Rna 3d structures. Medical search. Frequent questions

Like proteins, RNA molecules twist and fold into intricate 3D shapes that allow them to perform a wide range of cellular functions, including catalyzing reactions, regulating gene expression, modulating innate immunity, and sensing small molecules. (scienceboard.net)
However, while scientists' understanding of protein structure has made great strides in the last decade, their knowledge of RNA structure lags far behind, despite the fact that the fraction of the human genome transcribed to RNA is approximately 30 times as large as the fraction that codes for proteins. (scienceboard.net)
This is partly because RNA structures are currently not well understood and because RNA sequence information provides less information about 3D RNA structures than is the case for proteins. (scienceboard.net)
The code determines the recognition of RNA molecules by a superfamily of RNA-binding proteins called pentatricopeptide repeat (PPR) proteins. (scitechdaily.com)
This RNA is then used to make proteins that are required by the organism for all of its vital functions. (scitechdaily.com)
If a gene is defective, its RNA copy and the proteins made from this will also be defective. (scitechdaily.com)
RNA-binding PPR proteins could revolutionize the way we treat disease. (scitechdaily.com)
The new paper in PLOS Genetics describes for the first time how PPR proteins recognize their RNA targets via an easy-to-understand code. (scitechdaily.com)
What's more, we can now design our own synthetic proteins to target any RNA sequence we choose - this should allow us to control the expression of genes in new ways that just weren't available before. (scitechdaily.com)
Reference: "A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins" by Alice Barkan, Margarita Rojas, Sota Fujii, Aaron Yap, Yee Seng Chong, Charles S. Bond and Ian Small, 16 August 2012, PLOS Genetics . (scitechdaily.com)
The structure of the influenza virus's HA surface proteins is designed to fit the sialic acid receptors of the human cell, like a key to a lock. (cdc.gov)
In fact, evolutionary biologists hypothesize that RNA existed and self-replicated even before the appearance of DNA and the proteins encoded by it. (worldhealth.net)
Fast forward to modern-day humans: science has revealed that less than 3% of the human genome is transcribed into messenger RNA (mRNA) molecules that in turn are translated into proteins. (worldhealth.net)
This positive-sense RNA genome can be directly translated into viral proteins. (getjar.com)
The noncoding regions are removed and the coding regions, called exons, form a contiguous RNA sequence that will code for proteins. (embl.org)
Viral RNA as well as viral proteins interact with different components of the host cell, acting as key determinants of viral pathogenesis. (bionity.com)
The relatively new technique enables researchers to peer inside molecules to determine the 3D shape of proteins, which are often thousands of times smaller than the width of a human hair. (chicagobiomedicalconsortium.org)
However, some scientists think that before life adopted DNA and proteins, it relied primarily on RNA. (elifesciences.org)
Yet, some RNA strands can also fold to form ribozymes, 3D structures that could have guided life's chemical processes the way proteins do now. (elifesciences.org)
All life on Earth today uses a triplet RNA code to make proteins from DNA, and these experiments showed how RNA triplets might have helped RNA sustain early life forms. (elifesciences.org)
At its upper end, the λN protein is in contact with RNA (orange) and various regulatory proteins (yellow, blue and green). (phys.org)
The RNA Vaccines 3D Model Making Kit shows how RNA vaccines make vaccinated cells produce viral proteins (antigens), display them on their cell surface in Major Histocompatibility Complex (MHC) molecules and stimulate an immune response. (fishersci.com)
Next, during a process called RNA splicing, the introns are carefully removed, leaving only the exons to be later translated into the functional product - proteins. (mpg.de)
Residues that compose the RNA-binding surface are conserved in a subgroup of SAM domain-containing proteins, suggesting that the function of the domain is conserved from yeast to humans. (embl.de)
The contributors discuss the 3D organization of chromatin, the various nuclear bodies and compartments that have been identified, and the roles of RNA and actin in shaping nuclear organization, as well as how these structures interact with each other and with peripheral features (e.g., the nuclear pore complex and inner nuclear membrane proteins) to carry out the work of the nucleus. (cshlpress.com)
Small angle neutron scattering (SANS) provides unique insight into biomacromolecular complexes by combining solvent contrast variation (H2O:D2O exchange) with either natural contrast between different classes of biomolecules (proteins, RNA/DNA, lipids/detergents) and/or by applying artificial contrast, i.e. deuteration of specific biomolecules. (lu.se)

