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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...
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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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Related Experiment Video

Updated: May 15, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots.

Michaël Bon1, Cristian Micheletti, Henri Orland

  • 1Institut de Physique Théorique, CEA Saclay, CNRS URA 2306, 91191 Gif-sur-Yvette, France.

Nucleic Acids Research
|December 19, 2012
PubMed
Summary

McGenus predicts RNA secondary structures, including complex pseudoknots, using a novel genus-based classification and stochastic search. This advanced algorithm handles longer sequences and offers competitive performance against existing methods.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Predicting RNA secondary structures is crucial for understanding gene regulation and function.
  • Existing algorithms often struggle with complex structures like pseudoknots.
  • Topological properties of RNA structures offer a new perspective for prediction.

Purpose of the Study:

  • To develop McGenus, an algorithm for predicting RNA secondary structures with pseudoknots.
  • To utilize a topological genus classification for improved structure prediction.
  • To enable the prediction of minimum free energy structures for longer RNA sequences.

Main Methods:

  • Classification of RNA structures based on topological genus.
  • Monte Carlo algorithm with replica exchange for stochastic search.
  • Minimization of a scoring function incorporating free energy and a genus penalty.

Main Results:

  • McGenus successfully predicts RNA secondary structures with non-trivial pseudoknots.
  • Validation against TT2NE shows competitive performance for longer sequences.
  • Application to tmRNA database yields results comparable to existing algorithms.
  • The study identifies potential limitations in current free energy scoring functions.

Conclusions:

  • McGenus provides an effective approach for RNA secondary structure prediction, including pseudoknots.
  • The genus-based classification offers a valuable framework for RNA structure analysis.
  • The algorithm's performance suggests its utility for large-scale RNA studies.
  • McGenus is available as a web server for broader accessibility.