DNA Microarrays: An Easy Explanation for Beginners (2023)

This is the first installment in our series on DNA microarrays where I will introduce how this technology is used for the analysis of gene expression, the technology behind this technique, and explain the basics of the technique.

This is to give you a quick immersion if you are new to the subject, and maybe a refresher if you are an old hand at it.

Expressing the Story of Life From the Genetic Code

While humans contain about 25,000 genes, only a fraction of these are actively expressed as mRNAs at any one time. This makes sense since if all the genes were expressed all at once, we would get a garbled stream of unstructured information.

Just like forming words in a sentence, the expression of the genetic code reflects the specific context and the exact message that needs to be stated.

When we talk, we structure our words into a specific string that forms a sentence. Sentences could be arranged into a paragraph, paragraphs into passages, and so on. However, there must be a specific context and purpose to each sentence.

Similarly, specific genes are expressed under corresponding conditions to “update” the functional content of the organism, to respond to internal and external stimuli, resulting in growth, development, and survival. The set of all RNA molecules expressed in a cell at any given time, what it is “saying” at that time, is called the transcriptome.

The Technology

The development of DNA microarray technology in the mid-1990s allowed for the first time to simultaneously profile and study the transcriptome, in other words, to study cells’ real-time “chatter” in more detail. That is, microarrays are a tool for gene expression analysis.

The technology exploited the very same principle that makes nucleic acid so essential to information storage: hybridization to complementary sequences. Hybridization between the cDNA reverse transcribed from a biological sample to a pre-designed complementary DNA probe arranged on a slide, or array, is the basis of DNA microarrays. A microarray, therefore, consists of a pre-designed library of synthetic nucleic acid probes that are immobilized and spatially arrayed on a solid matrix.

(Video) Gene Expression Analysis and DNA Microarray Assays

The Evolution of DNA Microarrays

Microarrays evolved from a technique known as Southern blotting, where DNA fragments are attached to a substrate and then probed with a known gene sequence.

The first DNA arrays were constructed by immobilizing cDNAs onto filter paper.

However, it was not until 1995 that the first DNA microarrays capable of analyzing thousands of sequences were constructed by “spotting”, or attaching short synthetic probes to designated locations on the solid surface, usually glass or silicon chip (see Figure 1).

How DNA Arrays Are Produced

There are several ways that such spotted arrays can be produced.

Some methods basically use a robot to “print” pre-designed probes that have been attached to fine needles onto a chemical matrix surface using surface engineering (examples include fine-pointed pins, needles, and ink-jet printing).

Other methods employ photo-activated chemistry and masking to synthesize probes one nucleotide at a time on a solid surface in repeated steps to build up probes of specific sequences in designated locations.

Read more about how DNA microarrays are built.

(Video) DNA Microarray (DNA chip) technique

DNA Microarray Measurement of Gene Expression: A Step-By-Step Guide

Let’s walk through a basic protocol for using a DNA microarray for gene expression profiling.

Isolate and Purify

The first step is to isolate and purify mRNA from samples of interest. Since we are interested in comparing gene expression, one sample usually serves as a control, and another sample would be the experiment (e.g., healthy vs. disease)

Reverse Transcription and Labeling

The next step is to reverse transcribe and label the mRNA. In order to detect the transcripts by hybridization, they need to be labeled, and because starting material may be limited, an amplification step is also used.

Labeling usually involves performing a reverse transcription (RT) reaction to produce a complementary DNA strand (cDNA) and incorporating a fluorescent dye that has been linked to a DNA nucleotide, producing a fluorescent cDNA strand.

Disease and healthy samples can be labeled with different dyes and co-hybridized onto the same microarray in the following step. Some protocols do not label the cDNA but use a second step of amplification, where the cDNA from the RT step serves as a template to produce a labeled cRNA strand.


Now it’s time to hybridize the labeled target to the microarray. This step involves placing labeled cDNAs onto a DNA microarray where they will hybridize to their synthetic complementary DNA probes attached to the microarray.

A series of washes are used to remove non-bound sequences.

Scanning and Quantitation

The fluorescent tags on the bound cDNA are excited by a laser and the fluorescently labeled target sequences that bind to a probe generate a signal.

(Video) DNA microarrays

The total fluorescent intensity of the signal depends upon the amount of target sample binding to the probes present on that spot.

Thus, the amount of target sequence bound to each probe correlates to the expression level of various genes expressed in the sample. The signals are detected, the signal intensity is quantified, and used to create a digital image of the array.

DNA Microarrays: An Example Result

If we are trying to calculate relative expression between two samples, each labeled with a different dye (See figure 2, red for the experiment, green for the control), the resulting image is analyzed by calculating the ratio of the two dyes.

