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

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

16.8K
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
16.8K
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

14.9K
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...
14.9K
Complementary DNA01:44

Complementary DNA

31.8K
Overview
31.8K
DNA Helicases00:55

DNA Helicases

24.2K
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...
24.2K
Lagging Strand Synthesis01:59

Lagging Strand Synthesis

61.5K
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...
61.5K
The DNA Replication Fork01:02

The DNA Replication Fork

41.2K
An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication...
41.2K

You might also read

Related Articles

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

Sort by
Same author

Quasi-equilibrium translocation of short polymers through thin nanopores: Implications from forward flux sampling simulations.

The Journal of chemical physics·2026
Same author

Thermal Stability of IgG4 Monoclonal Antibodies: Ambiguous Roles of Cosolutes, Excipients, and Salts in Conformational and Colloidal States.

Molecular pharmaceutics·2026
Same author

Evolutionary change and adaptation as non-equilibrium thermodynamic processes.

Bio Systems·2026
Same author

Influence of Co-Solutes and Solvents on Diffusion Interaction Parameters in Multicomponent Solutions: New Insights through the Kirkwood-Buff Theory.

The journal of physical chemistry. B·2025
Same author

Chromatin-associated condensates as an inspiration for the system architecture of future DNA computers.

Annals of the New York Academy of Sciences·2025
Same author

Correction: Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning.

Journal of molecular evolution·2025

Related Experiment Video

Updated: Feb 12, 2026

Separation of Single-stranded DNA, Double-stranded DNA and RNA from an Environmental Viral Community Using Hydroxyapatite Chromatography
13:46

Separation of Single-stranded DNA, Double-stranded DNA and RNA from an Environmental Viral Community Using Hydroxyapatite Chromatography

Published on: September 29, 2011

32.4K

Preferential Binding of Urea to Single-Stranded DNA Structures: A Molecular Dynamics Study.

Ewa Anna Oprzeska-Zingrebe1, Jens Smiatek2

  • 1Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany.

Biophysical Journal
|April 12, 2018
PubMed
Summary

Urea accumulates around DNA, displacing water molecules. This binding, driven by electrostatic and dispersion forces, impacts DNA structure and function in biological systems.

More Related Videos

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

12.2K
Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

1.3K

Related Experiment Videos

Last Updated: Feb 12, 2026

Separation of Single-stranded DNA, Double-stranded DNA and RNA from an Environmental Viral Community Using Hydroxyapatite Chromatography
13:46

Separation of Single-stranded DNA, Double-stranded DNA and RNA from an Environmental Viral Community Using Hydroxyapatite Chromatography

Published on: September 29, 2011

32.4K
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

12.2K
Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

1.3K

Area of Science:

  • Biophysical Chemistry
  • Molecular Biology
  • Computational Chemistry

Background:

  • Biological processes like transcription termination rely on DNA secondary and tertiary structures.
  • Cellular cosolutes can significantly alter DNA structure stability.
  • Understanding cosolume-induced effects is crucial for molecular biology.

Purpose of the Study:

  • Investigate urea binding to DNA at various concentrations.
  • Analyze urea's local concentration around DNA hairpin vs. unfolded states.
  • Elucidate the mechanistic basis of cosolute effects on DNA.

Main Methods:

  • Molecular dynamics simulations of 7-nucleotide single-stranded DNA in aqueous solution.
  • Preferential binding model analysis.
  • Kirkwood-Buff theory application.

Main Results:

  • Urea shows pronounced accumulation around DNA structures.
  • Binding is driven by electrostatic and dispersion interactions.
  • Significant displacement of water molecules by urea was observed.

Conclusions:

  • Urea binding to DNA is concentration-dependent and involves water displacement.
  • Cosolute-induced effects on DNA structure are mechanistically complex.
  • This study provides foundational insights into cosolute interactions with nucleic acids.