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

Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures.

Pascale Hazel1, Gary N Parkinson, Stephen Neidle

  • 1CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, UK.

Nucleic Acids Research
|April 28, 2006
PubMed
Summary

Simulations reveal that lateral T3 loops are favored in dimeric DNA quadruplexes over diagonal loops. Loop length, not just G-quartet stability, influences observed dimer topology patterns.

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

DNA damaging properties of G-quadruplex ligand QN-302 are potentiated by the DNA repair inhibitor Olaparib and mitigated by the molecular helicase PhpC.

Genome biology·2026
Same author

Cellular adaptations impact the biological activity of naphthalene diimide G-quadruplex ligands in ALT-positive osteosarcoma cells.

Cell death & disease·2025
Same author

Structural and Functional Insights into Targeting GCCG Sites in the EGFR Promoter by Two DNA Intercalators to Inhibit Breast Cancer Metastasis.

Journal of medicinal chemistry·2025
Same author

The G-quadruplex experimental drug QN-302 impairs liposarcoma cell growth by inhibiting MDM2 expression and restoring p53 levels.

Nucleic acids research·2025
Same author

The G-quadruplex experimental drug QN-302 impairs liposarcoma cell growth by inhibiting MDM2 expression and restoring p53 levels.

Nucleic acids research·2025
Same author

Alternative Approach to Sequence-Specific Recognition of DNA: Cooperative Stacking of Dication Dimers─Sensitivity to Compound Curvature, Aromatic Structure, and DNA Sequence.

ACS chemical biology·2025

Area of Science:

  • Structural biology
  • Computational chemistry
  • Biophysics

Background:

  • Previous molecular dynamics (MD) simulations studied loop length effects on intramolecular quadruplex topology.
  • Recent crystal and NMR structures of dimeric DNA quadruplexes provide experimental data for comparison.

Purpose of the Study:

  • Predict favorable topologies and loop conformations of dimeric DNA quadruplexes with T2 or T3 loops.
  • Compare simulation results with experimental data for d(G4T3G4)2, d(G4BrUT2G4), and d(TG4T2G4T)2.

Main Methods:

  • Combination of simulated annealing (SA), molecular dynamics (MD), and locally enhanced sampling (LES).
  • MM-PBSA free-energy calculations.
  • Comparison with published crystal and NMR structures.

Related Experiment Videos

Main Results:

  • Lateral T3 loops are favored over diagonal loops, aligning with experimental findings.
  • Predicted loop conformations differ from experimentally observed ones.
  • Several lateral and diagonal loop conformations exhibit similar energies.
  • Simulations explain distinct dimer topology patterns based on loop length, not solely G-quartet stability.

Conclusions:

  • Loop length is a critical determinant of dimeric DNA quadruplex topology.
  • Computational methods provide insights into DNA quadruplex structures and dynamics.
  • Discrepancies between predicted and experimental loop conformations warrant further investigation.