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RNA Structure01:23

RNA Structure

79.2K
Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. 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): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
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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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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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RNA Stability01:53

RNA Stability

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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

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RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
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Related Experiment Video

Updated: Feb 11, 2026

A Structured Rehabilitation Protocol for Improved Multifunctional Prosthetic Control: A Case Study
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RNApdbee 2.0: multifunctional tool for RNA structure annotation.

Tomasz Zok1,2, Maciej Antczak1, Michal Zurkowski1

  • 1Institute of Computing Science, and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.

Nucleic Acids Research
|May 3, 2018
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Summary
This summary is machine-generated.

RNApdbee 2.0 is an advanced webserver for RNA structure annotation, enhancing secondary and 3D structure predictions. It offers new algorithms for pseudoknot recognition and visualization of complex RNA structures.

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Area of Science:

  • RNA structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Accurate RNA structure annotation is vital for secondary and 3D structure prediction.
  • The original RNApdbee webserver (2014) focused on extracting secondary structures from PDB files.

Purpose of the Study:

  • To present RNApdbee 2.0, an upgraded multifunctional tool for comprehensive RNA structure annotation.
  • To reveal the relationship between RNA secondary and 3D structures using PDB or PDBx/mmCIF data.
  • To incorporate advanced algorithms for pseudoknot recognition and analysis of base pair impact.

Main Methods:

  • Development of new algorithms for high-ordered pseudoknot recognition in large RNA structures.
  • Implementation of visualization tools for RNA secondary structures, including quadruplexes and non-canonical interactions.
  • Annotation of structural motifs (stems, loops, single-stranded fragments) for easier identification.

Main Results:

  • RNApdbee 2.0 provides advanced RNA structure annotation capabilities.
  • The tool effectively reveals the interplay between RNA secondary and 3D structures.
  • New algorithms enhance the recognition and classification of complex pseudoknots.

Conclusions:

  • RNApdbee 2.0 is a powerful, publicly available webserver for RNA structure analysis.
  • The intuitive interface facilitates the study of RNA structural biology and bioinformatics.
  • The enhanced features improve RNA secondary and 3D structure prediction accuracy.