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Related Concept Videos

RNA Structure01:23

RNA Structure

78.0K
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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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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Leaky Scanning02:28

Leaky Scanning

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Viral Mutations00:36

Viral Mutations

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A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
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Viruses with RNA Genomes01:29

Viruses with RNA Genomes

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RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
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Related Experiment Video

Updated: Dec 7, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
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Using SHAPE-MaP To Model RNA Secondary Structure and Identify 3'UTR Variation in Chikungunya Virus.

Emily A Madden1, Kenneth S Plante2, Clayton R Morrison2

  • 1Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA.

Journal of Virology
|October 1, 2020
PubMed
Summary

Chikungunya virus (CHIKV) RNA secondary structures are crucial for its lifecycle. This study mapped CHIKV genome structures, identifying 23 stable regions and novel 3'UTR variants, aiding future research on CHIKV replication and pathogenesis.

Keywords:
RNA structureSHAPE-MaPchikungunyaplus-strand RNA virus

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Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes
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Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes
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Area of Science:

  • Virology
  • Molecular Biology
  • Genomics

Background:

  • Chikungunya virus (CHIKV), a mosquito-borne alphavirus, causes debilitating arthralgia.
  • The role of RNA secondary structure in CHIKV replication is not well understood.
  • Previous studies showed limited RNA structure conservation among alphaviruses.

Purpose of the Study:

  • To investigate the impact of RNA secondary structure on CHIKV biology.
  • To identify and characterize functional RNA structures within the CHIKV genome.
  • To analyze RNA structures in 3'UTR variants affecting mosquito cell replication.

Main Methods:

  • Utilized SHAPE-MaP chemical probing to model CHIKV genomic RNA secondary structure.
  • Analyzed regions with high structural specificity for potential functional importance.
  • Examined RNA flexibility and secondary structures of multiple 3'UTR variants.

Main Results:

  • Identified 23 regions with higher than average structural stability in the CHIKV genome.
  • Confirmed functional importance of one identified RNA structure through mutagenesis.
  • Discovered novel RNA structures in 3'UTR variants, with a replication-enhancing duplication increasing unstructured RNA.

Conclusions:

  • The CHIKV genome possesses unique, specific RNA secondary structures.
  • Provides a strategy for testing the functional relevance of these structures in CHIKV replication.
  • Highlights the complexity of CHIKV RNA structures and their role in pathogenesis.