Zika virus has a nonsegmented, single-stranded, positive-sense RNA genome. (getjar.com)
It covers the analysis of genome activity from the 3D structure of chromosomes through to RNA and DNA-protein interactions. (abdn.ac.uk)
We discovered that CCCTC binding factor (CTCF) - a protein that can create chromatin loops between two distant sites in the genome - regulates which exons get included in the RNA by forming a loop. (embl.org)
Here we undertake a genome-scale analysis of these interactions in a genetically diverse population to systematically identify global genetic-epigenetic interaction, and reveal constraints imposed by chromatin structure. (elifesciences.org)
We show that stable 3D genome structure is an effective tool to guide searches for regulatory elements and, conversely, that regulatory elements in genetically diverse populations provide a means to infer 3D genome structure. (elifesciences.org)
Local regulatory mechanisms within the genome and their interaction with chromatin structure give rise to subtle variations in gene expression. (elifesciences.org)
Soon after infection, the single stranded positive RNA that constitutes the viral genome is efficiently translated using a cap-independent mechanism driven by the internal ribosome entry site element (IRES). (bionity.com)
Arteriviruses are small, enveloped, animal viruses with an icosahedral core containing a positive-sense RNA genome. (bionity.com)
Second, the polymerase plays a dual role switching between the RNA and DNA polymerizing activity during the processes of transcription and genome replication, respectively. (chicagobiomedicalconsortium.org)
The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of singleguide RNAs (sgRNAs) to enable genome editing 1 - 10 . (cdc.gov)

Unlike AlphaFold, which was trained on thousands of known protein structures, the ARES training data was limited to 18 RNA molecules for which experimentally determined structures were published between 1994 and 2006. (scienceboard.net)
many molecules have several possible three-dimensional structures, so predicting these structures remains out of reach unless obvious sequence and functional similarity to a known class of nucleic acid molecules, such as transfer RNA (tRNA) or microRNA (miRNA), is observed. (wikipedia.org)
Secondary structure of small RNA molecules is largely determined by strong, local interactions such as hydrogen bonds and base stacking . (wikipedia.org)
[6] For longer molecules, the number of possible secondary structures is huge: a sequence of 100 nucleotides has more than 10 25 possible secondary structures. (wikipedia.org)
This reservoir has dramatically increased in the past few years and it now contains over 1700 tertiary RNA structures, both, in the form of isolated molecules as well as RNA-protein and ligand complexes. (biomedcentral.com)
In contrast, 82% of it is transcribed into RNA molecules with other functions many of which still remain enigmatic. (worldhealth.net)
However, these techniques cannot be applied to RNA molecules with nearly the same effectiveness because their molecular composition and structural flexibility prevent them from easily forming crystals. (worldhealth.net)
Now, a research collaboration led by Wyss Core Faculty member Peng Yin, Ph.D. at the Wyss Institute for Biologically Inspired Engineering at Harvard University, and Maofu Liao, Ph.D. at Harvard Medical School (HMS), has reported a fundamentally new approach to the structural investigation of RNA molecules. (worldhealth.net)
ROCK, as it is called, uses an RNA nanotechnological technique that allows it to assemble multiple identical RNA molecules into a highly organized structure, which significantly reduces the flexibility of individual RNA molecules and multiplies their molecular weight. (worldhealth.net)
ROCK is breaking the current limits of RNA structural investigations and enables 3D structures of RNA molecules to be unlocked that are difficult or impossible to access with existing methods, and at near-atomic resolution," said Yin, who together with Liao led the study. (worldhealth.net)
They hypothesized that such strategies could also be used to assemble naturally occurring RNA molecules into highly ordered circular complexes in which their freedom to flex and move is highly restricted by specifically linking them together. (worldhealth.net)
We speculated that these higher-order rings could be analyzed with high resolution by cryo-EM, which had been applied to RNA molecules with first success. (worldhealth.net)
The recent improvements of such parameters have made them suitable for the analysis of nucleic acids and for characterizing conformational changes in RNA molecules. (loria.fr)
Called a polymerase, the enzyme assembles RNA molecules. (chicagobiomedicalconsortium.org)
During her doctoral work at the Max Planck Institute for Molecular Genetics (MPIMG) and Freie Universität Berlin, Annita Louloupi within a team of scientists developed a new methodology to detect and analyze N 6 -methyladenosine (m 6 A) modifications on precursor RNA molecules. (mpg.de)

