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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...

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Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...

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Related Experiment Video

Updated: Jun 27, 2026

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

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Modeling the sequence-dependent diffusion coefficients of short DNA molecules.

O Gonzalez¹, J Li

¹Department of Mathematics, University of Texas, Austin, Texas 78712, USA. og@math.utexas.edu

The Journal of Chemical Physics

|December 3, 2008

Summary

This study introduces a new computational model for DNA, revealing that DNA sequence affects its movement in solution. This finding impacts understanding DNA

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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: March 1, 2022

Area of Science:

Biophysics
Computational Biology
Molecular Modeling

Background:

Understanding the hydrodynamic properties of DNA is crucial for various biological processes.
Previous models often simplified DNA structure, neglecting sequence-dependent variations.
Accurate modeling requires considering DNA's flexibility and hydration shell.

Purpose of the Study:

To develop a computational model for predicting sequence-dependent hydrodynamic properties of short DNA molecules.
To investigate the impact of DNA sequence on translational and rotational diffusion.
To refine parameters for DNA structural models in solution.

Main Methods:

A boundary element model was employed to simulate the hydrated surface of DNA as a curved tube.
The DNA sequence determined the local curvature and length using a rigid basepair model.
Diffusion coefficients were computed for various random and periodic DNA sequences.

Main Results:

Sequence-dependent DNA curvature significantly impacts translational and rotational diffusion coefficients.
These effects are measurable even in short DNA fragments (under 150 basepairs).
Current estimates of DNA's hydrated radius may be underestimated.

Conclusions:

The developed model provides a more accurate representation of DNA hydrodynamics.
Sequence-based structural variations play a critical role in DNA dynamics.
The findings offer a method to refine DNA structural parameters and hydrated radius estimations.