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

12.9K
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...
12.9K
DNA as a Genetic Template02:05

DNA as a Genetic Template

22.2K
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...
22.2K
The DNA Helix01:16

The DNA Helix

129.4K
Overview
129.4K
The DNA Helix01:07

The DNA Helix

19.9K
Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...
19.9K
Nucleic Acid Structure01:25

Nucleic Acid Structure

8.1K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
8.1K
DNA Helicases00:55

DNA Helicases

19.4K
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...
19.4K

You might also read

Related Articles

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

Sort by
Same author

Structural commonalities determined by physicochemical principles in the complex polymorphism of the amyloid state of proteins.

The Biochemical journal·2024
Same author

A scale-invariant log-normal droplet size distribution below the critical concentration for protein phase separation.

eLife·2024
Same author

Tetrapod sperm length evolution in relation to body mass is shaped by multiple trade-offs.

Nature communications·2024
Same author

Large bubble drives circular DNA melting.

Physical chemistry chemical physics : PCCP·2024
Same author

Being heterogeneous is disadvantageous: Brownian non-Gaussian searches.

Physical review. E·2024
Same author

Being Heterogeneous Is Advantageous: Extreme Brownian Non-Gaussian Searches.

Physical review letters·2024

Related Experiment Video

Updated: May 2, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.3K

Melting behavior and different bound states in three-stranded DNA models.

Jaya Maji1, Somendra M Bhattacharjee1, Flavio Seno2

  • 1Institute of Physics, Bhubaneswar 751005, India.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|March 4, 2014
PubMed
Summary

Researchers explored three-stranded DNA melting using coarse-grained models. They discovered a novel "mixed state" phase alongside the predicted Efimov-DNA-like state, revealing complex DNA binding behaviors.

More Related Videos

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

2.5K
Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

14.8K

Related Experiment Videos

Last Updated: May 2, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.3K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

2.5K
Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

14.8K

Area of Science:

  • Statistical mechanics
  • Polymer physics
  • Biophysics

Background:

  • Coarse-grained models, like Poland and Scheraga, study DNA thermal denaturation by simulating base pairing with attractive interactions.
  • Previous studies predicted a three-stranded DNA bound state (Efimov-DNA) in certain conditions, analogous to the Efimov effect in nuclear physics.

Purpose of the Study:

  • Investigate three-stranded DNA melting on a Sierpinski gasket with fractal dimension d<2.
  • Analyze the influence of fork opening/closing weights on DNA melting dynamics.
  • Identify and characterize novel DNA binding phases beyond the Efimov-DNA state.

Main Methods:

  • Utilized coarse-grained polymer models on a Sierpinski gasket lattice (d<2).
  • Introduced specific weight factors for fork openings and closings to model two-strand DNA melting.
  • Analyzed phase transitions and thermodynamic properties of the system.

Main Results:

  • Replicated the existence of an Efimov-DNA-like state under modified conditions.
  • Discovered a new 'mixed state' characterized by pairwise strand binding without three-chain contacts.
  • Differentiated the Efimov-DNA as a melting crossover and the mixed state as a distinct thermodynamic phase.

Conclusions:

  • The study extends understanding of DNA binding phenomena in complex topological spaces.
  • Introduces a novel mixed state, expanding the known phase diagram for multi-stranded DNA systems.
  • Highlights the potential for complex, non-intuitive binding behaviors in DNA under varying structural constraints.