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 Experiment Videos

A model of DNA sequence evolution.

D G Arquès1, C J Michel

  • 1Université de Franche-Comté, Laboratoire d'Informatique de Besançon, Unité Associée CNRS No 822, France.

Bulletin of Mathematical Biology
|January 1, 1990
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Sport science for salmon and other species: ecological consequences of metabolic power constraints.

Ecology letters·2015
Same author

A computer method for identifying patterns in electroencephalogram signals.

Journal of medical engineering & technology·2003
Same author

[Determinants of long-term follow-up after stent implantation in acute myocardial infarction].

Zeitschrift fur Kardiologie·2002
Same author

Analysis of a circular code model.

Journal of theoretical biology·2002
Same author

Risk factors for the development of restenosis following stent implantation of venous bypass grafts.

Heart (British Cardiac Society)·2001
Same author

Intracoronary administration of dipyridamole prior to percutaneous transluminal coronary angioplasty provides a protective effect exceeding that of ischemic preconditioning.

Coronary artery disease·2000
Same journal

Effects of Seasonal Births and Predation on Disease Spread.

Bulletin of mathematical biology·2026
Same journal

Identifiability, Sensitivity, and Genetic Algorithms in Bacterial Biofilm Selection Models.

Bulletin of mathematical biology·2026
Same journal

Slow Evolution Towards Generalism in a Model of Variable Dietary Range.

Bulletin of mathematical biology·2026
Same journal

CBINN: Cancer Biology-Informed Neural Network for Unknown Parameter Estimation and Missing Physics Identification.

Bulletin of mathematical biology·2026
Same journal

A Cost-Sensitive Behavioral Modeling Analysis of the Early Identification and Control of Infectious Diseases.

Bulletin of mathematical biology·2026
Same journal

Tracking Dynamics of Superspreading Through Contacts, Exposures, and Transmissions in Edge-Based Network Epidemics.

Bulletin of mathematical biology·2026
See all related articles

The YRY(N)6YRY motif is a primitive DNA oligonucleotide with a central role in evolution. Its preferential occurrence and periodicities across diverse gene populations are explained by a simple Markov model, offering insights into DNA sequence evolution and the origin of life.

Area of Science:

  • Genomics
  • Molecular Evolution
  • Bioinformatics

Background:

  • Statistical studies revealed a non-uniform occurrence of the i-motif YRY(N)iYRY in various gene populations, with a maximum at i=6.
  • This 'universality' suggested YRY(N)6YRY as a primitive oligonucleotide crucial for DNA sequence evolution.

Purpose of the Study:

  • To validate and extend the observation of YRY(N)6YRY preferential occurrence in a wider range of gene populations.
  • To develop and test a model explaining DNA sequence evolution based on oligonucleotide composition and mixing.
  • To classify gene populations using YRY(N)6YRY occurrence and periodicity patterns.

Main Methods:

  • Analysis of updated gene databases to confirm and expand YRY(N)6YRY occurrence patterns.
  • Development of a Markov model simulating DNA sequence evolution through the mixing of YRY(N)6 and YRY(N)3 oligonucleotides.

Related Experiment Videos

  • Comparison of model simulations with real biological data to assess correlation and explanatory power.

    • Main Results:

    • Confirmed preferential occurrence of YRY(N)6YRY (maximum at i=6) in previously studied and newly analyzed gene populations (e.g., chloroplast and mitochondrial 5' regions, small nuclear RNA genes).
    • Successfully classified 18 gene populations based on YRY(N)6YRY occurrence and periodicity.
    • Demonstrated that statistical features, including YRY(N)6YRY occurrence and periodicities, can be reproduced by a Markov model based on oligonucleotide mixing.
    • Identified oligonucleotide mixing as an independent process and showed that various features are functions of a single parameter.
    • Observed a strong correlation between model simulations and biological reality regarding alternating purine/pyrimidine stretches and periodicities.

    Conclusions:

    • The YRY(N)6YRY motif's prevalence is a key feature of DNA sequence evolution.
    • A simple Markov model based on oligonucleotide mixing effectively explains observed statistical properties of gene populations.
    • The presence or absence of alternating purine/pyrimidine stretches can be explained by the mixing of specific oligonucleotides.
    • This approach provides a foundational step towards a unified model of DNA sequence evolution, linking molecular mechanisms to the origin of life and current biological reality.