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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...

Position-effect Variegation

Position-effect Variegation

In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.

Labeling DNA Probes

Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...

Southern Blot

Southern Blot

Agarose gel electrophoresis is very useful in separating DNA fragments by size. Running a DNA ladder containing fragments of the known length alongside the sample helps determine the approximate length of the sample DNA fragments. However, additional steps are needed to verify the sequence identity of the sample DNA fragments.
Denatured DNA fragments must be transferred onto a carrier membrane from the gel to make it accessible to a probe - a small ssDNA fragment complementary to the target DNA...

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Related Experiment Video

Updated: May 30, 2026

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

Published on: March 15, 2011

Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in

Doris Steger¹, David Berry, Susanne Haider

¹Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Wien, Austria.

|August 23, 2011

Summary

Researchers identified a spatial bias in DNA microarray hybridization, where boundary spots show higher signal intensity due to target molecule diffusion. Adjusting chamber size minimizes this bias for more accurate results.

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Area of Science:

Molecular Biology
Biotechnology
Genomics

Background:

DNA microarray hybridization is crucial for parallel target detection in biological research.
Current DNA microarray technology faces reproducibility issues due to biases in surface hybridization.
The mechanisms behind non-random spatial variations in microarray hybridizations are not fully understood.

Purpose of the Study:

To identify and explain the systematic spatial bias observed in DNA microarray hybridization intensity.
To investigate the underlying mechanisms causing increased signal intensity at the boundaries of spotted areas.

Main Methods:

Utilized a simplified single-probe block array format for observations.
Developed and employed a mathematical model to predict hybridization patterns.
Conducted numerical simulations to analyze the influence of microarray well geometry.

Main Results:

Identified a systematic spatial bias with increased signal intensity at the boundaries of spotted areas.
Determined that position-dependent lateral diffusion of target molecules causes this bias.
Numerical simulations confirmed that microarray well geometry significantly impacts spatial bias.

Conclusions:

Adjusting microarray hybridization chamber size to probe area effectively minimizes diffusion-based bias.
This adjustment leads to improved uniformity and accuracy in quantitative DNA microarray hybridization.
Understanding and mitigating spatial bias enhances the reliability of microarray-based analyses.