Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

554
Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
554
Viruses with RNA Genomes01:29

Viruses with RNA Genomes

603
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...
603
DNA Base Pairing02:27

DNA Base Pairing

32.6K
Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,
32.6K
DNA Base Pairing02:27

DNA Base Pairing

31.2K
31.2K
Leaky Scanning02:28

Leaky Scanning

5.5K
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...
5.5K
Nucleic Acid Structure01:25

Nucleic Acid Structure

8.2K
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...
8.2K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

COVID-19 vaccination induces cross-neutralisation of sarbecoviruses related to SARS-CoV-2.

NPJ vaccines·2026
Same author

Studying the Deep Evolution of Viruses in the Era of Artificial Intelligence Structure Prediction.

Annual review of virology·2026
Same author

A proposed new virus in the genus Marafivirus detected from Oriental persimmon 'Kumemaru'.

Archives of virology·2026
Same author

Virological characteristics of SARS-CoV-2-related coronaviruses dynamically circulating in Southeast Asia.

Cell·2026
Same author

From single-sequences to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2.

Nature communications·2026
Same author

Inferring context-specific site variation with evotuned protein language models.

NAR genomics and bioinformatics·2026

Related Experiment Video

Updated: Dec 23, 2025

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
18:10

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Published on: June 16, 2011

30.0K

Synonymous Dinucleotide Usage: A Codon-Aware Metric for Quantifying Dinucleotide Representation in Viruses.

Spyros Lytras1, Joseph Hughes1

  • 1MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.

Viruses
|April 25, 2020
PubMed
Summary

Viral genomes show distinct dinucleotide patterns. A new metric, synonymous dinucleotide usage (SDU), reveals vertebrate viruses significantly suppress CpG dinucleotides, offering insights into viral genome evolution and host immune interactions.

Keywords:
CpG suppressionFlaviviridaeRhabdoviridaebioinformaticsdinucleotidespython packagesynonymous codon usage

More Related Videos

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
05:45

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

9.2K
A Quantitative Dot Blot Assay for AAV Titration and Its Use for Functional Assessment of the Adeno-associated Virus Assembly-activating Proteins
14:49

A Quantitative Dot Blot Assay for AAV Titration and Its Use for Functional Assessment of the Adeno-associated Virus Assembly-activating Proteins

Published on: June 12, 2018

14.2K

Related Experiment Videos

Last Updated: Dec 23, 2025

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
18:10

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Published on: June 16, 2011

30.0K
Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
05:45

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

9.2K
A Quantitative Dot Blot Assay for AAV Titration and Its Use for Functional Assessment of the Adeno-associated Virus Assembly-activating Proteins
14:49

A Quantitative Dot Blot Assay for AAV Titration and Its Use for Functional Assessment of the Adeno-associated Virus Assembly-activating Proteins

Published on: June 12, 2018

14.2K

Area of Science:

  • Virology
  • Genomics
  • Bioinformatics

Background:

  • Viral genomes exhibit characteristic dinucleotide composition patterns, including CpG and UpA suppression.
  • Vertebrate immune systems possess mechanisms that target viruses based on specific dinucleotide content.
  • Systematic analysis of viral dinucleotide composition is crucial for understanding viral evolution and host interactions.

Purpose of the Study:

  • To develop a novel metric, synonymous dinucleotide usage (SDU), for quantifying dinucleotide representation in coding sequences.
  • To statistically assess dinucleotide abundance against a null hypothesis of equal synonymous codon usage.
  • To analyze dinucleotide composition in vertebrate and invertebrate flaviviruses and rhabdoviruses.

Main Methods:

  • Development of the synonymous dinucleotide usage (SDU) metric.
  • Implementation of the SDU metric and related analyses in a Python 3 package named DinuQ.
  • Application of SDU to datasets of invertebrate- and vertebrate-specific flaviviruses and rhabdoviruses.

Main Results:

  • Vertebrate viruses consistently show a greater under-representation of CpG dinucleotides across all three codon positions.
  • The SDU metric provides a statistically interpretable value by comparing observed dinucleotide frequency to a codon table-based null expectation.
  • Analysis confirmed distinct dinucleotide profiles between vertebrate and invertebrate viruses.

Conclusions:

  • The SDU metric offers a robust and statistically grounded approach to quantifying dinucleotide composition in viral genomes.
  • Vertebrate viruses demonstrate a significant selection against CpG dinucleotides, potentially linked to host immune pressures.
  • The DinuQ package and SDU method are applicable to analyzing coding sequences from various organisms, not just viruses.