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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...

Chromatin Packaging

Chromatin Packaging

Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...

Chromatin Packaging

Chromatin Packaging

Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter?
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.

The Nucleosome

The Nucleosome

Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...

The Nucleosome

The Nucleosome

DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...

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...

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Related Experiment Video

Updated: May 14, 2026

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

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

Can we model DNA at the mesoscale?

S Cuesta-López¹, J Errami, F Falo

¹Dept. Física de la Materia Condensada, Universidad de Zaragoza, c/Pedro Cerbuna s/n 50009 Zaragoza, Spain ; Laboratoire de Physique, Ecole Normale Supérieure de Lyon, 46 allée d'Iltalie, 69364 Lyon cedex 07, France ; Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain.

Journal of Biological Physics

|January 25, 2013

Summary

This summary is machine-generated.

Developing mesoscale models for DNA is crucial for understanding its complex properties. These models capture biological sequence details while remaining computationally feasible for studying DNA denaturation and self-assembly kinetics.

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Area of Science:

Biophysics
Computational Biology
Molecular Modeling

Background:

Understanding DNA properties requires models beyond molecular dynamics due to scale limitations.
Mesoscale models offer a balance between detail (e.g., biological sequence) and computational tractability.

Purpose of the Study:

To present mesoscale modeling approaches for DNA.
To illustrate applications in DNA mechanical denaturation and self-assembly.

Main Methods:

Development of a dynamical model for DNA mechanical denaturation.
Creation of a DNA self-assembly model focusing on hairpin formation kinetics.

Main Results:

The denaturation model probes DNA sequence effects across various scales.
The self-assembly model enables the study of hairpin formation kinetics.

Conclusions:

Mesoscale modeling is essential for bridging the gap between molecular detail and large-scale DNA phenomena.
These models provide valuable insights into DNA mechanics and assembly processes.