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Related Concept Videos

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 Structure01:19

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...
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
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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Related Experiment Video

Updated: Jul 6, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

A rule-based approach for RNA pseudoknot prediction.

X Z Fu1, H Wang, R W Harrison

  • 1Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA. xfu1@gsu.edu

International Journal of Data Mining and Bioinformatics
|April 11, 2008
PubMed
Summary

We developed a novel RNA pseudoknot structure prediction method using term rewriting. This approach accurately identifies complex RNA structures, achieving over 90% accuracy for most pseudoknots.

Related Experiment Videos

Last Updated: Jul 6, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Area of Science:

  • Computational Biology
  • Molecular Biology
  • Bioinformatics

Background:

  • RNA is crucial for cellular information transfer, with pseudoknots being vital structural motifs.
  • Accurate prediction of RNA pseudoknot structures is essential for understanding their function.

Purpose of the Study:

  • To present a new method for predicting RNA pseudoknot structures using term rewriting.
  • To evaluate the accuracy and potential of this novel approach in RNA structure prediction.

Main Methods:

  • RNA structures are represented as terms.
  • Term rewriting rules are developed for pseudoknot prediction.
  • The method is implemented using Mfold and the Maude language.

Main Results:

  • The method was tested on 211 pseudoknots from PseudoBase.
  • Achieved an average accuracy of 74.085% compared to experimental structures.
  • Most predicted pseudoknots showed accuracy above 90%.

Conclusions:

  • Term rewriting demonstrates significant potential for RNA structure prediction.
  • This method can be applied to predict pseudoknots and discover higher-level RNA structures.
  • Highlights the utility of term rewriting in complex RNA tertiary interaction analysis.