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

Thermodynamic parameters for DNA sequences with dangling ends.

S Bommarito1, N Peyret, J SantaLucia

  • 1Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.

Nucleic Acids Research
|April 11, 2000
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

Digital twin with augmented state extended Kalman filters for forecasting electric power consumption of industrial production systems.

Heliyon·2024
Same author

Effect of image compression of digital lateral cephalograms on the reproducibility of cephalometric points.

Dento maxillo facial radiology·2009
Same author

Evaluation of optical density of the midpalatal suture 3 months after surgically assisted rapid maxillary expansion.

Dento maxillo facial radiology·2007
Same author

Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA. II. NMR solution structure.

Journal of molecular biology·2001
Same author

Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA. III. Functional analysis of the 690 loop.

Journal of molecular biology·2001
Same author

Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA: analysis of the stem nucleotides.

Journal of molecular biology·2000
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

Single-nucleotide dangling ends significantly stabilize DNA duplexes, with some contributing as much as a Watson-Crick base pair. These findings impact DNA probe design and hybridization prediction algorithms.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Thermodynamics

Background:

  • DNA duplex formation is crucial for molecular interactions.
  • Understanding the stability of DNA structures informs various biological and biotechnological applications.
  • Thermodynamic contributions of nucleotide sequences to DNA stability are key to predicting structure and function.

Purpose of the Study:

  • To quantify the thermodynamic contributions of all 32 possible single-nucleotide dangling ends to DNA duplex formation.
  • To compare the stabilizing effects of dangling ends with Watson-Crick nearest-neighbor interactions.
  • To explore the implications of these findings for DNA probe design and hybridization prediction.

Main Methods:

  • Thermodynamic analysis of single-nucleotide dangling ends on Watson-Crick pairs.

Related Experiment Videos

  • Calculation of free energy contributions for various dangling end configurations.
  • Comparative analysis of DNA and RNA dangling-end motifs.

    • Main Results:

    • Most dangling ends are stabilizing, with free energy contributions ranging from +0.48 to -0.96 kcal/mol.
    • Some dangling ends provide stability comparable to a Watson-Crick A-T base pair.
    • Stabilization is largely determined by the closing base pair, with adenine dangling ends showing greater or equal stability.
    • 5' dangling ends are generally more stabilizing than 3' counterparts.
    • DNA 5' dangling ends are as or more stabilizing than RNA counterparts, while RNA 3' dangling ends are as or more stabilizing than DNA counterparts.

    Conclusions:

    • Single-nucleotide dangling ends play a significant role in DNA duplex stability.
    • The sequence context, particularly the closing base pair, dictates dangling-end stability.
    • These thermodynamic data are valuable for improving DNA secondary structure and hybridization prediction algorithms like DNA MFOLD and HYTHER.