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

Sequence-dependent DNA torsional rigidity: a tetranucleotide code.

Francesco Pedone1, Filomena Mazzei, Daniele Santoni

  • 1Istituto Nazionale di Fisica della Materia, Università La Sapienza, Rome, Italy. francesco.pedone@uniroma1.it

Biophysical Chemistry
|October 27, 2004
PubMed
Summary

Researchers measured DNA torsional constants using fluorescence polarization anisotropy (FPA), revealing sequence-dependent rigidity profiles. Many DNA sequences exhibit common 20/30 bp modulations, potentially impacting nucleosome function.

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

Human gut microbiota from acute coronary syndrome patients promotes plaque vulnerability in a mouse model of atherosclerosis.

Scientific reports·2026
Same author

Single-cell profiling reveals a novel CAF subpopulation linking stromal heterogeneity to immune suppression in breast cancer subtypes.

Journal of translational medicine·2026
Same author

A DNABERT based deep learning framework for predicting transcription factor binding sites.

Scientific reports·2026
Same author

Transcripts derived from AmnSINE1 repetitive sequences are depleted in the cortex of autism spectrum disorder patients.

Frontiers in bioinformatics·2025
Same author

A review on the applications of Transformer-based language models for nucleotide sequence analysis.

Computational and structural biotechnology journal·2025
Same author

HDAC6 inhibition disrupts HDAC6-P300 interaction reshaping the cancer chromatin landscape.

Clinical epigenetics·2024

Area of Science:

  • Biophysics
  • Molecular Biology
  • Genomics

Background:

  • DNA mechanical properties are crucial for its biological functions.
  • Understanding DNA sequence-dependent mechanics is essential for predicting its behavior in cellular processes.
  • Nucleosome formation and function are influenced by DNA structural flexibility.

Purpose of the Study:

  • To quantify the torsional constant for all unique DNA tetranucleotides.
  • To develop a method for generating DNA rigidity profiles based on sequence.
  • To investigate the relationship between DNA torsional properties and nucleosome formation.

Main Methods:

  • Utilized fluorescence polarization anisotropy (FPA) to measure DNA torsional constants.
  • Calculated torsional constants for 136 unique tetranucleotide sequences.

Related Experiment Videos

  • Developed and applied computational analysis to derive DNA rigidity profiles.

    • Main Results:

    • Established a comprehensive dataset of DNA torsional constants across various sequences.
    • Identified a common 20 and/or 30 base pair (bp) modulation in the torsional constant for over 50% of studied DNA sequences.
    • Observed diverse rigidity profiles, suggesting sequence-specific DNA mechanical behaviors.

    Conclusions:

    • DNA sequence significantly dictates its torsional properties and rigidity.
    • The identified modulations in torsional constant may play a role in nucleosome organization and function.
    • The developed rigidity profiling method offers insights into DNA mechanics relevant to chromatin studies.