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DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Order and interactions in DNA arrays: Multiscale molecular dynamics simulation.

Julija Zavadlav^1,2,3, Rudolf Podgornik^4,5, Matej Praprotnik^6,7

¹Department of Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001, Ljubljana, Slovenia.

Scientific Reports

|July 8, 2017

Summary

Dense DNA arrays transition between hexagonal and orthorhombic packing. Hydration forces drive this phase transition at high densities, influencing DNA, counterion, and solvent ordering.

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Area of Science:

Biophysics
Computational Biology
Materials Science

Background:

DNA arrays exhibit hexagonal and orthorhombic local packings.
The phase transition mechanism between these packings at high densities is not fully understood.
Accurate modeling requires atomistic resolution to capture DNA, counterion, and solvent interactions.

Purpose of the Study:

To elucidate the mechanism governing the hexagonal-orthorhombic phase transition in dense DNA arrays.
To characterize the structural ordering of DNA, counterions, and solvent under osmotic stress.
To determine the primary interaction forces driving DNA packing at high densities.

Main Methods:

Multiscale simulation of 16 atomistically resolved DNA molecules within a semi-permeable membrane.
Mimicking osmotic stress using a bathing solution of monovalent salt and multivalent counterions.
Varying DNA density, local packing symmetry, and counterion type.

Main Results:

Obtained the osmotic equation of state for dense DNA arrays.
Observed and characterized the hexagonal-orthorhombic phase transition.
Provided a full structural characterization of DNA positional/orientational fluctuations, counterion distributions, and solvent dielectric response.

Conclusions:

The hydration force is identified as the primary interaction mechanism governing dense DNA arrays at high densities.
Multiscale simulations effectively capture the complex interplay of forces in DNA condensation.
Understanding these forces is crucial for comprehending DNA organization in biological systems and synthetic materials.