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Related Concept Videos

RNA Structure01:23

RNA Structure

71.8K
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 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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Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

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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,...
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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
DNA...
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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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Updated: Aug 10, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

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Pseudoknots in RNA Structure Prediction.

Andrew Hollar1, Hunter Bursey1, Hosna Jabbari1

  • 1Department of Computer Science, University of Victoria, Victoria, Canada.

Current Protocols
|February 13, 2023
PubMed
Summary
This summary is machine-generated.

Computational methods for RNA pseudoknot prediction are crucial for understanding RNA function in biotechnology and medicine. This overview highlights current methods and their applications for improved accuracy and efficiency.

Keywords:
RNA interaction predictionRNA secondary structure predictionRNA-RNARNA-proteinisolated RNApseudoknot

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Chemistry

Background:

  • RNA molecules are vital in cellular processes, with function dictated by structure.
  • Experimental RNA structure determination is complex and resource-intensive.
  • Existing computational methods often overlook pseudoknotted structures, which are functionally significant.

Purpose of the Study:

  • To provide an overview of computational pseudoknot prediction methods.
  • To discuss the best-use cases for various pseudoknot prediction tools.
  • To highlight the ongoing challenges and advancements in RNA structure prediction.

Main Methods:

  • Review and categorization of existing pseudoknot prediction algorithms.
  • Analysis of method performance based on application scope (single RNA, RNA-RNA, RNA-protein interactions).
  • Discussion of limitations related to structure class and length.

Main Results:

  • Pseudoknots play critical roles in RNA function and interactions.
  • Many computational methods focus on secondary structures, neglecting pseudoknots.
  • Specialized methods improve accuracy for specific pseudoknot types and lengths.

Conclusions:

  • Accurate pseudoknot prediction is essential for advancing RNA-based biotechnology and medicine.
  • The development of efficient computational tools is crucial for RNA structure analysis.
  • Ongoing research aims to enhance the accuracy and scope of pseudoknot prediction methods.