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Related Concept Videos

RNA Structure01:19

RNA Structure

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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RNA Editing02:23

RNA Editing

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
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Nucleic Acids02:43

Nucleic Acids

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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
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The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Updated: Jun 15, 2025

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
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An ontology-based knowledge graph for representing interactions involving RNA molecules.

Emanuele Cavalleri1, Alberto Cabri1, Mauricio Soto-Gomez1

  • 1AnacletoLab, Computer Science Department, University of Milan, Milan, 20133, Italy.

Scientific Data
|August 22, 2024
PubMed
Summary
This summary is machine-generated.

We developed RNA-KG, a comprehensive knowledge graph integrating RNA data from over 60 databases. This resource centralizes information on RNA molecules, genes, proteins, and chemicals, aiding RNA world research and drug discovery.

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • The study of RNA molecules is crucial for understanding biological processes and diseases.
  • Current RNA data is fragmented across numerous public repositories.
  • A unified and semantically consistent representation of RNA-related knowledge is lacking.

Purpose of the Study:

  • To create RNA-KG, a centralized knowledge graph for the
  • RNA world
  • .
  • To integrate diverse RNA data with genes, proteins, and chemicals.
  • To provide a resource for exploring and analyzing RNA-related biomedical knowledge.

Main Methods:

  • Data integration from over 60 public databases.
  • Development of a meta-graph for ontological description.
  • Utilization of a semantically abstracted knowledge model for ontological alignment.
  • Creation of a SPARQL endpoint for querying RNA-KG.

Main Results:

  • RNA-KG integrates biological knowledge about coding and non-coding RNAs.
  • The knowledge graph connects RNA molecules with genes, proteins, and chemicals.
  • Topological analysis of RNA-KG offers insights into the
  • RNA world
  • .
  • RNA-KG is available for download and direct exploration.

Conclusions:

  • RNA-KG provides a centralized, semantically consistent resource for RNA research.
  • The knowledge graph facilitates the discovery of new drugs and personalized medicine.
  • RNA-KG can be updated with new data and adapted for specific biomedical problems.