A common problem for researchers working with RNA is to determine the three-dimensional structure of the molecule given only a nucleic acid sequence. (wikipedia.org)
However, in the case of RNA much of the final structure is determined by the secondary structure or intra-molecular base pairing interactions of the molecule. (wikipedia.org)
A molecular model of a PPR protein recognizing a specific RNA molecule. (scitechdaily.com)
The identity of specific amino acid residues in the protein (colored sticks) determines the sequence of the RNA molecule it can bind. (scitechdaily.com)
Their secret is their versatility - they can find and bind a specific RNA molecule, and have the capacity to correct it if it is defective, or destroy it if it is detrimental. (scitechdaily.com)
We live in a world made and run by RNA, the equally important sibling of the genetic molecule DNA. (worldhealth.net)
To understand what an individual RNA molecule does, its 3D structure needs to be deciphered at the level of its constituent atoms and molecular bonds. (worldhealth.net)
For early life to be built on RNA, though, this molecule must have had the ability to make copies of itself. (elifesciences.org)
A gene, the basic unit of heredity, is a segment of DNA containing all the information necessary to synthesize a polypeptide (protein) or a functional RNA molecule. (msdmanuals.com)
A gene is a segment of DNA that provides the code to construct a protein or RNA molecule. (msdmanuals.com)

The main goal of this PhD project is to elucidate the conformational dynamics of protein-RNA complexes and to develop a method for understanding their allosteric communications. (loria.fr)
This approach is a prerequisite for the design of new therapeutics that target protein-RNA complexes. (loria.fr)
In this PhD the goal is to design and implement a method for characterizing the conformational dynamics of protein-RNA complexes using the set of trajectories generated from MD simulations in a systematic way. (loria.fr)
In the proposed PhD project, the main goal is to adapt such methods to analyse protein-RNA complexes. (loria.fr)
In this paper, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the "σ-finger" of the bacterial transcription initiation factor σ. (osti.gov)
My background is mainly in structural biology (biomolecular crystallography and cryo electron-microscopy) where I developed methodology for 3D reconstruction of biomolecular complexes. (lu.se)
In a first couple of examples, I will show how distance and shape restraints from SANS have helped to improve the uniqueness of structural models for two multi-protein-RNA complexes, in combination with NMR restraints and building blocks from crystallography [1, 2]. (lu.se)

Accompanying recent advances in determining RNA secondary structure is the growing appreciation for the importance of relatively simple topological constraints, encoded at the secondary structure level, in defining the overall architecture, folding pathways, and dynamic adaptability of RNA. (duke.edu)

This model learned how to accurately predict protein structures from their amino acid sequences by leveraging the sequence-structure relationships in thousands of known protein structures. (scienceboard.net)
The single sequence methods mentioned above have a difficult job detecting a small sample of reasonable secondary structures from a large space of possible structures. (wikipedia.org)
Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. (wikipedia.org)
Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known). (wikipedia.org)
We used long- and short-read RNA-seq technology to deeply sequence samples and compared the performance of a range of analysis tools on these data. (nature.com)
1mms is a 4 chain structure with sequence from Atcc 43589 . (proteopedia.org)
When DNA of a gene is transcribed, the entire sequence is copied into RNA, which is then spliced. (embl.org)
The likelihood of interaction was most strongly defined by the three-dimensional (3D) domain structure rather than linear DNA sequence. (elifesciences.org)
Using three-letter 'triplet' building blocks, this new ribozyme can copy various folded RNA strands, including the active part of its own sequence. (elifesciences.org)
Similar to DNA, RNA consists of four different nucleotides whose sequence encodes the genes. (mpg.de)
Anteroposterior patterning in Drosophila melanogaster is dependent on the sequence-specific RNA-binding protein Smaug, which binds to and regulates the translation of nanos (nos) mRNA. (embl.de)
Using homology modeling and site-directed mutagenesis, we have localized the RNA-binding surface of the Smaug SAM domain and have elaborated the RNA consensus sequence required for binding. (embl.de)
We find that SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of mismatches. (cdc.gov)

Understanding, verifying and implementing Emergency Use Authorization molecular diagnostics for the detection of SARS-CoV-2 RNA. (cdc.gov)

