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

Homologous Recombination02:31

Homologous Recombination

50.4K
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...
50.4K
Lagging Strand Synthesis01:59

Lagging Strand Synthesis

51.1K
During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...
51.1K
DNA Helicases00:55

DNA Helicases

21.3K
DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
21.3K
DNA Topoisomerases02:02

DNA Topoisomerases

31.2K
Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types. ...
31.2K
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

6.0K
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...
6.0K
DNA as a Genetic Template02:05

DNA as a Genetic Template

21.9K
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
21.9K

You might also read

Related Articles

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

Sort by
Same author

Yeast condensin acts as a transient intermolecular crosslinker in entangled DNA.

Nucleic acids research·2026
Same author

Organisation and dynamics of individual DNA segments in topologically complex genomes.

Nucleic acids research·2025
Same author

Spontaneously directed loop extrusion in SMC complexes emerges from broken detailed balance and anisotropic DNA search.

Nucleic acids research·2025
Same author

Topologically-crosslinked hydrogels based on γ-cyclodextrins.

Communications chemistry·2025
Same author

Topological linking determines elasticity in limited valence networks.

Nature materials·2025
Same author

Kinetoplast DNA: a polymer physicist's topological Olympic dream.

Nucleic acids research·2024
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

Related Experiment Video

Updated: Jun 24, 2025

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

15.4K

Loops are geometric catalysts for DNA integration.

Cleis Battaglia1, Davide Michieletto1,2

  • 1School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.

Nucleic Acids Research
|June 12, 2024
PubMed
Summary
This summary is machine-generated.

DNA integration is not random. Loops in DNA act as catalysts, guiding where DNA elements insert and influencing genome evolution and engineering.

More Related Videos

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
09:32

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Published on: April 12, 2019

6.4K
Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

11.7K

Related Experiment Videos

Last Updated: Jun 24, 2025

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

15.4K
Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
09:32

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Published on: April 12, 2019

6.4K
Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

11.7K

Area of Science:

  • Genomics
  • Molecular Biology
  • Biophysics

Background:

  • Unregulated DNA insertion contributes to genetic diversity and disease.
  • The mechanisms of DNA integration site selection are not fully understood.
  • DNA elements like viral DNA and transposons integrate into genomes.

Purpose of the Study:

  • To investigate the physical mechanisms of DNA element integration.
  • To explore the role of DNA loops in integration site selection.
  • To understand how DNA conformation affects integration patterns.

Main Methods:

  • Molecular Dynamics (MD) simulations were employed.
  • Simulations studied DNA insertion into naked DNA and chromatin substrates.
  • The influence of DNA loops and nucleosomes on integration was analyzed.

Main Results:

  • DNA loops function as 'geometric catalysts' for DNA integration by lowering the energy barrier for substrate deformation.
  • The 1D and 3D structure of DNA loops significantly impacts integration site distribution.
  • DNA loops compete with nucleosomes for attracting DNA integrations.

Conclusions:

  • DNA loops play a crucial role in directing DNA integration.
  • Understanding these mechanisms can inform genome evolution and engineering strategies.
  • Experimental validation of these simulation findings is feasible.