How are DNA Microarrays Used in the Study of Genomics

A DNA microarray is a collection of DNA spots attached to a solid surface. In the study of genomics, DNA microarrays can be used either to simultaneously measure the expression levels of a large number of genes or to study the different regions of a genome.

The microscopic chips used in DNA microarrays consist of highly specific probes that are complementary to target DNA sequences. These probes can be a part of genes. Hence, each DNA spot can hold a particular DNA fragment of a genome. The information about the genome sequences can be used to analyze the complete transcriptional program of a particular organism during developmental processes or specific physiological responses.

Key Areas Covered

1. What are DNA Microarrays
     – Definition, Purpose, Spots
2. How are DNA Microarrays Used in the Study of Genomics
     – Analysis of Transcription

Key Terms: cDNA, DNA Microarray, Fluorescence, Genome Sequences, mRNA, Transcription

How are DNA Microarrays Used in the Study of Genomics - Infographic (1)

What are DNA Microarrays

DNA microarray refers to a collection of high density, single-stranded DNA molecules attached to a solid surface. It is used in the analysis of the expression of thousands of genes simultaneously. Generally, around 1 kb portion from the coding region of each gene is applied to closely-spaced spots on the surface of a microscopic slide. Typically, an array/gene chip of 2×2 cm contains around 6000 spots of DNA. A DNA microarray chip is shown in figure 1.

How are DNA Microarrays Used in the Study of Genomics

Figure 1: DNA Microarray

How are DNA Microarrays Used in the Study of Genomics

DNA microarrays can be used to identify the expression of genes in the genome. This process includes isolation of the total mRNA of a particular type of cells under a defined physiological condition. Then reverse transcription reactions are carried out to produce cDNA from mRNA. Here, DNA primers are used along with DNA nucleotides that contain a low concentration of labeled nucleotides with green fluorescent dye. This cDNA is hybridized with the complementary DNA probes in the chip. If two genomes are to be compared, the cDNA of the second genome can be labeled with a fluorescent dye of another color such as red. The procedure of DNA microarray is shown in figure 2.

How are DNA Microarrays Used in the Study of Genomics_Figure 2

Figure 2: DNA Microarray Procedure

The gene chip can be analyzed under the scanning laser microscope for the emission of fluorescence. The proper hybridization of target DNA with DNA probes in the DNA microarray gives the corresponding color of fluorescence. Since the DNA microarray is produced by applying known DNA sequences, the expressed genes in the genome can be identified. The knowledge of DNA sequences obtained through genomics is critical in the production of DNA microarrays, specifically for a particular target genome.


DNA microarrays are microscopic chips that contain spots of defined DNA probes. These spots can be hybridized with the DNA prepared from a target genome to identify the levels of expression under a specific physiological condition.


1. Lodish, Harvey. “DNA Microarrays: Analyzing Genome-Wide Expression.” Molecular Cell Biology. 4th Edition., U.S. National Library of Medicine, 1 Jan. 1970, Available here.

Image Courtesy:

1. “DNA microarray” By Guillaume Paumier (user:guillom) – Own work (CC BY-SA 3.0) via Commons Wikimedia
2. “Microarray-schema” By User:Larssono – Own work by the original uploader (Public Domain) via Commons Wikimedia

About the Author: Lakna

Lakna, a graduate in Molecular Biology and Biochemistry, is a Molecular Biologist and has a broad and keen interest in the discovery of nature related things. She has a keen interest in writing articles regarding science.

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