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

A palindromic repeat sequence adopts a stable fold back structure under supercoiling.

Arun K Shukla1, Kunal B Roy

  • 1Centre for Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-67, India.

Journal of Biochemistry
|January 24, 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

Orchestrating the signaling-bias at the protease-activated receptor, PAR1.

Trends in cell biology·2026
Same author

Molecular mechanisms of naturally encoded signaling bias at the complement anaphylatoxin receptors.

Molecular cell·2026
Same author

Q&A with Arun K. Shukla.

Cell reports·2026
Same author

De novo design of miniproteins targeting GPCRs.

Nature·2026
Same author

Integrating techniques and disciplines to drive structural and chemical biology forward.

Trends in biochemical sciences·2026
Same author

The Concise Guide to PHARMACOLOGY 2025/26: G protein-coupled receptors.

British journal of pharmacology·2025
Same journal

Estrogen-related receptor γ functions as a novel corepressor of androgen receptor by destabilizing receptor conformation and blocking coactivator recruitment.

Journal of biochemistry·2026
Same journal

Chromatin dynamics and cellular energy homeostasis.

Journal of biochemistry·2026
Same journal

Nutrigenomic Regulation of One-Carbon Metabolism and the Circadian Clock in Health and Disease.

Journal of biochemistry·2026
Same journal

Time to rethink circadian rhythms beyond the transcriptome.

Journal of biochemistry·2026
Same journal

BNIP3/NIX-dependent mitophagy: molecular mechanisms and physiological roles.

Journal of biochemistry·2026
Same journal

Regulatory mechanism of heme-regulated inhibitor through autophosphorylation-driven activation and heme-induced deactivation.

Journal of biochemistry·2026
See all related articles

A synthetic DNA sequence forms a parallel four-stranded structure. When cloned, supercoiling induces a stable fold-back quadruplex, distinct from G-quadruplexes, offering insights into DNA recombination.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Deoxyoligonucleotides can form non-canonical DNA structures.
  • G-quadruplexes are known DNA secondary structures involving G-tetrads.
  • Supercoiling in plasmids can influence DNA conformation.

Purpose of the Study:

  • To investigate the structural properties of a synthetic deoxyoligonucleotide with palindromic repeats.
  • To characterize the DNA structure formed by the oligonucleotide under supercoiling conditions.
  • To explore potential non-G-quartet tetraplex motifs in DNA.

Main Methods:

  • Synthesis of a deoxyoligonucleotide with five GGATCC palindromic repeats.
  • Analysis of DNA structures using gel electrophoresis and S1 nuclease sensitivity.

Related Experiment Videos

  • Dimethyl sulfate (DMS) modification assays to probe guanine accessibility.
  • Circular dichroism (CD) spectroscopy to characterize DNA conformation.

    • Main Results:

    • The oligonucleotide self-assembles into a parallel four-stranded G-tetrad structure with distinct electrophoretic mobility.
    • Supercoiling of the cloned oligonucleotide induces a stable fold-back quadruplex structure.
    • This fold-back quadruplex exhibits unique properties, including S1 nuclease sensitivity and DMS modification patterns.
    • Circular dichroism spectra suggest a fold-back quadruplex with A.T.A.T and G.C.G.C tetrads, lacking G-quartets.

    Conclusions:

    • The study demonstrates the formation of a novel fold-back quadruplex structure induced by supercoiling.
    • This structure represents a potential generalized tetraplex motif, distinct from G-quadruplexes.
    • Findings suggest implications for understanding DNA structural dynamics and generalized recombination mechanisms.