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 Concept Videos

Long-patch Base Excision Repair01:02

Long-patch Base Excision Repair

Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
Gene Conversion02:08

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
Gene Conversion02:08

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Cryo-EM structure determination of amyloid fibrils: Methodology, insights, and practical tools.

Methods in enzymology·2026
Same author

Stochastic misfolding drives the emergence of distinct α-synuclein strains.

Neuron·2026
Same author

Two-photon excitation enables single-molecule detection of a fluorescent base analogue in DNA with high photostability.

Chemical science·2026
Same author

Cryo-EM studies of amyloid-β fibrils from human and murine brains carrying the Uppsala APP mutation (Δ690-695).

Acta neuropathologica communications·2025
Same author

Anle138b binds predominantly to the central cavity in lipidic Aβ₄₀ fibrils and modulates fibril formation.

Nature communications·2025
Same author

Resolution of physics and deep learning-based protein engineering filters: A case study with a lipase for industrial substrate hydrolysis.

PloS one·2025

Related Experiment Video

Updated: May 25, 2026

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
07:55

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae

Published on: September 11, 2022

Branchpoint expansion in a fully complementary three-way DNA junction.

Tara Sabir1, Anita Toulmin, Long Ma

  • 1The School of Chemistry, Alan Turing Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.

Journal of the American Chemical Society
|February 15, 2012
PubMed
Summary

Researchers studied DNA three-way junctions (3WJs), finding they form a Y-shaped structure with an internal cavity. This discovery advances understanding of DNA structure for applications in nanoscience.

More Related Videos

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector
12:08

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector

Published on: March 28, 2018

Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning
08:31

Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning

Published on: February 5, 2021

Related Experiment Videos

Last Updated: May 25, 2026

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
07:55

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae

Published on: September 11, 2022

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector
12:08

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector

Published on: March 28, 2018

Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning
08:31

Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning

Published on: February 5, 2021

Area of Science:

  • Molecular Biology
  • Biophysics
  • Nanoscience

Background:

  • Branched nucleic acids, like DNA three-way junctions (3WJs), are crucial in biological processes such as DNA replication, recombination, and repair.
  • These structures also find applications in RNA architecture and as building blocks in nanoscience.

Purpose of the Study:

  • To elucidate the local and global structure of DNA three-way junctions (3WJs) in solution.
  • To understand the structural basis for the observed flexibility and reactivity of 3WJs.

Main Methods:

  • High-resolution single-molecule Förster Resonance Energy Transfer (FRET)
  • Time-resolved spectroscopy
  • Molecular modeling

Main Results:

  • The DNA 3WJ adopts a Y-shaped, pyramidal conformation in solution.
  • Bases adjacent to the branchpoint remain unpaired, despite full Watson-Crick complementarity.
  • This unpairing creates a nanoscale cavity at the junction's center.

Conclusions:

  • The determined structure explains previous observations regarding 3WJ flexibility and reactivity.
  • These findings provide a structural basis for designing novel DNA-based supramolecular receptors and nanosystems.