Conserved RNA motifs of EMCV IRES as potential building blocks to design RNA nanostructures

2012 ◽  
Vol 48 (94) ◽  
pp. 11573 ◽  
Author(s):  
Kwong Kit Chan ◽  
Vasudevan Ramesh
Keyword(s):  
2014 ◽  
Author(s):  
Paul P Gardner ◽  
Hisham Eldai

RNA performs a diverse array of important functions across all cellular life. These functions include important roles in translation, building translational machinery and maturing messenger RNA. More recent discoveries include the miRNAs and bacterial sRNAs that regulate gene expression, the thermosensors, riboswitches and other cis-regulatory elements that help prokaryotes sense their environment and eukaryotic piRNAs that suppress transposition. However, there can be a long period between the initial discovery of a RNA and determining its function. We present a bioinformatic approach to characterise RNA motifs, which are the central building blocks of RNA structure. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterised RNAs. Moreover, we introduce a new profile-based database of RNA motifs - RMfam - and illustrate its application for investigating the evolution and functional characterisation of RNA. All the data and scripts associated with this work is available from: https://github.com/ppgardne/RMfam


2021 ◽  
Vol 118 (33) ◽  
pp. e2109085118
Author(s):  
Steve L. Bonilla ◽  
Sarah K. Denny ◽  
John H. Shin ◽  
Aurora Alvarez-Buylla ◽  
William J. Greenleaf ◽  
...  

Despite RNA’s diverse secondary and tertiary structures and its complex conformational changes, nature utilizes a limited set of structural “motifs”—helices, junctions, and tertiary contact modules—to build diverse functional RNAs. Thus, in-depth descriptions of a relatively small universe of RNA motifs may lead to predictive models of RNA tertiary conformational landscapes. Motifs may have different properties depending on sequence and secondary structure, giving rise to subclasses that expand the universe of RNA building blocks. Yet we know very little about motif subclasses, given the challenges in mapping conformational properties in high throughput. Previously, we used “RNA on a massively parallel array” (RNA-MaP), a quantitative, high-throughput technique, to study thousands of helices and two-way junctions. Here, we adapt RNA-MaP to study the thermodynamic and conformational properties of tetraloop/tetraloop receptor (TL/TLR) tertiary contact motifs, analyzing 1,493 TLR sequences from different classes. Clustering analyses revealed variability in TL specificity, stability, and conformational behavior. Nevertheless, natural GAAA/11ntR TL/TLRs, while varying in tertiary stability by ∼2.5 kcal/mol, exhibited conserved TL specificity and conformational properties. Thus, RNAs may tune stability without altering the overall structure of these TL/TLRs. Furthermore, their stability correlated with natural frequency, suggesting thermodynamics as the dominant selection pressure. In contrast, other TL/TLRs displayed heterogenous conformational behavior and appear to not be under strong thermodynamic selection. Our results build toward a generalizable model of RNA-folding thermodynamics based on the properties of isolated motifs, and our characterized TL/TLR library can be used to engineer RNAs with predictable thermodynamic and conformational behavior.


1997 ◽  
Vol 161 ◽  
pp. 23-47 ◽  
Author(s):  
Louis J. Allamandola ◽  
Max P. Bernstein ◽  
Scott A. Sandford

