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

Stacking energies in DNA.

S G Delcourt1, R D Blake

  • 1Department of Biochemistry, Microbiology, and Molecular Biology, University of Maine, Orono 04469-0131.

The Journal of Biological Chemistry
|August 15, 1991
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

Experimental DNA melting behavior of the three major Schistosoma species.

Molecular and biochemical parasitology·2000
Same author

High-resolution calorimetric and optical melting profiles of DNA plasmids: resolving contributions from intrinsic melting domains and specifically designed inserts.

Biopolymers·1999
Same author

Statistical mechanical simulation of polymeric DNA melting with MELTSIM.

Bioinformatics (Oxford, England)·1999
Same author

Comparison of experimental to MELTSIM calculated DNA melting of the (A+T) rich Dictyostelium discoideum genome: denaturation maps distinguish exons from introns.

Journal of biomolecular structure & dynamics·1998
Same author

Thermal stability of DNA.

Nucleic acids research·1998
Same author

Repetitive sequence families in Alces alces americana.

Journal of molecular evolution·1997
Same journal

Isotope-Edited ESEEM: A New Method for Probing Copper Binding Sites in Neurodegenerative Proteins.

The Journal of biological chemistry·2026
Same journal

Introduction to the Thematic Review Series on Intracellular Protein Degradation. The ubiquitous biology of intracellular protein degradation: a tribute to Alfred L. ("Fred") Goldberg.

The Journal of biological chemistry·2026
Same journal

Correction: Aromatic residue-rich amino-terminal segments of temporin L self-assemble into collagen-mimetic peptides with cell-adhesion properties.

The Journal of biological chemistry·2026
Same journal

YhbO is a DJ-1 family glyoxalase and α-oxoaldehyde hydratase that confers resistance to reactive carbonyl stress (112).

The Journal of biological chemistry·2026
Same journal

ARMH3 acts as a central scaffold at the Golgi/TGN through interactions with Arl5, GBF1, and PI4KB.

The Journal of biological chemistry·2026
Same journal

PAX8 controls proximal tubule epithelial identity and stress response through epigenetic modification of distal regulatory elements.

The Journal of biological chemistry·2026
See all related articles

This study quantifies DNA stacking energies for all 10 base pair combinations, revealing their impact on DNA helix stability and melting temperatures. These new thermodynamic values improve predictions of DNA melting curves and identify structural variations.

Area of Science:

  • Molecular Biology
  • Biophysics
  • Thermodynamics

Background:

  • DNA stability is influenced by base stacking interactions.
  • Accurate thermodynamic data for DNA neighbor pairs are crucial for understanding helix stability.
  • Previous methods for determining stacking energies have limitations.

Purpose of the Study:

  • To precisely determine the stacking energies (TMN) for all 10 unique DNA nearest-neighbor pairs.
  • To establish a reliable thermodynamic model for DNA helix stability.
  • To compare newly derived stacking energies with previously reported values and quantum chemical calculations.

Main Methods:

  • Matrix decomposition of linear algebraic expressions relating melting temperatures (Tm) and fractional neighbor frequencies (fMN).

Related Experiment Videos

  • Analysis of high-resolution melting profiles of modified pBR322 DNA constructs (deleted and recombinant forms).
  • Employing site-specific cleavage, domain deletion, and domain addition to resolve subtransitions.

    • Main Results:

    • A unique set of stacking energy values (TMN) was determined with high precision (sigma = +/- 0.23°C).
    • Calculated Tm values closely matched experimental data (average difference +/- 0.17°C).
    • Free energy differences (delta delta G) showed distinct stability trends based on purine-pyrimidine arrangements, with purine-pyrimidine pairs being most stable.

    Conclusions:

    • The derived stacking energies provide a quantitative thermodynamic model for DNA helix stability.
    • These values differ significantly from prior determinations and show poor correlation with quantum chemical predictions.
    • The methodology allows for the identification of altered DNA structures and unusual helix dissociation modes.