If a gene is over-expressed in the experimental sample, then more of that sample cDNA than control cDNA will hybridize to the spot representing that expressed gene. In turn, the spot will fluoresce red with greater intensity than it will fluoresce green. The red-to-green fluorescence ratio thus indicates which gene is up or downregulated in the appropriate sample.

DNA Microarrays: An Easy Explanation for Beginners (2)

What Have Microarrays Done for Us?

Microarray technology propelled functional genomics, a discipline that strives to identify the role of genes in cellular processes, into the spotlight because it allowed functional analysis of genome-wide differential RNA expression between different samples, states, and cell types to gain insights into molecular mechanisms that regulate cell fate, development, and disease progression.

Microarray data is used for gene expression profiling, which serves as a determinant of protein levels and therefore cellular function between biological samples.

A single experiment can provide information on the expression of thousands of genes, virtually the entire human genome, to compare expression patterns between any two states.

(Video) An Introduction to DNA Microarrays

Microarray experiments can indicate which genes are up- or down-regulated between samples from normal and diseased tissue, or two samples in the absence and presence of a certain stimulus.

It is easy to see why this technology might be appealing for understanding complex biological systems as well as drug discovery, disease diagnosis, novel gene identification.

DNA Microarrays Considerations and Caveats

While DNA microarrays have been an excellent genomic tool, and have allowed for some great advances in our understanding of diseases and biological processes, there are some notable limitations to the technology.

Because the targets are preselected, there is little room for discovery (e.g., identification of new gene mutations or unknown sequences), although there are explorative probe design strategies available, which could allow for the detection of mutations.

However, newer techniques, such as RNA-Seq for gene expression profiling, are far more suited to this type of discovery.

Chip redesign can also be costly and time-consuming, meaning this technology can be slow to adapt to newly discovered targets.

Do you still use microarrays in your research? Let us know in the comments below.

Originally published July 13, 2011. Reviewed and updated October 2021.

(Video) Microarray Technique || DNA Microarray || Gene expression analysis using microarray

Further Reading

Trevino V, Falciani F & Barrera-Saldaña H.A. DNA Microarrays: a Powerful Genomic Tool for Biomedical and Clinical Research.Mol Med13,527–541 (2007).

Written by Yevgeniy Grigoryev


What is DNA microarray in simple words? ›

The DNA microarray is a tool used to determine whether the DNA from a particular individual contains a mutation in genes like BRCA1 and BRCA2. The chip consists of a small glass plate encased in plastic. Some companies manufacture microarrays using methods similar to those used to make computer microchips.

How do microarrays work simple? ›

The principle behind microarrays is that complementary sequences will bind to each other. The unknown DNA molecules are cut into fragments by restriction endonucleases; fluorescent markers are attached to these DNA fragments. These are then allowed to react with probes of the DNA chip.

What is a question that could be answered by a DNA microarray? ›

DNA microarray analysis is a technique that scientists use to determine whether genes are on or off. Scientists know a gene is on in a cell if its mRNA is present.

What are the main steps of DNA microarray? ›

There are four main steps to a DNA microarray analysis: Sample isolation/preparation, hybridization, washing, and image analysis. Hybridization occurs when the samples (target and control) bond to probes with a complementary sequence.

What is the main purpose of microarray? ›

A microarray is a laboratory tool used to detect the expression of thousands of genes at the same time. DNA microarrays are microscope slides that are printed with thousands of tiny spots in defined positions, with each spot containing a known DNA sequence or gene.

What is the purpose of a microarray? ›

A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome.

How are DNA microarrays used? ›

DNA microarrays are commonly used to genotype multiple regions of a genome or to generate lists of expressed genes from a cell. Microarray technology allows for the multiple analysis of gene expression in a single reaction.

What are DNA microarrays quizlet? ›

DNA Microarray. Used to screen a patient for a pattern of genes expressed in a particular condition and to develop patient's risk of disease.

What is the conclusion of microarray? ›

Conclusion. Microarray technology is a powerful technology that will substantially increase the speed at which differential gene expression can be analyzed and gene functions are elucidated.

What Cannot be detected by microarray? ›

Microarray analysis can detect submicroscopic deletions and duplications of genetic material across all chromosomes. It provides a higher resolution analysis than a karyotype study, but doesn't provide positional information e.g. it cannot detect genetically balanced rearrangements.

What kind of information can a DNA microarray analysis provide? ›

DNA microarrays help in gene discovery, their expression profiling, their regulation, genetic disease screening, SNP discrimination, microbial detection and typing, and observe variation between transcript levels of genes under different conditions.

What can microarray not detect? ›

For example, microarray analysis cannot detect balanced chromosome rearrangements (eg, inversions or translocations), which do not result in deletion or duplication of genetic material, or cases of low-level tissue mosaicism.

