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DNA as a Genetic Template

DNA as a Genetic Template

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...

DNA as a Genetic Template

DNA as a Genetic Template

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...

The DNA Helix

The DNA Helix

The DNA Helix

The DNA Helix

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...

The DNA Helix

The DNA Helix

DNA Helicases

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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...

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Related Experiment Video

Updated: May 14, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA

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Published on: April 26, 2013

Dynamic approach to DNA breathing.

Ralf Metzler¹, Tobias Ambjörnsson

¹NORDITA - Nordic Institute for Theoretical Physics, Blegdamsvej 17, DK-2100 Copenhagen Ø, Denmark.

Journal of Biological Physics

|January 25, 2013

Summary

DNA double-helix spontaneously denatures, forming transient DNA-bubbles. This study models DNA bubble dynamics using a Fokker-Planck equation, providing insights into DNA breathing and protein interactions.

Keywords:

DNA denaturation DNA-bubbles Poland-Scheraga free energy single molecule dynamics

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Area of Science:

Biophysics
Molecular Biology
Chemical Physics

Background:

DNA exists as a double helix but locally denatures into single strands.
These transient single-stranded regions are known as DNA-bubbles.
DNA bubble dynamics are crucial for understanding DNA-protein interactions.

Purpose of the Study:

To present a dynamical description of DNA-bubble breathing.
To model DNA bubble dynamics using a Fokker-Planck equation.
To investigate the lifetime of DNA-bubbles and their interaction with proteins.

Main Methods:

Developed a dynamical description of DNA-bubble breathing.
Utilized the Poland-Scheraga free energy for DNA denaturation.
Applied a Fokker-Planck equation to model bubble size dynamics.
Introduced a master equation approach for comparison.

Main Results:

Obtained basic quantities like the lifetime of DNA-bubbles.
The dynamical model aligns with single-molecule measurements of bubble fluctuations.
Compared the Fokker-Planck description with a master equation approach.

Conclusions:

The Fokker-Planck model provides a valid dynamical description of DNA-bubble breathing.
The calculated bubble lifetime is key for understanding DNA-protein interactions.
Both Fokker-Planck and master equation approaches offer insights into DNA breathing dynamics.