These images provide a 3D graphical representation of the biology and structure of a generic influenza virus, and are not specific to the 2009 H1N1 virus. (cdc.gov)
RNA-catalyzed RNA replication is widely believed to have supported a primordial biology. (elifesciences.org)
The Forschungsverbund Berlin e.V. (FVB) is granting this year's Marthe Vogt Award to Dr. Annita Louloupi for her outstanding contributions to the fundamental understanding of RNA biology. (mpg.de)
Our facilities provide the opportunity to study protein structure, molecular probes and drug design, system biology and molecular interactions in cells and tissues. (lu.se)
RNA Biology. (lu.se)
A fundamental challenge in biology is to understand how protein subunits have evolved the remarkable ability to spontaneously self-assembly into complex structures and to characterize the interactions, assembly pathway and three-dimensional structures of such protein assemblies. (lu.se)
With the rapid progress and improvements in the fields of macromolecular crystallography, Cryo-EM, small angle scattering, electron diffraction and use of XFELs, the new LINXS theme INTEGRATIVE STRUCTURAL BIOLOGY is formed to advance cutting-edge research and to encourage new users to utilize integrative structure biology to address key scientific questions. (lu.se)

We expect this advance to invigorate many areas of fundamental research and drug development, including the burgeoning field of RNA therapeutics. (worldhealth.net)

A new view is emerging in which tertiary interactions do not define RNA 3D structure, but rather, help select specific conformers from an already narrow, topologically pre-defined conformational distribution. (duke.edu)
Studies are providing fundamental insights into the nature of these topological constraints, how they are encoded by the RNA secondary structure, and how they interplay with other interactions, breathing new meaning to RNA secondary structure. (duke.edu)
For example, miRNAs regulate protein coding gene expression by binding to 3' UTRs, small nucleolar RNAs guide post-transcriptional modifications by binding to rRNA, U4 spliceosomal RNA and U6 spliceosomal RNA bind to each other forming part of the spliceosome and many small bacterial RNAs regulate gene expression by antisense interactions E.g. (wikipedia.org)
Summing the free energy for such interactions should provide an approximation for the stability of a given structure. (wikipedia.org)
The proposed deep learning model will be set up to address the characterization of dynamic properties of protein-RNA interactions at the 3D level. (loria.fr)
The team benefits from experts in RNA-protein interactions and structural bioinformatics, as well as in computer science. (loria.fr)
Moreover, by leveraging the large amounts of data generated by MD simulations, experimental and computational techniques [3], deep learning can help uncover the underlying mechanisms that govern protein-RNA interactions. (loria.fr)
Gene expression is known to be affected by interactions between local genetic variation and DNA accessibility, with the latter organized into three-dimensional chromatin structures. (elifesciences.org)

An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. (biomedcentral.com)
An instant visualization of the 3D RNA structures is provided. (biomedcentral.com)

All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. (osti.gov)
Inside of the virus, its ribonucleoproteins (RNPs) were shown in white, with their coiled structures, and three-bulbed polymerase complex on the ends. (cdc.gov)
Hence, a recent paper in PNAS, titled "Structure of a paramyxovirus polymerase complex reveals a unique methyltransferase-CTD conformation," published by a team of NU scientists led by Drs. Lamb and He is a very timely one, as it provides answers to some key questions about the virus replication mechanisms. (chicagobiomedicalconsortium.org)
Using a relatively novel technique, cryogenic electron microscopy (cryo-EM), the NU scientists were able to reconstruct a 3D structure of a multi-protein complex of paramyxovirus RNA polymerase. (chicagobiomedicalconsortium.org)
Structure of a paramyxovirus polymerase complex. (chicagobiomedicalconsortium.org)
We report RNA-catalysed RNA synthesis on structured templates when using trinucleotide triphosphates (triplets) as substrates, catalysed by a general and accurate triplet polymerase ribozyme that emerged from in vitro evolution as a mutualistic RNA heterodimer. (elifesciences.org)
3D structure of the complex consisting of the bacterial RNA polymerase (light and dark gray) and the viral λN protein (red). (phys.org)
The lower end of the λN reaches inside the RNA polymerase, linking its two halves. (phys.org)
RNA polymerase, a protein complex responsible for transcribing genetic information, would normally stop reading this information at the end of the bacterial gene and would ignore any viral genes inserted behind it. (phys.org)
The virus uses a trick that prevents the RNA polymerase from terminating the transcription process: It introduces 'lambda-N' (λN), a tiny protein that attaches itself to the host 's RNA polymerase and forces it to continue transcription of the viral genes . (phys.org)
Until now, and despite intensive efforts, researchers had failed to identify how this tiny protein can achieve such a feat. A Berlin-based team of researchers has now been able to visualize the 3-D structure of the RNA polymerase-λN-complex using high-resolution imaging, enabling them to provide a detailed explanation of this viral exploitation. (phys.org)
The nature of this structure told us that the small viral λN protein seals together the two halves of the RNA polymerase, thus preventing it from falling apart once it reaches the stop signal at the end of the bacterial gene," explains one of the study's first authors, Ferdinand Krupp, who is a doctoral student at Charité's Institute of Medical Physics and Biophysics. (phys.org)
Because of this, the RNA polymerase continues transcribing even once it reaches the viral genes. (phys.org)

