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 base pair opening in DNA double helix.

Andrew Krueger1, Ekaterina Protozanova, Maxim D Frank-Kamenetskii

  • 1Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA.

Biophysical Journal
|February 28, 2006
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

College Student-Athlete Preferences for the Gender Identity, Race, and Ethnicity of Their Athletic Trainers and Team Physicians.

Clinical journal of sport medicine : official journal of the Canadian Academy of Sport Medicine·2026
Same author

A Phase 2, Open-Label, Multicenter Study of the Safety and Efficacy of TAK-007 in Adult Patients with Relapsed/Refractory B-cell Non-Hodgkin Lymphoma.

Blood cancer discovery·2026
Same author

Postsurgical Disorders of the Gut-Brain Axis and the Need for Multidisciplinary Treatment Approach: Authors' Reply.

Neurogastroenterology and motility·2026
Same author

Survival in Patients With Low Expression of Wild-Type Homologous Recombination Genes: Refining the Homologous Recombination Paradigm in Colorectal Cancer.

JCO precision oncology·2026
Same author

Overlap of Structural Gastrointestinal Disorders in Children With Disorders of Gut-Brain Interaction.

Neurogastroenterology and motility·2026
Same author

The prevalence and impact of gluten-free food insecurity in pediatric celiac disease.

Journal of pediatric gastroenterology and nutrition·2025
Same journal

Tau protein differentially affects Piezo1 and Kir2.1 channels in brain capillary endothelial cells.

Biophysical journal·2026
Same journal

Emergent Intercellular Junction Stability during Cyclic Tissue Loading.

Biophysical journal·2026
Same journal

Enhanced-Sampling Simulations Reveal Distinct Intermediates in SARS-CoV-2 FSE Pseudoknot Interconversion.

Biophysical journal·2026
Same journal

Structure-based simulations of the full Flock House virus capsid reveal pathways and energetics of an infection-critical peptide externalization event.

Biophysical journal·2026
Same journal

Quantifying the Peripheral Surface Information Entropy from Conformational Ensembles of Globular Protein-Peptide Complexes.

Biophysical journal·2026
Same journal

Anisotropic unbinding and location-dependent hovering of a kinesin motor head over microtubule.

Biophysical journal·2026
See all related articles

DNA basepair opening, or "breathing", allows DNA modification. Our thermodynamic model predicts sequence-dependent opening probabilities, revealing nonobvious patterns crucial for genetic information preservation.

Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • DNA's double helix structure shields nucleobases.
  • Thermal fluctuations cause infrequent DNA basepair opening events.
  • This opening exposes normally buried groups for modification and protein interactions.

Purpose of the Study:

  • To predict sequence-dependent basepair opening probabilities in DNA.
  • To model the thermodynamic contributions to DNA double helix stability.
  • To understand the implications of basepair opening for genetic information.

Main Methods:

  • Separating contributions of base pairing and base stacking to helix stability.
  • Utilizing a partition function to calculate basepair opening probability.
  • Incorporating a 'ring factor' for unfavorable exposed base positioning.

Related Experiment Videos

  • Calibrating the model using NMR spectroscopy data on short DNA duplexes.

    • Main Results:

    • Developed a thermodynamic model for DNA basepair opening.
    • Identified sequence-dependent basepair opening probabilities.
    • Quantified the impact of base stacking and pairing on opening events.
    • Determined the 'ring factor' from experimental data.

    Conclusions:

    • Thermodynamic parameters reveal nonobvious sequence-dependent basepair opening probabilities.
    • DNA breathing is influenced by base sequence and helix stability.
    • Understanding these probabilities is key to DNA preservation and function.