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Showing 1 to 20 of 59 for “"RNA Structure"”.
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Graphical methods in RNA structure matching
… almost every base can be found in an RNA transcript. This is a surprising observation since most of the genome does not encode proteins. This RNA must serve an important regulatory function – important because producing non-coding RNA is an energy intensive process, and in the absence …
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RNA structure analysis : algorithms and applications
… thesis, efficient algorithms for aligning RNA secondary structures and mining unknown RNA motifs are presented. As the major contribution, a structure alignment algorithm, which combines both primary and secondary structure information, can find the optimal alignment between two given …
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Algorithm development for RNA structure prediction in RNA viruses
RNA structures play many different roles in the life cycles of RNA viruses, including in directing translational control, genome replication, subgenomic RNA synthesis, and encapsidation. However, predicting these structures can be challenging, especially when it comes to pseudoknots, long-range …
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A new approach to feature extraction for RNA structure comparision
In recent years, RNA structural comparison becomes a crucial problem in bioinformatics research. Generally, it is a popular approach for representing the RNA secondary structures with arc-annotation sets. Several methods can be used to compare two RNA structures, such as tree edit distance, longest …
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Generative Machine Learning Models for RNA Structure Prediction and Design
Ribonucleic acid (RNA) is a fundamental molecule in biology, central to the regulation and execution of life’s most essential processes. Its diverse roles range from encoding genetic information to catalyzing biochemical reactions. Beyond its modern biological functions, RNA is also believed to …
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A bioinformatics framework for RNA structure mining, motif discovery and polyadenylation analysis
The RNA molecules play various important roles in the cell and their functionality depends not only on the sequence information but to a large extent on their structure. The development of computational and predictive approaches to study RNA molecules is extremely valuable. In this research, a tool …
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Click Chemistry on DNA and Targeting RNA structure with Peptide Boronic Acids
… boronic acid libraries. It is well known that RNA ligands incorporating basic and intercalating moieties display high RNA affinity. Unfortunately, these ligands are also often plagued by promiscuous binding to off-target substrates. Due to the potential utility of RNA ligands in biology and …
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A Predictive Model for Secondary RNA Structure Using Graph Theory and a Neural Network.
… a graph-theoretic representation of secondary RNA structure found in the database RAG: RNA-As-Graphs. We model the bonding of two RNA secondary structures to form a larger structure with a graph operation called merge. The resulting data from each tree merge operation is summarized and …
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The analysis of a conserved RNA structure in the 3D polymerase encoding region of Human Parechovirus 1
Picornaviruses are important causes of human illness and it is necessary to understand more about how these viruses function. Human parechoviruses (HPeV) are common pathogens and studies have shown that 95% of people become infected with HPeV at a very early age, usually with symptoms such as mild …
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Point mutational examination of eukaryotic initiation factor 4E (eIF4E), inclusion bodies analysis, and Barley Yellow Dwarf Virus (BYDV) exonuclease resistant RNA structure mapping and prediction
… factor 4E (eIF4E) binds the 5’m7GTP cap structure of mRNA in order to facilitate effective translation. Recessive eIF4E alleles harboring naturally occurring point mutations have been associated with resistance to viral infection, particularly in members of the genus Potyvirus. Resistance …
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The role of RNA structures in the evolution of respiratory RNA virus genomes.
RNA secondary structures in RNA viral genomes play important roles in a range of functions, including packaging, protection from cellular nucleases, and regulating viral replication. Furthermore, RNA structures have been shown to be immunostimulatory. In the case of Influenza A virus (IAV), during …
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The conformational landscape of RNA translational regulators and their potential as drug discovery targets
RNA is an underutilized target for drug discovery. Once thought to be a passive carrier of genetic information, RNA is now known to play a critical role in essentially all aspects of biology including signaling, gene regulation, catalysis, and retroviral infection. It is now well-established that …
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M6A Reshapes the Folding and Recognition Landscape of RNAs
<p>Ribonucleic acid (RNA) is a versatile and dynamic biomolecule that serves as an indispensable component in the central dogma of molecular biology. The realization that RNA plays a wide variety of roles in gene expression and regulation has been accompanied by the discovery that virtually all …
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CHARACTERIZATION OF THE FUNCTION OF THE DEAD-BOX RNA HELICASE DBP2
… there are highly coupled mechanisms that require RNA-binding proteins to facilitate gene expression. Proper RNA structure and ribonucleoprotein (RNP) complex formation are critical for gene expression. DEAD-box proteins are the largest class of RNA helicases that play fundamental roles in RNA and …
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Binding Determinants of HIV-1 REV RNA to the Pokeweed Antiviral Protein
… residue from the sarcin/ricin loop (SRL) of rRNA through a process called depurination. PAP has also been shown to depurinate the ORF of Rev RNA of HIV-1 in vivo without causing toxicity. The sequence and structure of Rev RNA that PAP interacts is identified and compared to the sarcin/ricin …
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The synthesis and in vitro evaluation of chemically modified siRNAs that contain internal azobenzene derivative spacers for selective and tunable photocontrol of activity
Short interfering RNAs (siRNAs) are biopolymers that are used as post-transcriptional gene regulators and as a natural endogenous defense against attack from viruses. These molecules hold a great deal of interest as pharmaceuticals for the knockdown of unregulated genes, such as in cancers. Through …
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A Predictive Model Which Uses Descriptors of RNA Secondary Structures Derived from Graph Theory.
<p>The secondary structures of ribonucleic acid (RNA) have been successfully modeled with graph-theoretic structures. Often, simple graphs are used to represent secondary RNA structures; however, in this research, a multigraph representation of RNA is used, in which vertices represent stems and …
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Detection of RNA structural heterogeneity : computational analysis and development of web-based tool
… in protein formation, the linear sequence on RNA is capable of folding into higher order structures which may interact with other molecules and play key functional roles in the cell. Current methods in characterizing RNA structure via experimental probing are limited to the population average, …
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Exploring conformational variability of an rna domain in the ribosome: from structure and function to potential antibiotic targeting
<p>RNA in nature is modified at many specific sites to order to gain extra functions or to expand the genetic code. One of such RNAs is ribosomal RNA (rRNA), which contains several modified bases, particularly around the functionally significant sites. We have focused on understanding the …
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A data science approach to pattern discovery in complex structures with applications in bioinformatics
… for discovering patterns or motifs from complex structures, particularly complex RNA structures. RNA secondary and tertiary structure motifs are very important in biological molecules, which play multiple vital roles in cells. A lot of work has been done on RNA motif annotation. However, pattern …
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