The highly compact RNA has both familiar and novel structural motifs. (proteopedia.org)
One of the most difficult issues in mining available structural data is the search of RNA structural motifs and fragments in a conformational space. (biomedcentral.com)

The second one finds all base pairs and multiplets in the RNA structure and offers the classification of canonical and non-canonical base-pairs. (biomedcentral.com)

The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. (biomedcentral.com)
The library of RNA secondary structures (and their graphics) is made available. (biomedcentral.com)
The triplets cooperatively invaded and unraveled even highly stable RNA secondary structures, and support non-canonical primer-free and bidirectional modes of RNA synthesis and replication. (elifesciences.org)

Researchers at Princeton University have discovered the 3D structure of an enzyme that cuts to ribbons the genetic material of viruses and helps defend against bacteria. (princeton.edu)
Interferon relays distress signals from infected cells to neighboring healthy cells, thereby activating RNase L to turn on its ability to slice through RNA, a type of genetic material that is similar to DNA. (princeton.edu)
These findings provide evidence that genetic and epigenetic factors operate within the context of three-dimensional chromatin structure. (elifesciences.org)
Like DNA, strands of RNA contain genetic data. (elifesciences.org)
Although such modifications do not alter the genetic information carried by RNA, they can affect its functionality. (mpg.de)

The sites of mutations conferring resistance to thiostrepton and micrococcin line a narrow cleft between the RNA and the N-terminal domain. (proteopedia.org)
Now that we have the human RNase L structure, we can begin to understand the effects of carcinogenic mutations in the RNase L gene. (princeton.edu)
The newly found structure reveals the positions of these mutations and explains why some of these mutations could be detrimental, perhaps leading to cancer, Korennykh said. (princeton.edu)

However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. (osti.gov)
CoV transcription involves a discontinuous RNA synthesis (template switch) during the extension of a negative copy of the subgenomic mRNAs. (bionity.com)
The challenge facing Annita Louloupi at the beginning of her doctoral work was to develop new analytical techniques that would be accurate and sensitive enough to detect m 6 A-modified RNA during its brief "nascent" state, i.e. during the short phase immediately after transcription yet before RNA undergoes RNA splicing. (mpg.de)
It houses the cell's DNA and is the hub for DNA replication, transcription, and RNA processing. (cshlpress.com)

Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. (embl.de)

New approaches have been developed that take advantage of topological constraints in determining RNA backbone conformation based on secondary structure, and a limited set of other, easily accessible constraints. (duke.edu)
While the methods are similar, there are slight differences in the approaches to RNA and DNA structure prediction. (wikipedia.org)

RL11_THEMA ] This protein binds directly to 23S ribosomal RNA. (proteopedia.org)
While the C-terminal domain of L11 binds RNA tightly, the N-terminal domain makes only limited contacts with RNA and is proposed to function as a switch that reversibly associates with an adjacent region of RNA. (proteopedia.org)
We show here that the SAM domain of Saccharomyces cerevisiae Vts1 binds RNA with the same specificity as Smaug and that Vts1 induces transcript degradation through a mechanism involving the cytoplasmic deadenylase CCR4. (embl.de)

Discovering this novel mechanism that regulates RNA splicing is relevant basic knowledge and adds to the functional roles that chromatin structure plays in gene regulation - from development to disease processes. (embl.org)
Her main goal was to understand how m 6 A regulates RNA splicing and, more specifically, the rate of splicing. (mpg.de)

When CTCF does not bind to one of the sides, and thus no loop is formed, the resulting RNA is different. (embl.org)
For example, these triplets work together to bind tightly to RNA strands and unravel structures that block RNA copying. (elifesciences.org)