AbstractInfrared observations, combined with realistic laboratory simulations, have revolutionized our understanding of interstellar ice and dust, the building blocks of comets. Since comets are thought to be a major source of the volatiles on the primative earth, their organic inventory is of central importance to questions concerning the origin of life. Ices in molecular clouds contain the very simple molecules H2O, CH3OH, CO, CO2, CH4, H2, and probably some NH3and H2CO, as well as more complex species including nitriles, ketones, and esters. The evidence for these, as well as carbonrich materials such as polycyclic aromatic hydrocarbons (PAHs), microdiamonds, and amorphous carbon is briefly reviewed. This is followed by a detailed summary of interstellar/precometary ice photochemical evolution based on laboratory studies of realistic polar ice analogs. Ultraviolet photolysis of these ices produces H2, H2CO, CO2, CO, CH4, HCO, and the moderately complex organic molecules: CH3CH2OH (ethanol), HC(= O)NH2(formamide), CH3C(= O)NH2(acetamide), R-CN (nitriles), and hexamethylenetetramine (HMT, C6H12N4), as well as more complex species including polyoxymethylene and related species (POMs), amides, and ketones. The ready formation of these organic species from simple starting mixtures, the ice chemistry that ensues when these ices are mildly warmed, plus the observation that the more complex refractory photoproducts show lipid-like behavior and readily self organize into droplets upon exposure to liquid water suggest that comets may have played an important role in the origin of life.


Author(s):  
D.E. Brownlee ◽  
A.L. Albee

Comets are primitive, kilometer-sized bodies that formed in the outer regions of the solar system. Composed of ice and dust, comets are generally believed to be relic building blocks of the outer solar system that have been preserved at cryogenic temperatures since the formation of the Sun and planets. The analysis of cometary material is particularly important because the properties of cometary material provide direct information on the processes and environments that formed and influenced solid matter both in the early solar system and in the interstellar environments that preceded it.The first direct analyses of proven comet dust were made during the Soviet and European spacecraft encounters with Comet Halley in 1986. These missions carried time-of-flight mass spectrometers that measured mass spectra of individual micron and smaller particles. The Halley measurements were semi-quantitative but they showed that comet dust is a complex fine-grained mixture of silicates and organic material. A full understanding of comet dust will require detailed morphological, mineralogical, elemental and isotopic analysis at the finest possible scale. Electron microscopy and related microbeam techniques will play key roles in the analysis. The present and future of electron microscopy of comet samples involves laboratory study of micrometeorites collected in the stratosphere, in-situ SEM analysis of particles collected at a comet and laboratory study of samples collected from a comet and returned to the Earth for detailed study.


Author(s):  
Yeshayahu Talmon

To achieve complete microstructural characterization of self-aggregating systems, one needs direct images in addition to quantitative information from non-imaging, e.g., scattering or Theological measurements, techniques. Cryo-TEM enables us to image fluid microstructures at better than one nanometer resolution, with minimal specimen preparation artifacts. Direct images are used to determine the “building blocks” of the fluid microstructure; these are used to build reliable physical models with which quantitative information from techniques such as small-angle x-ray or neutron scattering can be analyzed.To prepare vitrified specimens of microstructured fluids, we have developed the Controlled Environment Vitrification System (CEVS), that enables us to prepare samples under controlled temperature and humidity conditions, thus minimizing microstructural rearrangement due to volatile evaporation or temperature changes. The CEVS may be used to trigger on-the-grid processes to induce formation of new phases, or to study intermediate, transient structures during change of phase (“time-resolved cryo-TEM”). Recently we have developed a new CEVS, where temperature and humidity are controlled by continuous flow of a mixture of humidified and dry air streams.


2016 ◽  
Vol 37 (3) ◽  
pp. 181-193 ◽  
Author(s):  
Aire Mill ◽  
Anu Realo ◽  
Jüri Allik

Abstract. Intraindividual variability, along with the more frequently studied between-person variability, has been argued to be one of the basic building blocks of emotional experience. The aim of the current study is to examine whether intraindividual variability in affect predicts tiredness in daily life. Intraindividual variability in affect was studied with the experience sampling method in a group of 110 participants (aged between 19 and 84 years) during 14 consecutive days on seven randomly determined occasions per day. The results suggest that affect variability is a stable construct over time and situations. Our findings also demonstrate that intraindividual variability in affect has a unique role in predicting increased levels of tiredness at the momentary level as well at the level of individuals.


Sign in / Sign up

Export Citation Format

Share Document