What are the two types of microarray? ›

Three basic types of microarrays: (A) Spotted arrays on glass, (B) self assembled arrays and (C) in-situ synthesized arrays.

What are the advantages of using DNA microarray? ›

In contrast to other DNA hybridization techniques developed earlier, such as Southern blotting, DNA microarrays have the advantages of high specificity, high sensitivity, and high throughput; and thousands of genes can be analyzed simultaneously.

Which is the most common use of microarrays in research? ›

Although microarrays have many uses, a common use is to measure gene expression. Gene expression arrays contain thousands of different genes, each represented by one or more gene fragments that are deposited on the array.

Why are DNA microarrays so important for studying genetic diseases? ›

This type of analysis is essential because it provides the simplest characterization of the specific molecular differences that are associated to a specific biological effect. These signatures can be used to generate new hypothesis and guide the design of further experiments.

Are microarrays used for sequencing? ›

DNA microarrays containing hundreds of thousands or millions of probes can be used to interrogate genomic sequence.

What does a microarray look at? ›

Also called a Detailed Chromosome Test or Array

A microarray is a special genetic test that looks in detail at a person's chromosomes to see if there are any extra or missing sections which might account for problems they have been experiencing.

What are 3 limitations of microarrays? ›

The most significant disadvantages of microarrays include the high cost of a single experiment, the large number of probe designs based on sequences of low-specificity, as well as the lack of control over the pool of analyzed transcripts since most of the commonly used microarray platforms utilize only one set of ...

What do the results from a microarray tell you? ›

The test's results may lead to: finding the genetic cause for your child's medical condition. changes in your child's health care. learning the risk for your child to pass down a genetic change to their children.

What do the red spots on the microarray mean? ›

• A red spot indicates that that gene was strongly expressed in cancer cells. (In your experiment these spots will be dark pink.) • A green spot indicates that that gene was strongly repressed in cancer cells.

What are two limitations of microarray? ›

Limitations of microarrays

limited dynamic range of detection owing to both background and saturation signals. comparing expression levels across different experiments is often difficult and can require complicated normalisation methods.

What is a major limitations of DNA microarray technology? ›

Limitations of DNA microarray technology include the initial high cost for the synthesis of gene-specific primers necessary to amplify each gene in a genome, for spotting and for the fluorophores used in the labeling reactions.

How accurate is a microarray? ›

In samples with a normal karyotype, microarray analysis revealed clinically relevant deletions or duplications in 6.0% with a structural anomaly and in 1.7% of those whose indications were advanced maternal age or positive screening results.

What is a DNA microarray quizlet? ›

DNA microarray. A glass slide carrying thousands of different kinds of single-stranded DNA fragments arranged in an array (grid). A DNA microarray is used to detect and measure the expression of thousands genes at one time.

What is DNA microarray technology used to measure? ›

This chapter provides an overview of DNA microarrays. Microarrays are a technology in which 1000's of nucleic acids are bound to a surface and are used to measure the relative concentration of nucleic acid sequences in a mixture via hybridization and subsequent detection of the hybridization events.

What is a microarray quizlet? ›

Definition. 1 / 13. -Glass microscope slides or nylon (synthetic) membranes containing an orderly arrangement of 1000's of "spots" (less than 2 microns in diameter) with known DNA sequences. -Machines print presynthesized DNA molecules or synthesize oligonucleotides onto the slides/membranes.

What is the meaning of Micro DNA? ›

MicroDNA is the most abundant subtype of Extrachromosomal Circular DNA (eccDNA) in humans, typically ranging from 200-400 base pairs in length and enriched in non-repetitive genomic sequences with a high density of exons.

What does a DNA microarray contain? ›

A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Each DNA spot contains many thousands of copies of a specific DNA sequence, known as probes. These usually correspond to a short section of a gene – generally at the 3′ end.

How does microarray genetic testing work? ›

“Microarray” refers to a microchip-based testing platform that allows high-volume, automated analysis of many pieces of DNA at once. CMA chips use labels or probes that bond to specific chromosome regions. Computer analysis is used to compare a patient's genetic material to that of a reference sample.

Why is PCR used in microarray? ›

Microarray detection is usually combined with PCR to detect specific amplicons. The inclusion of many different “probe” sequences on one microarray allows simultaneous detection of different organisms, or differences between organisms of the same species.

What are the advantages of microarray? ›

Microarray is a new powerful tool for studying the molecular basis of interactions on a scale that is impossible using conventional analysis. This technique makes it possible to examine the expression of thousands of genes simultaneously.

What is the disadvantage of microarray? ›

The most significant disadvantages of microarrays include the high cost of a single experiment, the large number of probe designs based on sequences of low-specificity, as well as the lack of control over the pool of analyzed transcripts since most of the commonly used microarray platforms utilize only one set of ...


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