Secondary structure can be predicted from one or several nucleic acid sequences. (wikipedia.org)
We performed northern blot analyses for the guide RNA truncations and found increased levels of expression for the longer tracrRNA sequences, suggesting that improved target cleavage was at least partially due to higher sgRNA expression or stability ( Fig. 1c ). (cdc.gov)

Scientists have revealed the 3D structure of the molecular transporter TSPO for the first time, opening the door to novel paths for the diagnosis and treatment of brain diseases. (scitechdaily.com)
Now, for the first time, scientists in Göttingen have solved the high-resolution structure of the molecular transporter TSPO, which introduces cholesterol into mitochondria. (scitechdaily.com)
Therefore, characterizing the structure, dynamics and conformational changes of biomolecules can help understand the molecular mechanisms of underlying diseases, and hopefully prevent them by designing drugs. (loria.fr)
Molecular modeling is the field of characterizing structure of biomolecules. (loria.fr)
The course provides a detailed exploration of the structure and function of genes at the molecular and biochemical level. (abdn.ac.uk)
With the help of various forms of mass spectrometry, synchrotron radiation, protein production & labelling, and bioinformatics, our facilities provide the opportunity to study protein structure and dynamics, molecular probes and drug design. (lu.se)

In vivo , DNA structures are more likely to be duplexes with full complementarity between two strands, while RNA structures are more likely to fold into complex secondary and tertiary structures such as in the ribosome , spliceosome , or transfer RNA . (wikipedia.org)
A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. (biomedcentral.com)

Structures that have been conserved by evolution are far more likely to be the functional form. (wikipedia.org)
Our 3D paints really open up the ability to print different functional or structural objects to make habitats beyond Earth. (innovationtoronto.com)
They show for the first time the functional impact of the 3D structure of chromatin - the tightly-packed structure that the long DNA thread adopts to fit into the cell's nucleus - on the RNA-regulating splicing mechanism. (embl.org)
In order for these "instructions" (genes) to be converted into a functional product, the DNA is first copied - or transcribed - into RNA (ribonucleic acid). (mpg.de)
When put onto a specific region within the "nascent" RNA, the m 6 A acts as a "fast-track ticket" in the processing queue - RNA with such a ticket will develop into "mature" functional RNA faster than that without a ticket. (mpg.de)

Applied to well-known model RNAs with different sizes and functions as benchmarks, the team showed that their method enables the structural analysis of the contained RNA subunits with a technique known as cryo-electron microscopy (cryo-EM). (worldhealth.net)

In cryo-EM, many single particles are flash-frozen at cryogenic temperatures to prevent any further movements, and then visualized with an electron microscope and the help of computational algorithms that compare the various aspects of a particle's 2D surface projections and reconstruct its 3D architecture. (worldhealth.net)

The advance, described by Stanford University researchers in a paper in Science on August 26, may help scientists uncover the biological functions of RNA and pave the way to the discovery of novel RNA-targeted drugs. (scienceboard.net)
According to the rules of RNA-Puzzles, when scientists in the community discover a new RNA structure experimentally, they withhold publication of the details until other RNA-Puzzles participants have submitted their structural predictions, which are then judged based on how closely they match the experimentally determined structure. (scienceboard.net)
Using nuclear magnetic resonance spectroscopy, two teams working with the Göttingen-based scientists Markus Zweckstetter and Stefan Becker have now shown the complex three-dimensional structure of the protein "at work" in atomic detail. (scitechdaily.com)
this has led scientists to try to artificially create RNA replicase ribozymes that could copy themselves. (elifesciences.org)

The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. (embl.de)

The structures reveal that-for both the primary σ-factor and extracytoplasmic (ECF) σ-factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA-the "σ-finger" is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from ~5 nt to ~10 nt. (osti.gov)

August 26, 2021 -- A new deep-learning system called Atomic Rotationally Equivariant Scorer (ARES) significantly improves the prediction of RNA structures over previous artificial intelligence (AI) models. (scienceboard.net)
Next, the researchers entered ARES' predictions into four new rounds of the RNA-Puzzles blind structure prediction challenge. (scienceboard.net)
This list of RNA structure prediction software is a compilation of software tools and web portals used for RNA structure prediction. (wikipedia.org)
This article is about the computational prediction of nucleic acid structure. (wikipedia.org)
Many secondary structure prediction methods rely on variations of dynamic programming and therefore are unable to efficiently identify pseudoknots . (wikipedia.org)
The structure prediction methods can follow a completely theoretical approach, or a hybrid one incorporating experimental data. (wikipedia.org)

