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

DNA sequence specificity of triplex-binding ligands.

Melanie D Keppler1, Peter L James, Stephen Neidle

  • 1Division of Biochemistry & Molecular Biology, School of Biological Sciences, University of Southampton, UK.

European Journal of Biochemistry
|December 5, 2003
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

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

Synthesis, SAR, and biophysical mechanism of action of cyclopropabenzindole-pyridinobenzodiazepine (CBI-PDD) guanine-adenine DNA cross-linking agents.

European journal of medicinal chemistry·2025
Same author

Synthesis and Evaluation of DNA Cross-linkers by Click Chemistry-Mediated Heterodimerization of Nor-Tomaymycins.

Chemistry (Weinheim an der Bergstrasse, Germany)·2025
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

A novel DNA sequence-selective, guanine mono-alkylating ADC payload suitable for solid tumour treatment.

RSC medicinal chemistry·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 journal

Comparison of expression patterns and cell adhesion properties of the mouse biliary glycoproteins Bgp1 and Bgp2.

European journal of biochemistry·2020
Same journal

AB 3.1.1.1 (or EC 3.1.1.?).

European journal of biochemistry·2020
Same journal

Cdk5.

European journal of biochemistry·2018
Same journal

Structure of the core oligosaccharide of a rough-type lipopolysaccharide of Pseudomonas syringae pv. phaseolicola.

European journal of biochemistry·2004
Same journal

Monitoring ligand-mediated nuclear receptor-coregulator interactions by noncovalent mass spectrometry.

European journal of biochemistry·2004
Same journal

Solution structure of long neurotoxin NTX-1 from the venom of Naja naja oxiana by 2D-NMR spectroscopy.

European journal of biochemistry·2004
See all related articles

Three aromatic ligands were tested for their ability to stabilize parallel DNA triplexes. Naphthylquinoline and anthraquinone derivatives showed selective stabilization of specific DNA sequences, unlike BePI.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • DNA triplexes are three-stranded nucleic acid structures with potential applications in gene therapy and diagnostics.
  • Ligand binding to DNA triplexes can modulate their stability and function.
  • Understanding sequence-specific ligand interactions is crucial for designing effective triplex-based technologies.

Purpose of the Study:

  • To investigate the stabilizing effects of naphthylquinoline, a 2,7-disubstituted anthraquinone, and BePI (benzo[e]pyridoindole) on parallel DNA triplexes.
  • To determine the sequence selectivity of these ligands for different DNA base compositions within triplex structures.
  • To elucidate the structural basis for differential ligand binding and stabilization of DNA triplexes.

Main Methods:

Related Experiment Videos

  • Fluorescence melting studies were employed to assess triplex stability with both inter- and intramolecular triplexes.
  • DNase I footprinting assays were utilized to confirm ligand binding and protection of DNA regions.
  • Analysis of triplexes with varying third-strand compositions, including (TAT)n, (TC)n, (CCT)n, (TTC)n, and (CCTT)n.

    • Main Results:

    • All three ligands, naphthylquinoline, anthraquinone, and BePI, stabilized DNA triplexes containing blocks of TAT triplets.
    • Naphthylquinoline selectively stabilized triplexes with (TTC)n sequences, while the anthraquinone derivative stabilized (TC)n, (CCT)n, and (TTC)n sequences.
    • BePI showed limited stabilization and slightly destabilized triplexes with (TC)n, (CCT)n, and (TTC)n sequences, suggesting charge-dependent binding interactions.

    Conclusions:

    • Naphthylquinoline and BePI appear to bind preferentially between adjacent TAT triplets, possibly due to their positive charge.
    • The anthraquinone ligand exhibits broader sequence selectivity, potentially due to the absence of a positive charge.
    • Optimal triplex stabilization occurs with alternating charged and uncharged residues, and ligands do not stabilize triplexes with alternating C+GC and TAT triplets.