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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...

Nucleosome Remodeling

Nucleosome Remodeling

Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
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Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...

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

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DNA Topoisomerases

DNA Topoisomerases

Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
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Homologous Recombination

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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

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Related Experiment Video

Updated: Jul 11, 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

Simple combined model for nonlinear excitations in DNA.

D L Hien¹, N T Nhan, V Thanh Ngo

¹Institute of Physics and Electronics, P. O. Box 429, Boho, Hanoi 10000, Vietnam.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics

|October 13, 2007

Summary

This study introduces a combined model for DNA denaturation, showing that DNA strand separation and kink velocity are influenced by coupling strength and temperature. This research advances our understanding of DNA dynamics.

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Last Updated: Jul 11, 2026

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

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Published on: June 28, 2014

Area of Science:

Molecular Biology
Biophysics
Computational Biology

Background:

DNA denaturation is a fundamental process in molecular biology.
Existing models, like the pendulum and Peyrard-Bishop models, offer insights into DNA dynamics but have limitations.

Purpose of the Study:

To propose a novel, simplified 'combined model' for DNA denaturation.
To investigate the influence of key parameters on DNA denaturation dynamics.

Main Methods:

Developed a combined model integrating pendulum and Peyrard-Bishop approaches.
Analyzed the impact of coupling constant (k), hydrogen bond stretching (y*), and damping/force ratio (gamma/F).
Examined the dependence of unpaired base length (L) and kink velocity (v) on model parameters.

Main Results:

The length of unpaired DNA bases (L) is dependent on both coupling constant (k) and temperature (T).
The velocity of DNA kinks (v) is also significantly influenced by coupling constant (k) and temperature (T).
Model predictions show good agreement with existing experimental and theoretical findings.

Conclusions:

The proposed combined model offers a simplified yet effective framework for studying DNA denaturation.
Temperature and base-pairing strength are critical factors governing DNA strand separation and dynamics.
This model provides a valuable tool for further research into DNA mechanical properties and interactions.