Many RNAs fold in complex yet predictable ways, with small segments base-pairing with each other. (worldhealth.net)
In this apparent paradox, a ribozyme needs to fold to copy RNA, but when folded, is itself copied poorly. (elifesciences.org)

Advances in understanding ribosome structure and function are shaping new directions in proteomic discovery. (genengnews.com)
The 3D image is a model of the human ribosome. (genengnews.com)

Computational methods are developed to predict the 3D structure of protein assemblies at high resolution. (lu.se)

CoV N protein is required for coronavirus RNA synthesis, and has RNA chaperone activity that may be involved in template switch. (bionity.com)
Your students will learn about RNA vaccines in the context of coronavirus but the model can be used to teach RNA vaccines in other contexts too. (fishersci.com)

RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. (biomedcentral.com)

Of particular interest are basepairs files which describe canonical and non-canonical (non-Watson-Crick) base pairings in RNA secondary structure. (haskell.org)

RNA nucleotides can be biochemically modified during their life cycle. (mpg.de)
Crystal structures of tRNASec lacking nucleotides 72-76 of the acceptor stem were determined up to 2.0 Å resolution. (uni-goettingen.de)

CryoREAD uses deep learning to identify structure information and subsequently construct the 3D structure of nucleic acids. (nature.com)
Among several fixes and improvements, it mainly provides a new component to easily construct an RNA 2D: the bracket notation panel. (github.io)

In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. (biomedcentral.com)
A deep knowledge of complex three-dimensional folds of RNA structures is essential to understand the range of their biological functions. (biomedcentral.com)
the other is the peptide chain which formed the natural structure of protein through the folding process to obtain biological activity and express life information [ 2 ]. (ijpsonline.com)
As the expression vector of life information, the specific spatial structure formed by protein folding is the basis of its biological function. (ijpsonline.com)
They are involved in the formation of protein folding/degradation signalling pathway, maintaining the normal spatial structure and normal biological function of protein [ 3 ]. (ijpsonline.com)

Triplet substrates thus resolve a central incongruity of RNA replication, and here allow the ribozyme to synthesise its own catalytic subunit '+' and '-' strands in segments and assemble them into a new active ribozyme. (elifesciences.org)
RNA strands are made of four different letters attached to each other in a specific order. (elifesciences.org)
Biochemical techniques were used to engineer a ribozyme that copies RNA strands by adding letters not one-by-one, but three-by-three. (elifesciences.org)

The term Picornaviridae is derived from pico , which means small (typically, 18-30 nm), and RNA, referring to the single-stranded positive-sense RNA common to all members of the Picornaviridae family. (medscape.com)

To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human and show that they unwind structured substrates to promote degradation. (rcsb.org)
Competition for the exosome core may ensure that RNA is committed to degradation by DIS3 when engaged by MTR4. (rcsb.org)
The capsid-coat protein serves multiple functions, including (1) protecting the viral RNA from degradation by environmental RNase, (2) determining host and tissue tropism by recognition of cell-specific cell-membrane receptors, (3) penetrating target cells and delivering the viral RNA into the cell cytoplasm, and (4) selecting and packaging viral RNA. (medscape.com)

By comparison, the three other scoring methods included the correct structure less than 50% of the time. (scienceboard.net)
For experimental methods, see Nucleic acid structure determination . (wikipedia.org)
Most popular methods for predicting RNA and DNA's secondary structure involve dynamic programming . (wikipedia.org)
Few methods for three-dimensional structure modeling of nucleic acids from cryo-EM data exist. (nature.com)
In comparison to complementary methods such as single-crystal X-ray diffraction (SC-XRD), SAXS allows analysis of the structure of these materials in their native state. (anton-paar.com)

Using cryo- electron microscopy , the researchers took a total of 700,000 images of the protein complex from various angles, using these to compute its 3-D structure. (phys.org)

the CRISPR-associated nuclease Cas9 (SpCas9), a specificity-determining CRISPR RNA (crRNA), and an auxiliary trans-activating crRNA (tracrRNA) 11 . (cdc.gov)

