- A DNA microarray is a powerful molecular biology tool used to measure the expression levels of thousands of genes simultaneously or to detect variations within the genome. It consists of a solid surface—typically a glass slide or silicon chip—onto which thousands of DNA probes are fixed in a precise grid pattern. Each probe corresponds to a specific gene or DNA sequence of interest. When a sample containing fluorescently labeled nucleic acids is applied to the array, complementary base pairing allows sequences in the sample to hybridize to matching probes on the chip. By analyzing the pattern and intensity of fluorescence signals at each spot, researchers can determine which genes are active and to what extent.
- The development of DNA microarrays was a significant milestone in genomics, emerging in the mid-1990s as a response to the need for high-throughput methods to study gene expression. The principle of microarrays is based on nucleic acid hybridization, the same fundamental mechanism underlying techniques like Southern and Northern blotting. However, microarrays miniaturized and automated this process, enabling parallel analysis of thousands of genes at once. Early arrays were fabricated using robotic spotting of cDNA or oligonucleotides onto glass slides. Later advancements introduced photolithographic synthesis of oligonucleotides directly on the chip surface (as used in Affymetrix GeneChips), improving precision, reproducibility, and probe density.
- The process of performing a DNA microarray experiment generally involves several key steps. First, mRNA is isolated from cells or tissues of interest and converted into complementary DNA (cDNA) using reverse transcriptase. The cDNA is then fluorescently labeled, typically using different dyes (such as Cy3 and Cy5) to distinguish between samples—for example, a control and a treated sample. These labeled cDNAs are then hybridized to the microarray chip, where they bind to their complementary DNA probes. After hybridization and washing to remove unbound molecules, the chip is scanned using a laser-based fluorescence scanner, and the emitted light intensity at each spot reflects the relative abundance of the corresponding transcript in the sample.
- DNA microarrays have been used extensively in gene expression profiling, enabling scientists to compare expression patterns between healthy and diseased tissues, study responses to drugs, or understand developmental and environmental effects on gene activity. They have also been applied in genotyping, mutation analysis, SNP detection, and comparative genomic hybridization (CGH) to study genetic variation, copy number changes, and chromosomal abnormalities. The vast datasets generated by microarrays have contributed to the identification of disease biomarkers, molecular signatures of cancer subtypes, and insights into gene regulatory networks.
- Despite their transformative impact, DNA microarrays have some limitations. They rely on prior knowledge of gene sequences, meaning they cannot detect unknown transcripts or novel variants. Cross-hybridization and background noise can also affect specificity and quantitative accuracy. In recent years, RNA sequencing (RNA-seq) has largely replaced microarrays for gene expression analysis due to its higher sensitivity and ability to detect new transcripts. Nevertheless, DNA microarrays remain valuable for large-scale screening, clinical diagnostics, and educational purposes, offering a cost-effective and established platform for parallel genetic analysis.
