DNA MICROARRAYS: PROCEDURE AND APPLICATIONS - BIOLOGY - 2025

A DNA microarray, also called a DNA chip or DNA microarray, is made up of a series of DNA fragments anchored to a physical support of variable material, be it plastic or glass. Each piece of DNA represents a sequence complementary to a specific gene.

The main objective of microarrays is the comparative study of the expression of certain genes of interest. For example, it is common for this technique to be applied to two samples - one in healthy conditions and one pathological - in order to identify which genes are being expressed and which are not in the sample with the condition. Said sample can be a cell or a tissue.

By Paphrag at English Wikipedia (Transferred from en.wikipedia to Commons.), Via Wikimedia Commons

Generally the expression of genes can be detected and quantified thanks to the use of fluorescent molecules. The manipulation of the chips is carried out in most cases by robot and a large number of genes can be analyzed simultaneously.

This novel technology is useful for a wide range of disciplines, from medical diagnostics to various molecular biology studies in the fields of proteomics and genomics.

What does it consist of?

DNA (deoxyribonucleic acid) microarrays are a set of specific DNA segments attached to a solid matrix. These sequences are complementary to the genes that want to be studied and there can be up to 10,000 genes per cm ².

These characteristics allow the systematic and massive study of the gene expression of an organism.

The information that a cell needs to function is encoded in units called “genes”. Certain genes contain the instructions for creating essential biological molecules called proteins.

A gene is expressed if its DNA is transcribed into an intermediate messenger RNA molecule and the expression of the gene can vary depending on the level of transcription of this segment of DNA. In certain cases, the change in expression may be indicative of diseases.

The principle of hybridization makes the operation of microarrays possible. DNA is a molecule made up of four types of nucleotides: adenine, thymine, guanine, and cytosine.

To form the double helix structure, adenine groups with thymine and cytosine with guanine. Thus, two complementary chains can be joined by hydrogen bonds.

Types of microarrays

In terms of the structure of the microarrays, there are two variations: the custom made complementary DNA or oligonucleotides, and the commercial high-density microarrays manufactured by commercial companies, such as Affymetrix GeneChip.

The first type of microarray allows the analysis of RNA from two different samples on a single chip, while the second variation is of the commercial type and has a large number of genes (for example, the Affymetrix GeneChip has about 12,000 human genes) allowing to analyze a single sample.

Process

RNA isolation

The first step in conducting an experiment using microarray technology is the isolation and purification of the RNA molecules (it can be messenger RNA or other types of RNA).

If you want to compare two samples (healthy vs. sick, control vs. treatment, among others), the isolation of the molecule in both tissues must be performed.

Production and labeling of cDNA

Subsequently, the RNA is subjected to a reverse transcription process in the presence of labeled nucleotides and thus the complementary DNA or cDNA will be obtained.

The label can be fluorescent and must be distinguishable between the two tissues to be analyzed. In a traditional way, the fluorescent compounds Cy3 and Cy5 are used, since they emit fluorescence at different wavelengths. In the case of Cy3, it is a color close to red and Cy5 corresponds to the spectrum between orange and yellow.

Hybridization

The cDNAs are mixed and incubated in the DNA microarray to allow hybridization (ie, binding occurs) of the cDNA from both samples with the portion of DNA immobilized on the solid surface of the microarray.

A higher percentage of hybridization with the probe in the microarray is interpreted as a higher tissue expression of the corresponding mRNA.

System reading

The quantification of the expression is carried out by incorporating a reader system that assigns a color code to the amount of fluorescence emitted by each cDNA. For example, if red is used to mark the pathological condition and it hybridizes in a higher proportion, the red component will be the predominant one.

With this system, the overexpression or repression of each gene analyzed in both selected conditions can be known. In other words, the transcriptome of the samples evaluated in the experiment can be known.

Larssono, from Wikimedia Commons

Applications

Currently, microarrays are considered as very powerful tools in the medical field. This new technology allows the diagnosis of diseases and a better understanding of how gene expression is modified under different medical conditions.

Furthermore, it allows the comparison of a control tissue and a tissue treated with a certain drug, in order to study the effects of a possible medical treatment.

To do this, the normal state and the sick state are compared before and after the administration of the drug. By studying the effect of the drug on the genome in vivo, one has a better overview of its mechanism of action. Also, it can be understood why some particular drugs lead to unwanted side effects.

Cancer

Cancer tops the lists of diseases studied with DNA microarrays. This methodology has been used for the classification and prognosis of the disease, particularly in the cases of leukemias.

The field of investigation of this condition involves the compression and characterization of the molecular bases of cancer cells to find patterns of gene expression that result in failures in the regulation of the cell cycle and in the processes of cell death (or apoptosis).

Other diseases

Through the use of microarrays, it has been possible to elucidate the differential expression profiles of genes in medical conditions of allergies, primary immunodeficiencies, autoimmune diseases (such as rheumatoid arthritis) and infectious diseases.

References

1. Bednar, M. (2000). DNA microarray technology and application. Medical Science Monitor, 6 (4), MT796-MT800.
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3. Nguyen, DV, Bulak Arpat, A., Wang, N., & Carroll, RJ (2002). DNA microarray experiments: biological and technological aspects. Biometrics, 58 (4), 701-717.
4. Plous, CV (2007). DNA microarrays and their applications in biomedical research. CENIC Magazine. Biological Sciences, 38 (2), 132-135.
5. Wiltgen, M., & Tilz, GP (2007). DNA microarray analysis: principles and clinical impact. Hematology, 12 (4), 271-287.