To address this issue, the researchers, led by Raphael Townshend, a Stanford doctoral graduate and founder and CEO of Atomic AI, designed ARES to make its RNA structure predictions based on minimal assumptions. (scienceboard.net)
To assess the ability of ARES to identify accurate structural models of previously unseen RNAs, the Stanford researchers compiled a benchmark data set of seven years' worth of winning entries in the RNA-Puzzles contest, a long-running challenge organized by the RNA scientific community. (scienceboard.net)
For each RNA structure in the RNA-Puzzles data set, the researchers generated a minimum of 1,500 structural models using the Rosetta FARFAR2 sampling software. (scienceboard.net)
Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field. (biomedcentral.com)
The Göttingen researchers hope that detailed information about the transporter's structure will help to develop new TSPO-binding drugs. (scitechdaily.com)
Researchers at Princeton have deciphered the 3D structure of RNase L, an enzyme that slices through RNA and is a first responder in the innate immune system. (princeton.edu)
The researchers found that one protomer finds and attaches to the RNA, while the other protomer snips it. (princeton.edu)
To discover the enzyme's structure, the researchers first created a crystal of the RNase L enzyme. (princeton.edu)
Now that the human structure has been solved, researchers can explore ways to either enhance or dampen RNase L activity for medical and therapeutic uses, Korennykh said. (princeton.edu)
Northwestern University researchers have, for the first time, determined the 3D atomic structure of a key complex in paramyxoviruses, a family of viruses that includes mumps, human parainfluenza and respiratory syncytial virus (RSV). (chicagobiomedicalconsortium.org)
To find the unique structure, researchers used cryogenic electron microscopy (cryo-EM). (chicagobiomedicalconsortium.org)
Although the first documented case of mumps occurred in the 5th century and measles in the 9th century, researchers did not have the equipment to characterize their atomic structures until relatively recently. (chicagobiomedicalconsortium.org)

Such structures are often assembled spontaneously from individual components through the process of self-assembly. (lu.se)

CryoREAD automatically builds DNA-RNA atomic structure from cryo-EM maps. (nature.com)
CryoREAD, a fully automated DNA/RNA atomic structure modeling method based on deep learning, was developed to fill this gap. (nature.com)

This duplication is a chemical reaction that could be driven by an 'RNA replicase' ribozyme. (elifesciences.org)
When RNA is copied, one strand acts as a template, and a replicase ribozyme would accurately guide which letters are added to the strand under construction. (elifesciences.org)
Yet, although ribozymes can be made to copy straight RNA templates this way, folded RNA templates - including the replicase ribozyme itself - impede copying. (elifesciences.org)

Here we demonstrate that the sterile-alpha motif (SAM) domain of Smaug functions as an RNA-recognition domain. (embl.de)
RNA recognition via the SAM domain of Smaug. (embl.de)

for BVDV frequently nonhomologous RNA recombination events lead to the appearance of genetically distinct viruses that are lethal to the host. (bionity.com)
Although the paramyxoviruses constitute a different family than coronaviruses, both families are enveloped, RNA-type viruses, sharing many similarities between their replication and infection cycles. (chicagobiomedicalconsortium.org)

An influenza virus' RNP is composed of both RNA and protein. (cdc.gov)

However, RNA catalysis is dependent upon RNA folding, and this yields structures that can block replication of such RNAs. (elifesciences.org)

Here, we review recent advances in our understanding of topological constraints encoded by the RNA secondary structure. (duke.edu)

Anatomy8

Organisms10

Diseases1

Chemicals and Drugs98

Analytical, Diagnostic and Therapeutic Techniques and Equipment46

Psychiatry and Psychology1

Phenomena and Processes83

Disciplines and Occupations5

Technology, Industry, Agriculture1

Information Science25

Health Care5

Proteins26

Genome10

Molecules15

Molecule10

Complexes7

Determining RNA secondary structure1

Sequence13

SARS-CoV-2 RNA1

Biology7

Therapeutics1

Interactions8

Visualization2

Polymerase13

Structural motifs2

Classification1

Secondary structures3

Genetic5

Mutations3

TRANSCRIPTION4

HAIRPIN1

Approaches2

Binds3

Regulates2

Bind2

Sequences2

Molecular6

Tertiary structures2

Functional5

Enables1

Reconstruct1

Scientists4

Residues1

Nascent1

Prediction6

Fold2

Ribosome2

Computational1

Coronavirus2

Conformational1

Base pairings1

Nucleotides2

Construct2

Biological5

Strands3

Single stranded1

Degradation3

Methods5

Cryo-electron m1

Specificity1

Researchers12

Assembly1

Atomic structure2

Replicase3

Recognition2

Viruses2

Influenza Virus1

Catalysis1

Advances1