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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.

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...

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

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...

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Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Published on: April 12, 2019

Coarse-grained model DNA: structure, sequences, stems, circles, hairpins.

Lance E Edens¹, James A Brozik, David J Keller

¹Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, United States.

The Journal of Physical Chemistry. B

|November 20, 2012

Summary

A new coarse-grained DNA model accurately simulates base stacking and hydrogen bonding. This computational model captures essential DNA behaviors like double helix formation and elasticity, offering insights into molecular interactions.

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Area of Science:

Computational Biology
Biophysics
Molecular Modeling

Background:

Accurate modeling of DNA structure and dynamics is crucial for understanding biological processes.
Existing models often face limitations in capturing base-level interactions and emergent properties.

Purpose of the Study:

To develop a coarse-grained model for DNA that realistically simulates individual base behaviors.
To investigate the ability of the model to reproduce key DNA structural and dynamic properties.

Main Methods:

A coarse-grained model with residues composed of up to eight beads was developed.
Short-ranged pair potentials and an implicit solvent model were employed.
Simulations utilized Brownian dynamics without hydrodynamic coupling.

Main Results:

The model successfully formed stable double helices with B-form DNA parameters.
It accurately reproduced DNA elasticity, including bending and twisting persistence lengths.
Mismatched sequences and single-stranded DNA behaviors were realistically simulated.
Supercoiling and stem-loop formation/melting were observed in model DNA.

Conclusions:

The coarse-grained model effectively captures essential DNA properties from local base-level interactions.
This model provides a computationally efficient tool for studying DNA behavior at the molecular level.