time dependence of the logarithmic damping decrement is also an important characteristic of the concrete structure. The studies carried out make it possible to obtain serogypsum composites with the necessary performance characteristics and to manufacture elements of architectural décor, wall fencing products of increased aesthetics, durability and reliability from them.

scholarly journals Vesicle encapsulation stabilizes intermolecular association and structure formation of functional RNA and DNA

2021 ◽  
Author(s):  
Huan Peng ◽  
Amandine Lelievre ◽  
Katharina Landenfeld ◽  
Sabine Müller ◽  
Irene A. Chen
Keyword(s):  
Structure Formation ◽  
Intermolecular Association ◽  
Rna And Dna ◽  
Functional Rna

scholarly journals Kinetic Analysis of the Hydrolysis of Pentose-1-Phosphates Through Apparent Nucleoside Phosphorolysis Equilibrium Shifts

2020 ◽  
Author(s):  
Felix Kaspar ◽  
Peter Neubauer ◽  
Anke Kurreck
Keyword(s):  
Kinetic Analysis ◽  
Hydrolysis Kinetics ◽  
Equilibrium Thermodynamics ◽  
Apparent Increase ◽  
Equilibrium Conversion ◽  
Sugar Phosphates ◽  
Kinetics Of ◽  
Hydrolysis Of

<div>Ask what an equilibrium can do for you:</div><div>Hydrolysis of pentose-1-phosphates leads to an apparent increase of the equilibrium conversion in nucleoside phosphorolysis reactions. This information can be leveraged via equilibrium thermodynamics to determine the hydrolysis kinetics of in situ generated sugar phosphates, which are known to be elusive and difficult to quantify.<br></div>

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