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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

The DNA Helix

The DNA Helix

DNA as a Genetic Template

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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

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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 Replication Fork

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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 forks, one in...

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Related Experiment Video

Updated: May 14, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

A twist opening model for DNA.

M Barbi¹, S Cocco, M Peyrard

¹Dipartimento di Fisica, Università degli Studi di Firenze, Largo E. Fermi, 2 - 50125 Firenze, Italy.

Journal of Biological Physics

|January 25, 2013

Summary

This summary is machine-generated.

This study explores DNA

Keywords:

DNA modeling helix hydrogen bond stretching nonlinear dynamics solitons transcription initiation twist

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Last Updated: May 14, 2026

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Published on: April 26, 2013

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Published on: August 15, 2018

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Published on: April 12, 2019

Area of Science:

Molecular Biology
Biophysics
Computational Biology

Background:

The precise mechanisms governing DNA biological processes, such as transcription initiation, remain incompletely understood.
Understanding the formation of the open complex and enhancer binding protein activation is crucial for deciphering gene regulation.

Purpose of the Study:

To investigate the dynamical mechanisms underlying transcription activation.
To develop and analyze an extended DNA model incorporating angular variables for a more comprehensive representation of double helix geometry.

Main Methods:

Extension of the Peyrard Bishop (PB) model to include angular variables for DNA twist.
Application of generalized multiple scale expansion to derive analytical solutions for the extended DNA model.
Analysis of small amplitude, movable, and spatially localized solutions.

Main Results:

The developed extended DNA model effectively represents double helix geometry and structural features.
Analytical solutions reveal movable and spatially localized wave-like behaviors.
The calculated solution shapes align with expected coupled angular-radial distortions in DNA.

Conclusions:

Dynamical mechanisms involving DNA double chain distortions play a key role in transcription activation.
A mesoscopic dynamical approach provides deeper insights into complex biological processes like transcription.
The extended DNA model and its analytical solutions offer a valuable framework for studying DNA dynamics.