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Related Concept Videos

RNA Structure01:19

RNA Structure

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...
RNA Structure01:23

RNA Structure

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...
RNA Structure01:23

RNA Structure

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...
Nucleic Acid Structure01:25

Nucleic Acid Structure

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
DNA has a double-helix structure. The...
RNA Stability01:53

RNA Stability

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...
RNA Stability01:53

RNA Stability

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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Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
11:32

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

Topological classification of RNA structures.

Michael Bon1, Graziano Vernizzi, Henri Orland

  • 1Service de Physique Théorique, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France; Ecole Nationale Supérieure des Mines de Paris, 75006 Paris, France.

Journal of Molecular Biology
|May 20, 2008
PubMed
Summary
This summary is machine-generated.

We introduce a new method to classify RNA secondary structures with pseudoknots using topological genus. This classification helps identify novel RNA structural motifs and understand folding complexity.

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Area of Science:

  • * Molecular Biology
  • * Computational Biology
  • * Structural Biology

Background:

  • * RNA molecules fold into complex secondary structures essential for their function.
  • * Existing classification methods for RNA structures, especially those with pseudoknots, are limited.
  • * Topological properties offer a novel perspective for understanding RNA folding complexity.

Purpose of the Study:

  • * To present a novel topological classification for RNA secondary structures incorporating pseudoknots.
  • * To define and utilize the topological genus as a quantitative measure of RNA folding complexity.
  • * To identify and classify topological folding motifs in RNA structures.

Main Methods:

  • * Developed a classification system based on the topological genus of circular diagrams representing RNA base-pair structures.
  • * Analyzed RNA structures from the Worldwide Protein Data Bank and Pseudobase databases.
  • * Focused analysis on Watson-Crick and G-U wobble base pairs.

Main Results:

  • * Planar diagrams (zero genus) correspond to simple secondary structures, while non-planar diagrams (higher genus) represent pseudoknotted structures.
  • * Successfully classified known RNA structures based on their topological genus.
  • * Identified potential new RNA structural motifs through this topological classification.

Conclusions:

  • * Topological genus provides a robust metric for quantifying the complexity of RNA secondary structures.
  • * This classification framework enables the discovery of novel RNA structural motifs.
  • * The method offers a new avenue for analyzing and understanding RNA folding patterns.